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[Gsrc-commit] trunk r3733: big changes, added rest pkg from BioSrc
|
From: |
Carl Hansen |
|
Subject: |
[Gsrc-commit] trunk r3733: big changes, added rest pkg from BioSrc |
|
Date: |
Fri, 17 Jun 2016 20:01:58 +0000 (UTC) |
|
User-agent: |
Bazaar (2.6b2) |
------------------------------------------------------------
revno: 3733
revision-id: address@hidden
parent: address@hidden
committer: address@hidden
branch nick: trunk
timestamp: Fri 2016-06-17 13:01:53 -0700
message:
big changes, added rest pkg from BioSrc
added:
pkg/other/argtable/ argtable-20160617200040-lqf8h520dfq0rtk7-1
pkg/other/argtable/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-42
pkg/other/argtable/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-43
pkg/other/bambamc/ bambamc-20160617200040-lqf8h520dfq0rtk7-2
pkg/other/bambamc/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-44
pkg/other/bambamc/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-45
pkg/other/beagle-lib/ beaglelib-20160617200040-lqf8h520dfq0rtk7-3
pkg/other/beagle-lib/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-46
pkg/other/eigen/ eigen-20160617200040-lqf8h520dfq0rtk7-4
pkg/other/eigen/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-47
pkg/other/eigen/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-48
pkg/other/htslib/ htslib-20160617200040-lqf8h520dfq0rtk7-5
pkg/other/htslib/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-49
pkg/other/htslib/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-50
pkg/other/libgtextutils/ libgtextutils-20160617200040-lqf8h520dfq0rtk7-6
pkg/other/libgtextutils/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-51
pkg/other/libgtextutils/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-52
pkg/other/libsvm/ libsvm-20160617200040-lqf8h520dfq0rtk7-7
pkg/other/libsvm/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-53
pkg/other/libsvm/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-54
pkg/other/nlopt/ nlopt-20160617200040-lqf8h520dfq0rtk7-8
pkg/other/nlopt/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-55
pkg/other/nlopt/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-56
pkg/other/perl-bioperl/ perlbioperl-20160617200040-lqf8h520dfq0rtk7-9
pkg/other/perl-bioperl/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-57
pkg/other/perl-bioperl/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-58
pkg/other/perl-ensembl/ perlensembl-20160617200040-lqf8h520dfq0rtk7-10
pkg/other/perl-ensembl-compara/
perlensemblcompara-20160617200040-lqf8h520dfq0rtk7-11
pkg/other/perl-ensembl-compara/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-61
pkg/other/perl-ensembl-compara/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-62
pkg/other/perl-ensembl-funcgen/
perlensemblfuncgen-20160617200040-lqf8h520dfq0rtk7-12
pkg/other/perl-ensembl-funcgen/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-63
pkg/other/perl-ensembl-funcgen/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-64
pkg/other/perl-ensembl-variation/
perlensemblvariation-20160617200040-lqf8h520dfq0rtk7-13
pkg/other/perl-ensembl-variation/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-65
pkg/other/perl-ensembl-variation/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-66
pkg/other/perl-ensembl/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-59
pkg/other/perl-ensembl/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-60
pkg/other/python/ python-20160617200040-lqf8h520dfq0rtk7-14
pkg/other/python-biopython/
pythonbiopython-20160617200040-lqf8h520dfq0rtk7-15
pkg/other/python-biopython/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-70
pkg/other/python-biopython/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-71
pkg/other/python-matplotlib/
pythonmatplotlib-20160617200040-lqf8h520dfq0rtk7-16
pkg/other/python-matplotlib/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-72
pkg/other/python-matplotlib/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-73
pkg/other/python-networkx/
pythonnetworkx-20160617200040-lqf8h520dfq0rtk7-17
pkg/other/python-networkx/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-74
pkg/other/python-networkx/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-75
pkg/other/python-numpy/ pythonnumpy-20160617200040-lqf8h520dfq0rtk7-18
pkg/other/python-numpy/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-76
pkg/other/python-numpy/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-77
pkg/other/python-pandas/ pythonpandas-20160617200040-lqf8h520dfq0rtk7-19
pkg/other/python-pandas/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-78
pkg/other/python-pandas/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-79
pkg/other/python-scipy/ pythonscipy-20160617200040-lqf8h520dfq0rtk7-20
pkg/other/python-scipy/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-80
pkg/other/python-scipy/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-81
pkg/other/python-setuptools/
pythonsetuptools-20160617200040-lqf8h520dfq0rtk7-21
pkg/other/python-setuptools/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-82
pkg/other/python-setuptools/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-83
pkg/other/python-six/ pythonsix-20160617200040-lqf8h520dfq0rtk7-22
pkg/other/python-six/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-84
pkg/other/python-six/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-85
pkg/other/python-sqlalchemy/
pythonsqlalchemy-20160617200040-lqf8h520dfq0rtk7-23
pkg/other/python-sqlalchemy/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-86
pkg/other/python-sqlalchemy/gpg-keyring
gpgkeyring-20160617200040-lqf8h520dfq0rtk7-87
pkg/other/python-sqlalchemy/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-88
pkg/other/python/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-67
pkg/other/python/gpg-keyring gpgkeyring-20160617200040-lqf8h520dfq0rtk7-68
pkg/other/python/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-69
pkg/other/python2/ python2-20160617200040-lqf8h520dfq0rtk7-24
pkg/other/python2-biopython/
python2biopython-20160617200040-lqf8h520dfq0rtk7-25
pkg/other/python2-biopython/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-92
pkg/other/python2-biopython/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-93
pkg/other/python2-dateutil/
python2dateutil-20160617200040-lqf8h520dfq0rtk7-26
pkg/other/python2-dateutil/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-94
pkg/other/python2-dateutil/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-95
pkg/other/python2-htseq/ python2htseq-20160617200040-lqf8h520dfq0rtk7-27
pkg/other/python2-htseq/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-96
pkg/other/python2-htseq/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-97
pkg/other/python2-matplotlib/
python2matplotlib-20160617200040-lqf8h520dfq0rtk7-28
pkg/other/python2-matplotlib/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-98
pkg/other/python2-matplotlib/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-99
pkg/other/python2-networkx/
python2networkx-20160617200040-lqf8h520dfq0rtk7-29
pkg/other/python2-networkx/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-100
pkg/other/python2-networkx/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-101
pkg/other/python2-numpy/ python2numpy-20160617200040-lqf8h520dfq0rtk7-30
pkg/other/python2-numpy/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-102
pkg/other/python2-numpy/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-103
pkg/other/python2-pandas/
python2pandas-20160617200040-lqf8h520dfq0rtk7-31
pkg/other/python2-pandas/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-104
pkg/other/python2-pandas/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-105
pkg/other/python2-pysam/ python2pysam-20160617200040-lqf8h520dfq0rtk7-32
pkg/other/python2-pysam/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-106
pkg/other/python2-pysam/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-107
pkg/other/python2-scipy/ python2scipy-20160617200040-lqf8h520dfq0rtk7-33
pkg/other/python2-scipy/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-108
pkg/other/python2-scipy/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-109
pkg/other/python2-setuptools/
python2setuptools-20160617200040-lqf8h520dfq0rtk7-34
pkg/other/python2-setuptools/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-110
pkg/other/python2-setuptools/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-111
pkg/other/python2-six/ python2six-20160617200040-lqf8h520dfq0rtk7-35
pkg/other/python2-six/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-112
pkg/other/python2-six/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-113
pkg/other/python2-sqlalchemy/
python2sqlalchemy-20160617200040-lqf8h520dfq0rtk7-36
pkg/other/python2-sqlalchemy/Makefile
makefile-20160617200040-lqf8h520dfq0rtk7-114
pkg/other/python2-sqlalchemy/gpg-keyring
gpgkeyring-20160617200040-lqf8h520dfq0rtk7-115
pkg/other/python2-sqlalchemy/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-116
pkg/other/python2-toolz/ python2toolz-20160617200040-lqf8h520dfq0rtk7-37
pkg/other/python2-toolz/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-117
pkg/other/python2-toolz/sha256sums
sha256sums-20160617200040-lqf8h520dfq0rtk7-118
pkg/other/python2/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-89
pkg/other/python2/gpg-keyring gpgkeyring-20160617200040-lqf8h520dfq0rtk7-90
pkg/other/python2/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-91
pkg/other/seqan/ seqan-20160617200040-lqf8h520dfq0rtk7-38
pkg/other/seqan/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-119
pkg/other/seqan/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-120
pkg/other/sparsehash/ sparsehash-20160617200040-lqf8h520dfq0rtk7-39
pkg/other/sparsehash/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-121
pkg/other/sparsehash/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-122
pkg/other/xerces/ xerces-20160617200040-lqf8h520dfq0rtk7-40
pkg/other/xerces/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-123
pkg/other/xerces/gpg-keyring gpgkeyring-20160617200040-lqf8h520dfq0rtk7-124
pkg/other/xerces/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-125
pkg/other/zeptodb/ zeptodb-20160617200040-lqf8h520dfq0rtk7-41
pkg/other/zeptodb/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-126
pkg/other/zeptodb/gpg-keyring gpgkeyring-20160617200040-lqf8h520dfq0rtk7-127
pkg/other/zeptodb/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-128
=== added directory 'pkg/other/argtable'
=== added file 'pkg/other/argtable/Makefile'
--- a/pkg/other/argtable/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/argtable/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,42 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = argtable
+GARNAME = argtable
+GARVERSION = 2.13
+HOME_URL = http://argtable.sourceforge.net
+DESCRIPTION = An ANSI C command-line parser
+define BLURB
+Argtable is an ANSI C library for parsing GNU style command line
+options with a minimum of fuss.
+endef
+LICENSE = GPLv2 or later
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = argtable/files/$(GARNAME)/$(GARNAME)-$(GARVERSION)/
+DISTNAME = $(GARNAME)$(subst .,-,$(GARVERSION))
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/other/argtable/sha256sums'
--- a/pkg/other/argtable/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/argtable/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf
download/argtable2-13.tar.gz
=== added directory 'pkg/other/bambamc'
=== added file 'pkg/other/bambamc/Makefile'
--- a/pkg/other/bambamc/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/bambamc/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,46 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = bambamc
+GARNAME = bambamc
+GARVERSION = 0.0.50
+HOME_URL = https://github.com/gt1/bambamc
+DESCRIPTION = A C implementation of name-collating BAM file input and output
+define BLURB
+bambamc is a C library implementing functions for BAM file input and
+output.
+endef
+LICENSE = GPLv3+
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = gt1/$(GARNAME)/archive/
+DISTNAME = $(GARNAME)_$(subst .,_,$(GARVERSION))
+DISTFILES = $(DISTNAME).tar.gz
+WORKSRC = $(WORKDIR)/$(GARNAME)-$(DISTNAME)
+
+BUILDDEPS =
+LIBDEPS =
+
+USE_AUTORECONF = y
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/other/bambamc/sha256sums'
--- a/pkg/other/bambamc/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/bambamc/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+f1ca5b35ce115c3aa3a3630228293cab333d239b26476b271a056f038abdc7a5
download/bambamc_0_0_50.tar.gz
=== added directory 'pkg/other/beagle-lib'
=== added file 'pkg/other/beagle-lib/Makefile'
--- a/pkg/other/beagle-lib/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/beagle-lib/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,48 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = BEAGLE
+GARNAME = beagle-lib
+GARVERSION = 2.1.2
+SVN_REVISION = 1240
+HOME_URL = https://code.google.com/p/beagle-lib/
+DESCRIPTION = A library for evaluating the likelihoodof sequence evolution on
trees
+define BLURB
+BEAGLE is a library of functions for evaluating phylogenetic
+likelihoods, both via Bayesian samplers and Maximum Likelihood
+optimizers.
+endef
+LICENSE = LGPLv3 or later
+CITE = doi:10.1093/sysbio/syr100
+
+######################################################################
+
+MASTER_SITES = svnco://beagle-lib.googlecode.com/
+MASTER_SUBDIR = svn/trunk/
+SVN_PATH = $(subst svnco,http,$(MASTER_SITES))$(MASTER_SUBDIR)
+DISTFILES = $(DISTNAME).tar.gz
+NOCHECKSUM = $(DISTFILES)
+
+BUILDDEPS =
+LIBDEPS =
+
+USE_AUTORECONF = y
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added directory 'pkg/other/eigen'
=== added file 'pkg/other/eigen/Makefile'
--- a/pkg/other/eigen/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/eigen/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,44 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Eigen
+GARNAME = eigen
+GARVERSION = 3.2.1
+COMMIT = 6b38706d90a9
+HOME_URL = http://eigen.tuxfamily.org
+DESCRIPTION = A C++ template library for linear algebra
+define BLURB
+Eigen is a C++ template library for linear algebra. It can handle
+matrices, vectors, numerical solvers and related algorithms.
+endef
+LICENSE = MPL2
+
+######################################################################
+
+MASTER_SITES = http://bitbucket.org/
+MASTER_SUBDIR = $(GARNAME)/$(GARNAME)/get/
+DISTFILES = $(GARVERSION).tar.gz
+WORKSRC = $(WORKDIR)/$(GARNAME)-$(GARNAME)-$(COMMIT)
+WORKOBJ = $(WORKSRC)-build
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/cmake.mk
+include config.mk
=== added file 'pkg/other/eigen/sha256sums'
--- a/pkg/other/eigen/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/eigen/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+fa9b1821608d8fd3b364ac9db62102b797364923fa0c74e6cbc4f9ba36c43e44
download/3.2.1.tar.gz
=== added directory 'pkg/other/htslib'
=== added file 'pkg/other/htslib/Makefile'
--- a/pkg/other/htslib/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/htslib/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,46 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = HTSlib
+GARNAME = htslib
+GARVERSION = 1.0
+HOME_URL = https://github.com/samtools/htslib
+DESCRIPTION = C library for high-throughput sequencing data formats
+define BLURB
+HTSlib is a library for accessing common file formats used for high-
+throughput sequencing data, such as SAM, CRAM and VCF
+endef
+LICENSE = Expat License
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = samtools/files/samtools/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.bz2
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = $(WORKSRC)/Makefile
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+INSTALL_ARGS = prefix=$(packageprefix)
=== added file 'pkg/other/htslib/sha256sums'
--- a/pkg/other/htslib/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/htslib/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+3d53fb081fafd930cadfee6f950faacc1993a0f4a9fa329fc897865fc6b331bc
download/htslib-1.0.tar.bz2
=== added directory 'pkg/other/libgtextutils'
=== added file 'pkg/other/libgtextutils/Makefile'
--- a/pkg/other/libgtextutils/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/libgtextutils/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,41 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = libGTextUtils
+GARNAME = libgtextutils
+GARVERSION = 0.7
+HOME_URL = https://github.com/agordon/libgtextutils
+DESCRIPTION = A library of various text processing functions
+define BLURB
+libGTextUtils is a library containing various functions for processing
+text.
+endef
+LICENSE = AGPLv3 or later
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = agordon/$(GARNAME)/releases/download/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/other/libgtextutils/sha256sums'
--- a/pkg/other/libgtextutils/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/libgtextutils/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+792e0ea3c96ffe3ad65617a104b7dc50684932bc96d2adab501c952fd65c3e4a
download/libgtextutils-0.7.tar.gz
=== added directory 'pkg/other/libsvm'
=== added file 'pkg/other/libsvm/Makefile'
--- a/pkg/other/libsvm/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/libsvm/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,77 @@
+# Copyright © 2015 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = LIBSVM
+GARNAME = libsvm
+GARVERSION = 3.20
+HOME_URL = http://www.csie.ntu.edu.tw/~cjlin/libsvm/
+DESCRIPTION = A library for Support Vector Machines
+define BLURB
+LIBSVM is an integrated software for support vector classification,
+(C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution
+estimation (one-class SVM). It supports multi-class classification.
+endef
+LICENSE = 3-clause BSD
+CITE = doi:10.1145/1961189.1961199
+
+######################################################################
+
+MASTER_SITES = http://www.csie.ntu.edu.tw/
+MASTER_SUBDIR = ~cjlin/$(GARNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = bin lib header python java
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+MAKE_ARGS = lib all
+
+install-bin:
+ $(INSTALL_BIN) $(WORKSRC)/svm-train
+ $(INSTALL_BIN) $(WORKSRC)/svm-predict
+ $(INSTALL_BIN) $(WORKSRC)/svm-scale
+ $(MAKECOOKIE)
+
+install-lib:
+ $(INSTALL_LIB) $(WORKSRC)/libsvm.so.2
+ $(SYMLINK_LIB) libsvm.so.2 libsvm.so
+ $(MAKECOOKIE)
+
+install-header:
+ $(INSTALL_INCLUDE) $(WORKSRC)/svm.h
+ $(MAKECOOKIE)
+
+install-java:
+ install -D -m644 $(WORKSRC)/java/libsvm.jar
$(packageprefix)/share/java/libsvm.jar
+ $(MAKECOOKIE)
+
+install-python:
+ for f in svm.py svmutil.py; do \
+ sed -i '1s/python/python2/' $(WORKSRC)/python/$$f; \
+ install -D -m644 $(WORKSRC)/python/$$f
$(packageprefix)/lib/python2.7/$$f; \
+ done
+ for f in svm.py svmutil.py; do \
+ sed -i '1s/python2/python3/' $(WORKSRC)/python/$$f; \
+ install -D -m644 $(WORKSRC)/python/$$f
$(packageprefix)/lib/python3.4/$$f; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/other/libsvm/sha256sums'
--- a/pkg/other/libsvm/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/libsvm/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+0f122480bef44dec4df6dae056f468c208e4e08c00771ec1b6dae2707fd945be
download/libsvm-3.20.tar.gz
=== added directory 'pkg/other/nlopt'
=== added file 'pkg/other/nlopt/Makefile'
--- a/pkg/other/nlopt/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/nlopt/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,45 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = NLopt
+GARNAME = nlopt
+GARVERSION = 2.4.1
+HOME_URL = http://ab-initio.mit.edu/nlopt
+DESCRIPTION = A library for nonlinear optimization
+define BLURB
+NLopt is a library for nonlinear optimization, providing a common
+interface for a number of different optimization routines. It
+features bindings for a wide array of languages, such as C/C++,
+Python, and R.
+endef
+LICENSE = LGPLv2.1 or later
+CITE = Steven G. Johnson, The NLopt nonlinear-optimization package,
http://ab-initio.mit.edu/nlopt
+
+######################################################################
+
+MASTER_SITES = http://ab-initio.mit.edu/
+MASTER_SUBDIR = $(GARNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+SIGFILES =
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/other/nlopt/sha256sums'
--- a/pkg/other/nlopt/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/nlopt/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+fe9ade54ed79c87f682540c34ad4e610ff32c9a43c52c6ea78cef6adcd5c1319
download/nlopt-2.4.1.tar.gz
=== added directory 'pkg/other/perl-bioperl'
=== added file 'pkg/other/perl-bioperl/Makefile'
--- a/pkg/other/perl-bioperl/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/perl-bioperl/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,52 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Bioperl
+GARNAME = perl-bioperl
+UPSTREAMNAME = BioPerl
+GARVERSION = 1.6.923
+HOME_URL = http://www.bioperl.org
+DESCRIPTION = Perl code which is useful in biology
+define BLURB
+BioPerl is a collection of Perl modules that facilitate the development of Perl
+scripts for bioinformatics applications.
+endef
+LICENSE = Artistic License or GPLv3
+
+######################################################################
+
+MASTER_SITES = $(MASTER_CPAN)
+MASTER_SUBDIR = authors/id/C/CJ/CJFIELDS/
+DISTFILES = $(DISTNAME).tar.gz
+BUILD_SCRIPTS = $(WORKSRC)/Build.PL
+INSTALL_SCRIPTS = Build
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+build-$(WORKSRC)/Build.PL:
+ cd $(WORKSRC) && perl Build.PL --install_base $(packageprefix)
+ $(MAKECOOKIE)
+
+install-Build:
+ cd $(WORKSRC) && ./Build install
+ $(MAKECOOKIE)
=== added file 'pkg/other/perl-bioperl/sha256sums'
--- a/pkg/other/perl-bioperl/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/perl-bioperl/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+6f6ada4ebd51ad223662e4b1ddcccc37a4fb8c47f3ecbbf060e6844d361730cd
download/BioPerl-1.6.923.tar.gz
=== added directory 'pkg/other/perl-ensembl'
=== added directory 'pkg/other/perl-ensembl-compara'
=== added file 'pkg/other/perl-ensembl-compara/Makefile'
--- a/pkg/other/perl-ensembl-compara/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/perl-ensembl-compara/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,54 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Ensembl Compara
+GARNAME = perl-ensembl-compara
+UPSTREAMNAME = ensembl-compara
+GARVERSION = 78
+HOME_URL = http://www.ensembl.org
+DESCRIPTION = Ensembl Compara Perl API
+define BLURB
+The Ensembl Compara Perl API allows you to programmatically access the
+Ensembl Compara database.
+endef
+LICENSE = Apache License
+CITE = doi:10.1101/gr.073585.107
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = Ensembl/$(UPSTREAMNAME)/archive/release/
+DISTFILES = $(GARVERSION).zip
+WORKSRC = $(WORKDIR)/$(UPSTREAMNAME)-release-$(GARVERSION)
+INSTALL_SCRIPTS = modules
+
+BUILDDEPS =
+LIBDEPS = perl-bioperl
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+FILE_SITES = file://$(FILEDIR)/
+
+install-modules:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(UPSTREAMNAME)
modules.$(OFF)\n"
+ mkdir -p $(packageprefix)/lib/perl5/
+ cp -r $(WORKSRC)/modules/Bio $(packageprefix)/lib/perl5/
+ cp -r $(WORKSRC)/modules/t $(packageprefix)/lib/perl5
+ $(MAKECOOKIE)
=== added file 'pkg/other/perl-ensembl-compara/sha256sums'
--- a/pkg/other/perl-ensembl-compara/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/perl-ensembl-compara/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+a20a4917f2f2af43075dcdd5710f66f589970f73172d550d20d60d532eed0beb
download/78.zip
=== added directory 'pkg/other/perl-ensembl-funcgen'
=== added file 'pkg/other/perl-ensembl-funcgen/Makefile'
--- a/pkg/other/perl-ensembl-funcgen/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/perl-ensembl-funcgen/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,54 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Ensembl Funcgen
+GARNAME = perl-ensembl-funcgen
+UPSTREAMNAME = ensembl-funcgen
+GARVERSION = 78
+HOME_URL = http://www.ensembl.org
+DESCRIPTION = Ensembl Funcgen Perl API
+define BLURB
+The Ensembl Funcgen Perl API allows you to programmatically access the
+Ensembl Funcgen database.
+endef
+LICENSE = Apache License
+CITE = doi:10.1093/nar/gkt1196
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = Ensembl/$(UPSTREAMNAME)/archive/release/
+DISTFILES = $(GARVERSION).zip
+WORKSRC = $(WORKDIR)/$(UPSTREAMNAME)-release-$(GARVERSION)
+INSTALL_SCRIPTS = modules
+
+BUILDDEPS =
+LIBDEPS = perl-bioperl
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+FILE_SITES = file://$(FILEDIR)/
+
+install-modules:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(UPSTREAMNAME)
modules.$(OFF)\n"
+ mkdir -p $(packageprefix)/lib/perl5/
+ cp -r $(WORKSRC)/modules/Bio $(packageprefix)/lib/perl5/
+ cp -r $(WORKSRC)/modules/t $(packageprefix)/lib/perl5
+ $(MAKECOOKIE)
=== added file 'pkg/other/perl-ensembl-funcgen/sha256sums'
--- a/pkg/other/perl-ensembl-funcgen/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/perl-ensembl-funcgen/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+b63d12c26eae5ae0ef6c8eeb5d8a359467bb470b3d9765e5612869aad90e28a6
download/78.zip
=== added directory 'pkg/other/perl-ensembl-variation'
=== added file 'pkg/other/perl-ensembl-variation/Makefile'
--- a/pkg/other/perl-ensembl-variation/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/perl-ensembl-variation/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,61 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Ensembl Variation
+GARNAME = perl-ensembl-variation
+UPSTREAMNAME = ensembl-variation
+GARVERSION = 78
+HOME_URL = http://www.ensembl.org
+DESCRIPTION = Ensembl Variation Perl API
+define BLURB
+The Ensembl Variation Perl API allows you to programmatically access
+the Ensembl Variation database.
+endef
+LICENSE = Apache License
+CITE = doi:10.1093/nar/gkt1196
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = Ensembl/$(UPSTREAMNAME)/archive/release/
+DISTFILES = $(GARVERSION).zip
+WORKSRC = $(WORKDIR)/$(UPSTREAMNAME)-release-$(GARVERSION)
+BUILD_SCRIPTS = $(WORKSRC)/C_code/Makefile
+INSTALL_SCRIPTS = modules calc_genotypes
+
+BUILDDEPS =
+LIBDEPS = perl-bioperl
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+FILE_SITES = file://$(FILEDIR)/
+MAKE_ARGS = calc_genotypes
+
+install-calc_genotypes:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(UPSTREAMNAME)
calc_genotype.$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/C_code/calc_genotypes
+ $(MAKECOOKIE)
+
+install-modules:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(UPSTREAMNAME)
modules.$(OFF)\n"
+ mkdir -p $(packageprefix)/lib/perl5/
+ cp -r $(WORKSRC)/modules/Bio $(packageprefix)/lib/perl5/
+ cp -r $(WORKSRC)/modules/t $(packageprefix)/lib/perl5
+ $(MAKECOOKIE)
=== added file 'pkg/other/perl-ensembl-variation/sha256sums'
--- a/pkg/other/perl-ensembl-variation/sha256sums 1970-01-01 00:00:00
+0000
+++ b/pkg/other/perl-ensembl-variation/sha256sums 2016-06-17 20:01:53
+0000
@@ -0,0 +1,1 @@
+25674e07821a97d4978b97570dd7622ebdf1459f30c3794f0b558acc54c9eeaa
download/78.zip
=== added file 'pkg/other/perl-ensembl/Makefile'
--- a/pkg/other/perl-ensembl/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/perl-ensembl/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,54 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Ensembl
+GARNAME = perl-ensembl
+UPSTREAMNAME = ensembl
+GARVERSION = 78
+HOME_URL = http://www.ensembl.org
+DESCRIPTION = Ensembl Perl API
+define BLURB
+The Ensembl Perl API allows you to programmatically access the Ensembl
+database.
+endef
+LICENSE = Apache License
+CITE = doi:10.1093/nar/gkt1196
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = Ensembl/$(UPSTREAMNAME)/archive/release/
+DISTFILES = $(GARVERSION).zip
+WORKSRC = $(WORKDIR)/$(UPSTREAMNAME)-release-$(GARVERSION)
+INSTALL_SCRIPTS = modules
+
+BUILDDEPS =
+LIBDEPS = perl-bioperl
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+FILE_SITES = file://$(FILEDIR)/
+
+install-modules:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(UPSTREAMNAME)
modules.$(OFF)\n"
+ mkdir -p $(packageprefix)/lib/perl5/
+ cp -r $(WORKSRC)/modules/Bio $(packageprefix)/lib/perl5/
+ cp -r $(WORKSRC)/modules/t $(packageprefix)/lib/perl5
+ $(MAKECOOKIE)
=== added file 'pkg/other/perl-ensembl/sha256sums'
--- a/pkg/other/perl-ensembl/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/perl-ensembl/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+83bce553d81a3c393e2544c36b4decf413afa3534a14f70d029ee24d50b8b799
download/78.zip
=== added directory 'pkg/other/python'
=== added directory 'pkg/other/python-biopython'
=== added file 'pkg/other/python-biopython/Makefile'
--- a/pkg/other/python-biopython/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-biopython/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,49 @@
+# Copyright © 2013, 2014, 2015, 2016 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Biopython
+GARNAME = python-biopython
+UPSTREAMNAME = biopython
+GARVERSION = 1.67
+HOME_URL = http://www.biopython.org
+DESCRIPTION = A set of Python modules for biological computation
+define BLURB
+Biopython is a set of Python modules for biological computation.
+Biopython features include parsers for various Bioinformatics file
+formats, access to online services, interfaces to common and not-so-
+common programs, a standard sequence class, various clustering
+modules, and a KD tree data structure.
+endef
+LICENSE = BSD-like
+
+######################################################################
+
+MASTER_SITES = http://biopython.org/
+MASTER_SUBDIR = DIST/
+DISTFILES = $(DISTNAME).tar.gz
+BUILD_SCRIPTS = $(WORKSRC)/setup.py
+INSTALL_SCRIPTS = $(WORKSRC)/setup.py
+
+BUILDDEPS =
+LIBDEPS = python-numpy
+
+PYTHON ?= $(prefix)/bin/python
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
=== added file 'pkg/other/python-biopython/sha256sums'
--- a/pkg/other/python-biopython/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-biopython/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+1ab322fe4d2f79d2d999c9d8faf8b4e0b4c41c4e8b5f0a97912dfa0e3aa249e6
download/biopython-1.67.tar.gz
=== added directory 'pkg/other/python-matplotlib'
=== added file 'pkg/other/python-matplotlib/Makefile'
--- a/pkg/other/python-matplotlib/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-matplotlib/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,46 @@
+# Copyright © 2015 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Matplotlib
+GARNAME = python-matplotlib
+UPSTREAMNAME = matplotlib
+GARVERSION = 1.4.3
+HOME_URL = http://matplotlib.org
+DESCRIPTION = 2-D plotting library for Python
+define BLURB
+Matplotlib is a 2-D plotting library for python, which exposes many
+low-level functions to have a complete control over the creation of
+plots.
+endef
+LICENSE = PSF
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(UPSTREAMNAME)/files/$(UPSTREAMNAME)/$(DISTNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS = python-setuptools
+LIBDEPS = python-six python-numpy
+
+PYTHON ?= $(prefix)/bin/python
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python-matplotlib/sha256sums'
--- a/pkg/other/python-matplotlib/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-matplotlib/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+5b9544472d9d6ab3d47423bdb5a0e64fdf913e505c1c083f25283dd0362bc0b6
download/matplotlib-1.4.3.tar.gz
=== added directory 'pkg/other/python-networkx'
=== added file 'pkg/other/python-networkx/Makefile'
--- a/pkg/other/python-networkx/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-networkx/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,47 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = NetworkX
+GARNAME = python-networkx
+UPSTREAMNAME = networkx
+GARVERSION = 1.8.1
+HOME_URL = http://networkx.lanl.gov/
+DESCRIPTION = Python library for the creation, manipulation, and study of the
structure, dynamics, and functions of complex networks
+define BLURB
+NetworkX is a Python library for the creation, manipulation, and study
+of the structure, dynamics, and functions of complex networks. The
+library features the implementation of undirected and directed graphs,
+a rich set of analysis algorithms and the ability to import/export
+graphs in common-used formats.
+endef
+LICENSE = BSD-like
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/
+MASTER_SUBDIR = packages/source/n/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python
+
+PYTHON ?= $(prefix)/bin/python
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python-networkx/sha256sums'
--- a/pkg/other/python-networkx/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-networkx/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+b75ba675fd2831f60e3f5a028822a8f7b9993877854599e9694196f8b2f88233
download/networkx-1.8.1.tar.gz
=== added directory 'pkg/other/python-numpy'
=== added file 'pkg/other/python-numpy/Makefile'
--- a/pkg/other/python-numpy/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-numpy/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,73 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = NumPy
+GARNAME = python-numpy
+UPSTREAMNAME = numpy
+GARVERSION = 1.8.0
+HOME_URL = http://www.numpy.org
+DESCRIPTION = Numerical python
+define BLURB
+NumPy is a package for scientific computing with Python. Its central
+feature is an N-dimensional array object and efficient functions for
+manipulating instances of it. It also includes many other useful
+numerical functions, tools for integrating C/C++ and Fortran code,
+and linear algebra capabilities.
+endef
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(UPSTREAMNAME)/files/NumPy/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python
+
+PYTHON ?= $(prefix)/bin/python
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
+
+CONFIGURE_SCRIPTS = setup.py
+INSTALL_SCRIPTS += links
+PY_INSTALL_ARGS += --optimize=1
+BUILD_ENV += ATLAS=None
+LDFLAGS += -shared
+
+configure-%/setup.py:
+ @printf "[$(OK)configure$(OFF)] $(MSG)Running setup.py configure in
$(OFF)$*\n"
+ cd $* && $(CONFIGURE_ENV) $(PYTHON) setup.py config `$(PYTHON)-config
--includes --libs` $(OUTPUT)
+ $(MAKECOOKIE)
+
+build-%/setup.py:
+ @printf "[$(OK)build$(OFF)] $(MSG)Running setup.py build in $(OFF)$*\n"
+ cd $* && $(BUILD_ENV) $(PYTHON) setup.py config_fc --fcompiler=gnu95
build $(PY_BUILD_ARGS) $(OUTPUT) \
+ || $(BUILD_FAIL)
+ $(MAKECOOKIE)
+
+install-%/setup.py:
+ @printf "[$(OK)install$(OFF)] $(MSG)Running setup.py install in
$(OFF)$*\n"
+ mkdir -p $(packageDESTDIR)`python -c 'from distutils.sysconfig import
get_python_lib; print get_python_lib()'`
+ cd $* && $(INSTALL_ENV) $(PYTHON) setup.py config_fc --fcompiler=gnu95
install --root=$(packageDESTDIR) $(PY_INSTALL_ARGS) $(OUTPUT)
+ $(MAKECOOKIE)
+
+install-links:
+ ln -sf
$(prefix)/lib/python$(PYTHON3_VER)/site-packages/numpy/core/include/numpy
$(packageprefix)/include/python$(PYTHON3_VER)/numpy
+ $(MAKECOOKIE)
=== added file 'pkg/other/python-numpy/sha256sums'
--- a/pkg/other/python-numpy/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-numpy/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+2764d0819acc77e9ff81b060fe7f69530b0d85c26ac9d162639b787cb227d253
download/numpy-1.8.0.tar.gz
=== added directory 'pkg/other/python-pandas'
=== added file 'pkg/other/python-pandas/Makefile'
--- a/pkg/other/python-pandas/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-pandas/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,45 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Pandas
+GARNAME = python-pandas
+UPSTREAMNAME = pandas
+GARVERSION = 0.13.1
+HOME_URL = http://pandas.pydata.org/
+DESCRIPTION = Python data analysis library
+define BLURB
+pandas is an open source, BSD-licensed library providing
+high-performance, easy-to-use data structures and data analysis
+tools for the Python programming language.
+endef
+LICENSE = 3-clause BSD
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/
+MASTER_SUBDIR = packages/source/p/$(UPSTREAMNAME)/
+DISTFILES = $(UPSTREAMNAME)-$(GARVERSION).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python python-numpy python-setuptools
+
+PYTHON ?= $(prefix)/bin/python
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python-pandas/sha256sums'
--- a/pkg/other/python-pandas/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-pandas/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+6813746caa796550969ed98069f16627f070f6d8d60686cfb3fa0e66c2e0312b
download/pandas-0.13.1.tar.gz
=== added directory 'pkg/other/python-scipy'
=== added file 'pkg/other/python-scipy/Makefile'
--- a/pkg/other/python-scipy/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-scipy/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,70 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = SciPy
+GARNAME = python-scipy
+UPSTREAMNAME = scipy
+GARVERSION = 0.13.3
+HOME_URL = http://www.scipy.org
+DESCRIPTION = A mathematical library for Python
+define BLURB
+SciPy is a collection of mathematical algorithms and convenience
+functions for Python. It provides high-level commands and classes for
+manipulating and visualizing data.
+endef
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(UPSTREAMNAME)/files/$(UPSTREAMNAME)/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python python-numpy
+
+PYTHON = $(prefix)/bin/python
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
+
+CONFIGURE_SCRIPTS =
+PY_INSTALL_ARGS += --optimize=1
+BUILD_ENV += ATLAS=None
+LDFLAGS += -shared
+
+ifeq ($(PYTHON),$(prefix)/bin/python2)
+pre-configure:
+ sed -e "s|#![ ]*/usr/bin/python$$|#!/$(prefix)/bin/python2|" \
+ -e "s|#![ ]*/usr/bin/env python$$|#!/$(prefix)/bin/python2|" \
+ -e "s|#![ ]*/bin/env python$$|#!/$(prefix)/bin/python2|" \
+ -i $(shell find $(WORKSRC) -name '*.py')
+endif
+
+build-%/setup.py:
+ @printf "[$(OK)build$(OFF)] $(MSG)Running setup.py build in $(OFF)$*\n"
+ cd $* && $(BUILD_ENV) $(PYTHON) setup.py config_fc --fcompiler=gnu95
build $(PY_BUILD_ARGS) $(OUTPUT) \
+ || $(BUILD_FAIL)
+ $(MAKECOOKIE)
+
+install-%/setup.py:
+ @printf "[$(OK)install$(OFF)] $(MSG)Running setup.py install in
$(OFF)$*\n"
+ mkdir -p $(packageDESTDIR)`python -c 'from distutils.sysconfig import
get_python_lib; print get_python_lib()'`
+ cd $* && $(INSTALL_ENV) $(PYTHON) setup.py config_fc --fcompiler=gnu95
install --root=$(packageDESTDIR) $(PY_INSTALL_ARGS) $(OUTPUT)
+ $(MAKECOOKIE)
+
=== added file 'pkg/other/python-scipy/sha256sums'
--- a/pkg/other/python-scipy/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-scipy/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+a9e33c7ee060c35cd5c6ee3ac9e5e9bbb99219d7ea8c89537c2e80e581670266
download/scipy-0.13.3.tar.gz
=== added directory 'pkg/other/python-setuptools'
=== added file 'pkg/other/python-setuptools/Makefile'
--- a/pkg/other/python-setuptools/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-setuptools/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,44 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = setuptools
+GARNAME = python-setuptools
+UPSTREAMNAME = setuptools
+GARVERSION = 3.6
+HOME_URL = https://pypi.python.org/pypi/setuptools
+DESCRIPTION = Easily download, build, install, upgrade and uninstall Python
packages
+define BLURB
+Easily download, build, install, upgrade and uninstall Python packages
+endef
+LICENSE = Python Software Foundation License
+CITE =
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/packages/source/
+MASTER_SUBDIR = s/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python
+
+PYTHON = $(prefix)/bin/python
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python-setuptools/sha256sums'
--- a/pkg/other/python-setuptools/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-setuptools/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+afaf5f78b9b0b6439af11224601b2130494051701912e4d9915647e51d9de0e7
download/setuptools-3.6.tar.gz
=== added directory 'pkg/other/python-six'
=== added file 'pkg/other/python-six/Makefile'
--- a/pkg/other/python-six/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-six/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,46 @@
+# Copyright © 2015 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = six
+GARNAME = python-six
+UPSTREAMNAME = six
+GARVERSION = 1.9.0
+HOME_URL = https://pypi.python.org/pypi/six/
+DESCRIPTION = Python 2-to-3 compatibility utilities
+define BLURB
+six provides utilities for maintaining a codebase that is compatible
+with both Python 2 and 3.
+endef
+LICENSE = Expat
+CITE =
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/packages/source/
+MASTER_SUBDIR = s/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+SIGFILES =
+
+BUILDDEPS =
+LIBDEPS =
+
+PYTHON = $(prefix)/bin/python
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python-six/sha256sums'
--- a/pkg/other/python-six/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-six/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5
download/six-1.9.0.tar.gz
=== added directory 'pkg/other/python-sqlalchemy'
=== added file 'pkg/other/python-sqlalchemy/Makefile'
--- a/pkg/other/python-sqlalchemy/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-sqlalchemy/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,47 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = SQLAlchemy
+GARNAME = python-sqlalchemy
+UPSTREAMNAME = SQLAlchemy
+GARVERSION = 0.9.4
+HOME_URL = http://www.sqlalchemy.org
+DESCRIPTION = The Python SQL toolkit and Object Relational Mapper
+define BLURB
+SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that
+allows interfacing with SQL databases in a high-level manner using a
+simple Pythonic domain language with the full power of SQL.
+endef
+LICENSE = Expat License
+CITE =
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/packages/source/
+MASTER_SUBDIR = S/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+SIGFILES = $(DISTNAME).tar.gz.asc
+
+BUILDDEPS =
+LIBDEPS = python
+
+PYTHON = $(prefix)/bin/python
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python-sqlalchemy/gpg-keyring'
Binary files a/pkg/other/python-sqlalchemy/gpg-keyring 1970-01-01 00:00:00
+0000 and b/pkg/other/python-sqlalchemy/gpg-keyring 2016-06-17 20:01:53 +0000
differ
=== added file 'pkg/other/python-sqlalchemy/sha256sums'
--- a/pkg/other/python-sqlalchemy/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python-sqlalchemy/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,2 @@
+bc87674f5ac9962e0efe96f060ba22a07e2c61fbebf531efc383b82db5b291ec
download/SQLAlchemy-0.9.4.tar.gz
+ddb43c49249b99178c317af4df8fc3899322f0b4e7750b9cef4799c1ce8a3d38
download/SQLAlchemy-0.9.4.tar.gz.asc
=== added file 'pkg/other/python/Makefile'
--- a/pkg/other/python/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,63 @@
+# Copyright © 2014, 2015, 2016 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Python
+GARNAME = python
+UPSTREAMNAME = Python
+GARVERSION = 3.5.1
+BASEVERSION = 3.5
+HOME_URL = http://python.org
+DESCRIPTION = A general-purpose, high-level programming language
+define BLURB
+Python is a high-level programming language that emphasizes code
+readability and expressiveness. It features a large standard library
+that encompases a wide range of functionality. It supports multiple
+programming paradigms including object-oriented, imperative or
+procedural styles.
+endef
+LICENSE = Python Software Foundation License
+
+######################################################################
+
+MASTER_SITES = http://python.org/
+MASTER_SUBDIR = ftp/$(GARNAME)/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.xz
+SIGFILES = $(DISTNAME).tar.xz.asc
+INSTALL_SCRIPTS = $(WORKSRC)/Makefile links pth
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
+
+install-links:
+ ln -sf $(packagedir)/bin/python3 $(packageprefix)/bin/python
+ ln -sf $(packagedir)/bin/python3-config
$(packageprefix)/bin/python-config
+ ln -sf $(packagedir)/bin/pydoc3 $(packageprefix)/bin/pydoc
+ $(MAKECOOKIE)
+
+install-pth:
+ mkdir -p $(packageprefix)/lib/python$(BASEVERSION)/site-packages/
+ echo "$(prefix)/lib/python$(BASEVERSION)/site-packages"
>$(packageprefix)/lib/python$(BASEVERSION)/site-packages/biosrc.pth
+ $(MAKECOOKIE)
+
+post-install:
+ sed -i 's|$(packageprefix)|$(prefix)|'
$(packagedir)/bin/python$(BASEVERSION)-config
+ $(MAKECOOKIE)
=== added file 'pkg/other/python/gpg-keyring'
Binary files a/pkg/other/python/gpg-keyring 1970-01-01 00:00:00 +0000 and
b/pkg/other/python/gpg-keyring 2016-06-17 20:01:53 +0000 differ
=== added file 'pkg/other/python/sha256sums'
--- a/pkg/other/python/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,2 @@
+c6d57c0c366d9060ab6c0cdf889ebf3d92711d466cc0119c441dbf2746f725c9
download/Python-3.5.1.tar.xz
+0cee1b1b61dd1bc3201b978ab02fd3c17db97e1e6caf12748e9e74be923d8a63
download/Python-3.5.1.tar.xz.asc
=== added directory 'pkg/other/python2'
=== added directory 'pkg/other/python2-biopython'
=== added file 'pkg/other/python2-biopython/Makefile'
--- a/pkg/other/python2-biopython/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-biopython/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,49 @@
+# Copyright © 2013, 2014, 2015, 2016 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Biopython (Python 2)
+GARNAME = python2-biopython
+UPSTREAMNAME = biopython
+GARVERSION = 1.67
+HOME_URL = http://www.biopython.org
+DESCRIPTION = A set of Python modules for biological computation
+define BLURB
+Biopython is a set of Python modules for biological computation.
+Biopython features include parsers for various Bioinformatics file
+formats, access to online services, interfaces to common and not-so-
+common programs, a standard sequence class, various clustering
+modules, and a KD tree data structure. (Python 2 version)
+endef
+LICENSE = BSD-like
+
+######################################################################
+
+MASTER_SITES = http://biopython.org/
+MASTER_SUBDIR = DIST/
+DISTFILES = $(DISTNAME).tar.gz
+BUILD_SCRIPTS = $(WORKSRC)/setup.py
+INSTALL_SCRIPTS = $(WORKSRC)/setup.py
+
+BUILDDEPS =
+LIBDEPS = python2-numpy
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
=== added file 'pkg/other/python2-biopython/sha256sums'
--- a/pkg/other/python2-biopython/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-biopython/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+1ab322fe4d2f79d2d999c9d8faf8b4e0b4c41c4e8b5f0a97912dfa0e3aa249e6
download/biopython-1.67.tar.gz
=== added directory 'pkg/other/python2-dateutil'
=== added file 'pkg/other/python2-dateutil/Makefile'
--- a/pkg/other/python2-dateutil/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-dateutil/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,44 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Dateutil (Python 2)
+GARNAME = python2-dateutil
+UPSTREAMNAME = python-dateutil
+GARVERSION = 2.2
+HOME_URL = http://labix.org/python-dateutil
+DESCRIPTION = Extensions to the standard Python datetime module
+define BLURB
+The dateutil module provides powerful extensions to the datetime
+module available in the Python standard library (Python 2 version).
+endef
+LICENSE = Simplified BSD
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/
+MASTER_SUBDIR = packages/source/p/$(UPSTREAMNAME)/
+DISTFILES = $(UPSTREAMNAME)-$(GARVERSION).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python2 python2-setuptools
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python2-dateutil/sha256sums'
--- a/pkg/other/python2-dateutil/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-dateutil/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+eec865307ebe7f329a6a9945c15453265a449cdaaf3710340828a1934d53e468
download/python-dateutil-2.2.tar.gz
=== added directory 'pkg/other/python2-htseq'
=== added file 'pkg/other/python2-htseq/Makefile'
--- a/pkg/other/python2-htseq/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-htseq/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,49 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = HTSeq
+GARNAME = python2-htseq
+UPSTREAMNAME = HTSeq
+GARVERSION = 0.6.0
+HOME_URL = http://www-huber.embl.de/users/anders/HTSeq/
+DESCRIPTION = A framework to process and analyze high-throughput sequencing
data
+define BLURB
+HTSeq is a Python framework for processing and analyzing data from
+high-throughput sequencing assays. Its purpose is to allow you to
+write your own, customized analysis scripts without having to
+implement the basic functionality.
+endef
+LICENSE = GPLV3 or later
+CITE = doi:10.1101/002824
+
+######################################################################
+
+MASTER_SITES = http://pypi.python.org/packages/
+MASTER_SUBDIR = source/H/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+BUILD_SCRIPTS = $(WORKSRC)/setup.py
+INSTALL_SCRIPTS = $(WORKSRC)/setup.py
+
+BUILDDEPS =
+LIBDEPS = python2-numpy #python-setuptools
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
=== added file 'pkg/other/python2-htseq/sha256sums'
--- a/pkg/other/python2-htseq/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-htseq/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+d7af916c77ff2df13bb782db8276e0133a829656b77b51ecbffcc8b9aed420ed
download/HTSeq-0.6.0.tar.gz
=== added directory 'pkg/other/python2-matplotlib'
=== added file 'pkg/other/python2-matplotlib/Makefile'
--- a/pkg/other/python2-matplotlib/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-matplotlib/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,46 @@
+# Copyright © 2015 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Matplotlib
+GARNAME = python2-matplotlib
+UPSTREAMNAME = matplotlib
+GARVERSION = 1.4.3
+HOME_URL = http://matplotlib.org
+DESCRIPTION = 2-D plotting library for Python
+define BLURB
+Matplotlib is a 2-D plotting library for python, which exposes many
+low-level functions to have a complete control over the creation of
+plots.
+endef
+LICENSE = PSF
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(UPSTREAMNAME)/files/$(UPSTREAMNAME)/$(DISTNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS = python2-setuptools
+LIBDEPS = python2-six python2-numpy
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python2-matplotlib/sha256sums'
--- a/pkg/other/python2-matplotlib/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-matplotlib/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+5b9544472d9d6ab3d47423bdb5a0e64fdf913e505c1c083f25283dd0362bc0b6
download/matplotlib-1.4.3.tar.gz
=== added directory 'pkg/other/python2-networkx'
=== added file 'pkg/other/python2-networkx/Makefile'
--- a/pkg/other/python2-networkx/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-networkx/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,47 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = NetworkX (Python 2)
+GARNAME = python-networkx
+UPSTREAMNAME = networkx
+GARVERSION = 1.8.1
+HOME_URL = http://networkx.lanl.gov/
+DESCRIPTION = Python library for the creation, manipulation, and study of the
structure, dynamics, and functions of complex networks
+define BLURB
+NetworkX is a Python library for the creation, manipulation, and study
+of the structure, dynamics, and functions of complex networks. The
+library features the implementation of undirected and directed graphs,
+a rich set of analysis algorithms and the ability to import/export
+graphs in common-used formats. (Python 2 version)
+endef
+LICENSE = BSD-like
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/
+MASTER_SUBDIR = packages/source/n/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python2
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python2-networkx/sha256sums'
--- a/pkg/other/python2-networkx/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-networkx/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+b75ba675fd2831f60e3f5a028822a8f7b9993877854599e9694196f8b2f88233
download/networkx-1.8.1.tar.gz
=== added directory 'pkg/other/python2-numpy'
=== added file 'pkg/other/python2-numpy/Makefile'
--- a/pkg/other/python2-numpy/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-numpy/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,79 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = NumPy (Python 2)
+GARNAME = python2-numpy
+UPSTREAMNAME = numpy
+GARVERSION = 1.8.0
+HOME_URL = http://www.numpy.org
+DESCRIPTION = Numerical python
+define BLURB
+NumPy is a package for scientific computing with Python. Its central
+feature is an N-dimensional array object and efficient functions for
+manipulating instances of it. It also includes many other useful
+numerical functions, tools for integrating C/C++ and Fortran code,
+and linear algebra capabilities. (Python 2 version)
+endef
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(UPSTREAMNAME)/files/NumPy/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python2
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
+
+CONFIGURE_SCRIPTS = setup.py
+INSTALL_SCRIPTS += links
+PY_INSTALL_ARGS += --optimize=1
+BUILD_ENV += ATLAS=None
+LDFLAGS += -shared
+
+pre-configure:
+ sed -e "s|#![ ]*/usr/bin/python$$|#!/$(prefix)/bin/python2|" \
+ -e "s|#![ ]*/usr/bin/env python$$|#!/$(prefix)/bin/python2|" \
+ -e "s|#![ ]*/bin/env python$$|#!/$(prefix)/bin/python2|" \
+ -i $(shell find $(WORKSRC) -name '*.py')
+
+configure-%/setup.py:
+ @printf "[$(OK)configure$(OFF)] $(MSG)Running setup.py configure in
$(OFF)$*\n"
+ cd $* && $(CONFIGURE_ENV) $(PYTHON) setup.py config `$(PYTHON)-config
--includes --libs` $(OUTPUT)
+ $(MAKECOOKIE)
+
+build-%/setup.py:
+ @printf "[$(OK)build$(OFF)] $(MSG)Running setup.py build in $(OFF)$*\n"
+ cd $* && $(BUILD_ENV) $(PYTHON) setup.py config_fc --fcompiler=gnu95
build $(PY_BUILD_ARGS) $(OUTPUT) \
+ || $(BUILD_FAIL)
+ $(MAKECOOKIE)
+
+install-%/setup.py:
+ @printf "[$(OK)install$(OFF)] $(MSG)Running setup.py install in
$(OFF)$*\n"
+ mkdir -p $(packageDESTDIR)`python -c 'from distutils.sysconfig import
get_python_lib; print get_python_lib()'`
+ cd $* && $(INSTALL_ENV) $(PYTHON) setup.py config_fc --fcompiler=gnu95
install --root=$(packageDESTDIR) $(PY_INSTALL_ARGS) $(OUTPUT)
+ $(MAKECOOKIE)
+
+install-links:
+ ln -sf
$(prefix)/lib/python$(PYTHON2_VER)/site-packages/numpy/core/include/numpy
$(packageprefix)/include/python$(PYTHON2_VER)/numpy
+ $(MAKECOOKIE)
=== added file 'pkg/other/python2-numpy/sha256sums'
--- a/pkg/other/python2-numpy/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-numpy/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+2764d0819acc77e9ff81b060fe7f69530b0d85c26ac9d162639b787cb227d253
download/numpy-1.8.0.tar.gz
=== added directory 'pkg/other/python2-pandas'
=== added file 'pkg/other/python2-pandas/Makefile'
--- a/pkg/other/python2-pandas/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-pandas/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,45 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Pandas (Python 2)
+GARNAME = python2-pandas
+UPSTREAMNAME = pandas
+GARVERSION = 0.13.1
+HOME_URL = http://pandas.pydata.org/
+DESCRIPTION = Python data analysis library
+define BLURB
+pandas is an open source, BSD-licensed library providing
+high-performance, easy-to-use data structures and data analysis
+tools for the Python programming language (Python 2 version).
+endef
+LICENSE = 3-clause BSD
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/
+MASTER_SUBDIR = packages/source/p/$(UPSTREAMNAME)/
+DISTFILES = $(UPSTREAMNAME)-$(GARVERSION).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python2 python2-numpy python2-setuptools python2-dateutil
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python2-pandas/sha256sums'
--- a/pkg/other/python2-pandas/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-pandas/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+6813746caa796550969ed98069f16627f070f6d8d60686cfb3fa0e66c2e0312b
download/pandas-0.13.1.tar.gz
=== added directory 'pkg/other/python2-pysam'
=== added file 'pkg/other/python2-pysam/Makefile'
--- a/pkg/other/python2-pysam/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-pysam/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,46 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = PySam (Python 2)
+GARNAME = python2-pysam
+UPSTREAMNAME = pysam
+GARVERSION = 0.8.1
+HOME_URL = https://code.google.com/p/pysam/
+DESCRIPTION = A python module for reading and manipulating samfiles
+define BLURB
+Pysam is a python module for reading and manipulating files in the
+SAM/BAM format. The SAM/BAM format is a way to store efficiently
+large numbers of alignments, such as those routinely created by
+next-generation sequencing methods.
+endef
+LICENSE = BSD-like
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/
+MASTER_SUBDIR = packages/source/p/$(UPSTREAMNAME)/
+DISTFILES = $(UPSTREAMNAME)-$(GARVERSION).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python2
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python2-pysam/sha256sums'
--- a/pkg/other/python2-pysam/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-pysam/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+a9105a1aa65f5a93e1e2cfb0e3009190b7a8a82ad7fb29cceaaaffbba08966b9
download/pysam-0.8.1.tar.gz
=== added directory 'pkg/other/python2-scipy'
=== added file 'pkg/other/python2-scipy/Makefile'
--- a/pkg/other/python2-scipy/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-scipy/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,70 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = SciPy (Python 2)
+GARNAME = python-scipy
+UPSTREAMNAME = scipy
+GARVERSION = 0.13.3
+HOME_URL = http://www.scipy.org
+DESCRIPTION = A mathematical library for Python
+define BLURB
+SciPy is a collection of mathematical algorithms and convenience
+functions for Python. It provides high-level commands and classes for
+manipulating and visualizing data. (Python 2 version)
+endef
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(UPSTREAMNAME)/files/$(UPSTREAMNAME)/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python2 python2-numpy
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
+
+CONFIGURE_SCRIPTS =
+PY_INSTALL_ARGS += --optimize=1
+BUILD_ENV += ATLAS=None
+LDFLAGS += -shared
+
+ifeq ($(PYTHON),$(prefix)/bin/python2)
+pre-configure:
+ sed -e "s|#![ ]*/usr/bin/python$$|#!/$(prefix)/bin/python2|" \
+ -e "s|#![ ]*/usr/bin/env python$$|#!/$(prefix)/bin/python2|" \
+ -e "s|#![ ]*/bin/env python$$|#!/$(prefix)/bin/python2|" \
+ -i $(shell find $(WORKSRC) -name '*.py')
+endif
+
+build-%/setup.py:
+ @printf "[$(OK)build$(OFF)] $(MSG)Running setup.py build in $(OFF)$*\n"
+ cd $* && $(BUILD_ENV) $(PYTHON) setup.py config_fc --fcompiler=gnu95
build $(PY_BUILD_ARGS) $(OUTPUT) \
+ || $(BUILD_FAIL)
+ $(MAKECOOKIE)
+
+install-%/setup.py:
+ @printf "[$(OK)install$(OFF)] $(MSG)Running setup.py install in
$(OFF)$*\n"
+ mkdir -p $(packageDESTDIR)`python -c 'from distutils.sysconfig import
get_python_lib; print get_python_lib()'`
+ cd $* && $(INSTALL_ENV) $(PYTHON) setup.py config_fc --fcompiler=gnu95
install --root=$(packageDESTDIR) $(PY_INSTALL_ARGS) $(OUTPUT)
+ $(MAKECOOKIE)
+
=== added file 'pkg/other/python2-scipy/sha256sums'
--- a/pkg/other/python2-scipy/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-scipy/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+a9e33c7ee060c35cd5c6ee3ac9e5e9bbb99219d7ea8c89537c2e80e581670266
download/scipy-0.13.3.tar.gz
=== added directory 'pkg/other/python2-setuptools'
=== added file 'pkg/other/python2-setuptools/Makefile'
--- a/pkg/other/python2-setuptools/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-setuptools/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,44 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = setuptools
+GARNAME = python-setuptools
+UPSTREAMNAME = setuptools
+GARVERSION = 3.6
+HOME_URL = https://pypi.python.org/pypi/setuptools
+DESCRIPTION = Easily download, build, install, upgrade and uninstall Python
packages
+define BLURB
+Easily download, build, install, upgrade and uninstall Python packages
+endef
+LICENSE = Python Software Foundation License
+CITE =
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/packages/source/
+MASTER_SUBDIR = s/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python2
+
+PYTHON = $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python2-setuptools/sha256sums'
--- a/pkg/other/python2-setuptools/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-setuptools/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+afaf5f78b9b0b6439af11224601b2130494051701912e4d9915647e51d9de0e7
download/setuptools-3.6.tar.gz
=== added directory 'pkg/other/python2-six'
=== added file 'pkg/other/python2-six/Makefile'
--- a/pkg/other/python2-six/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-six/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,46 @@
+# Copyright © 2015 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = six
+GARNAME = python2-six
+UPSTREAMNAME = six
+GARVERSION = 1.9.0
+HOME_URL = https://pypi.python.org/pypi/six/
+DESCRIPTION = Python 2-to-3 compatibility utilities
+define BLURB
+six provides utilities for maintaining a codebase that is compatible
+with both Python 2 and 3.
+endef
+LICENSE = Expat
+CITE =
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/packages/source/
+MASTER_SUBDIR = s/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+SIGFILES =
+
+BUILDDEPS =
+LIBDEPS =
+
+PYTHON = $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python2-six/sha256sums'
--- a/pkg/other/python2-six/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-six/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5
download/six-1.9.0.tar.gz
=== added directory 'pkg/other/python2-sqlalchemy'
=== added file 'pkg/other/python2-sqlalchemy/Makefile'
--- a/pkg/other/python2-sqlalchemy/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-sqlalchemy/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,47 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = SQLAlchemy (Python 2)
+GARNAME = python2-sqlalchemy
+UPSTREAMNAME = SQLAlchemy
+GARVERSION = 0.9.4
+HOME_URL = http://www.sqlalchemy.org
+DESCRIPTION = The Python SQL toolkit and Object Relational Mapper
+define BLURB
+SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that
+allows interfacing with SQL databases in a high-level manner using a
+simple Pythonic domain language with the full power of SQL.
+endef
+LICENSE = Expat License
+CITE =
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/packages/source/
+MASTER_SUBDIR = S/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+SIGFILES = $(DISTNAME).tar.gz.asc
+
+BUILDDEPS =
+LIBDEPS = python2
+
+PYTHON = $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python2-sqlalchemy/gpg-keyring'
Binary files a/pkg/other/python2-sqlalchemy/gpg-keyring 1970-01-01 00:00:00
+0000 and b/pkg/other/python2-sqlalchemy/gpg-keyring 2016-06-17 20:01:53
+0000 differ
=== added file 'pkg/other/python2-sqlalchemy/sha256sums'
--- a/pkg/other/python2-sqlalchemy/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-sqlalchemy/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,2 @@
+bc87674f5ac9962e0efe96f060ba22a07e2c61fbebf531efc383b82db5b291ec
download/SQLAlchemy-0.9.4.tar.gz
+ddb43c49249b99178c317af4df8fc3899322f0b4e7750b9cef4799c1ce8a3d38
download/SQLAlchemy-0.9.4.tar.gz.asc
=== added directory 'pkg/other/python2-toolz'
=== added file 'pkg/other/python2-toolz/Makefile'
--- a/pkg/other/python2-toolz/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-toolz/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,47 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Toolz (Python 2)
+GARNAME = python2-toolz
+UPSTREAMNAME = toolz
+GARVERSION = 0.7.0
+HOME_URL = http://toolz.readthedocs.org/en/latest/
+DESCRIPTION = Utility functions for iterators, functions, dictionaries.
+define BLURB
+Toolz provides a set of utility functions for iterators, functions,
+and dictionaries. These functions interoperate well and form the
+building blocks of common data analytic operations. They extend the
+standard libraries itertools and functools and borrow heavily from the
+standard libraries of contemporary functional languages.
+endef
+LICENSE = BSD
+
+######################################################################
+
+MASTER_SITES = https://pypi.python.org/
+MASTER_SUBDIR = packages/source/t/$(UPSTREAMNAME)/
+DISTFILES = $(UPSTREAMNAME)-$(GARVERSION).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python2 python2-setuptools
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/other/python2-toolz/sha256sums'
--- a/pkg/other/python2-toolz/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2-toolz/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+8f88590f960c16db2146b6ecae31f9d048865612b69e197907e886c963fad6f3
download/toolz-0.7.0.tar.gz
=== added file 'pkg/other/python2/Makefile'
--- a/pkg/other/python2/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,69 @@
+# Copyright © 2014, 2015, 2016 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Python 2
+GARNAME = python2
+UPSTREAMNAME = Python
+GARVERSION = 2.7.11
+BASEVERSION = 2.7
+HOME_URL = http://python.org
+DESCRIPTION = A general-purpose, high-level programming language (Version 2)
+define BLURB
+Python is a high-level programming language that emphasizes code
+readability and expressiveness. It features a large standard library
+that encompases a wide range of functionality. It supports multiple
+programming paradigms including object-oriented, imperative or
+procedural styles.
+endef
+LICENSE = Python Software Foundation License
+
+######################################################################
+
+MASTER_SITES = http://python.org/
+MASTER_SUBDIR = ftp/python/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.xz
+SIGFILES = $(DISTNAME).tar.xz.asc
+INSTALL_SCRIPTS = $(WORKSRC)/Makefile links pth
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
+
+COLLISIONS = python-config
+
+install-links:
+ rm $(packageprefix)/bin/python2 $(packageprefix)/bin/python
+ ln -sf $(packagedir)/bin/python$(BASEVERSION)
$(packageprefix)/bin/python2
+ ln -sf $(packagedir)/bin/python$(BASEVERSION)-config
$(packageprefix)/bin/python2-config
+ mv $(packageprefix)/bin/idle $(packageprefix)/bin/idle2
+ mv $(packageprefix)/bin/pydoc $(packageprefix)/bin/pydoc2
+ mv $(packageprefix)/bin/2to3 $(packageprefix)/bin/2to3-2.7
+ $(MAKECOOKIE)
+
+install-pth:
+ mkdir -p $(packageprefix)/lib/python$(BASEVERSION)/site-packages/
+ echo "$(prefix)/lib/python$(BASEVERSION)/site-packages"
>$(packageprefix)/lib/python$(BASEVERSION)/site-packages/biosrc.pth
+ $(MAKECOOKIE)
+
+post-install:
+ sed -i 's|$(packageprefix)|$(prefix)|'
$(packagedir)/bin/python$(BASEVERSION)-config
+ $(MAKECOOKIE)
+
=== added file 'pkg/other/python2/gpg-keyring'
Binary files a/pkg/other/python2/gpg-keyring 1970-01-01 00:00:00 +0000 and
b/pkg/other/python2/gpg-keyring 2016-06-17 20:01:53 +0000 differ
=== added file 'pkg/other/python2/sha256sums'
--- a/pkg/other/python2/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/python2/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,2 @@
+962b4c45af50124ea61f11a30deb4342fc0bc21126790fa1d7f6c79809413f46
download/Python-2.7.11.tar.xz
+67a4ab927355ef156160663f0dcc610016254a52f4f3fe091cf33efd72cb8fe6
download/Python-2.7.11.tar.xz.asc
=== added directory 'pkg/other/seqan'
=== added file 'pkg/other/seqan/Makefile'
--- a/pkg/other/seqan/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/seqan/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,50 @@
+# Copyright © 2013, 2014, 2015 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = SeqAn
+GARNAME = seqan
+GARVERSION = 2.0.0
+HOME_URL = http://www.seqan.de
+DESCRIPTION = A C++ library for the analysis of sequences
+define BLURB
+SeqAn is a C++ library of algorithms and data structures for the
+analysis of sequences with the focus on biological data.
+endef
+LICENSE = 3-clause BSD
+CITE = doi:10.1186/1471-2105-9-11
+
+######################################################################
+
+MASTER_SITES = http://packages.seqan.de/
+MASTER_SUBDIR = $(GARNAME)-src/
+DISTFILES = $(GARNAME)-src-$(GARVERSION).tar.gz
+WORKSRC = $(WORKDIR)/$(GARNAME)-$(GARNAME)-v$(GARVERSION)
+BUILD_SCRIPTS = $(WORKOBJ)/Makefile
+INSTALL_SCRIPTS = $(WORKOBJ)/cmake_install.cmake headers
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/cmake.mk
+include config.mk
+
+install-headers:
+ mkdir -p $(packageprefix)/include
+ cp -r $(WORKSRC)/include/seqan $(packageprefix)/include
+ $(MAKECOOKIE)
=== added file 'pkg/other/seqan/sha256sums'
--- a/pkg/other/seqan/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/seqan/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+69cb39574e63de2f728715255ac7ffd26db6480d6ce33c8601eef05f282aed28
download/seqan-src-2.0.0.tar.gz
=== added directory 'pkg/other/sparsehash'
=== added file 'pkg/other/sparsehash/Makefile'
--- a/pkg/other/sparsehash/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/sparsehash/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,44 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = sparsehash
+GARNAME = sparsehash
+GARVERSION = 2.0.2
+HOME_URL = https://code.google.com/p/sparsehash/
+DESCRIPTION = An extremely memory-efficient hash_map implementation
+define BLURB
+sparsehash is a C++ library that implemnts several hash-map
+implementations, including ones that optimize for space or speed.
+It also contains code to serialize and unserialize hash-maps from
+disk.
+endef
+LICENSE = 3-clause BSD
+CITE =
+
+######################################################################
+
+MASTER_SITES = https://$(GARNAME).googlecode.com/
+MASTER_SUBDIR = files/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/other/sparsehash/sha256sums'
--- a/pkg/other/sparsehash/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/sparsehash/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,1 @@
+2ed639a7155607c097c2029af5f4287296595080b2e5dd2e2ebd9bbb7450b87c
download/sparsehash-2.0.2.tar.gz
=== added directory 'pkg/other/xerces'
=== added file 'pkg/other/xerces/Makefile'
--- a/pkg/other/xerces/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/xerces/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,46 @@
+# Copyright © 2015 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Xerces-C++
+GARNAME = xerces
+UPSTREAMNAME = xerces-c
+GARVERSION = 3.1.1
+HOME_URL = https://xerces.apache.org/xerces-c
+DESCRIPTION = A validating XML parser
+define BLURB
+Xerces-C++ is a validating XML parser written in a portable subset of
+C++. A shared library is provided for parsing, generating,
+manipulating, and validating XML documents using the DOM, SAX, and
+SAX2 APIs.
+endef
+LICENSE =
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_APACHE)
+MASTER_SUBDIR = $(GARNAME)/c/3/sources/
+DISTFILES = $(DISTNAME).tar.gz
+SIGFILES = $(DISTNAME).tar.gz.asc
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/other/xerces/gpg-keyring'
Binary files a/pkg/other/xerces/gpg-keyring 1970-01-01 00:00:00 +0000 and
b/pkg/other/xerces/gpg-keyring 2016-06-17 20:01:53 +0000 differ
=== added file 'pkg/other/xerces/sha256sums'
--- a/pkg/other/xerces/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/xerces/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,2 @@
+a42785f71e0b91d5fd273831c87410ce60a73ccfdd207de1b805d26d44968736
download/xerces-c-3.1.1.tar.gz
+f7a60bcc9855b965f37ad9ebbaeb4dc69d72de865e7683351d6829cf8eaeb7d4
download/xerces-c-3.1.1.tar.gz.asc
=== added directory 'pkg/other/zeptodb'
=== added file 'pkg/other/zeptodb/Makefile'
--- a/pkg/other/zeptodb/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/other/zeptodb/Makefile 2016-06-17 20:01:53 +0000
@@ -0,0 +1,45 @@
+# Copyright © 2014, 2016 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = zeptodb
+GARNAME = zeptodb
+GARVERSION = 3.0.1
+HOME_URL = http://zeptodb.invergo.net
+DESCRIPTION = Command-line DBM tools
+define BLURB
+zeptodb provides command-line tools for creating and manipulating DBM
+databases. DBM databases are non-relational databases consisting of
+key-value pairs; thus, they are disk-bound hash tables, providing
+constant, fast look-up time even in large databases.
+endef
+LICENSE = GPLv3 or later
+
+######################################################################
+
+MASTER_SITES = http://zeptodb.invergo.net/
+MASTER_SUBDIR = download/
+DISTFILES = $(DISTNAME).tar.gz
+SIGFILES = $(DISTNAME).tar.gz.sig
+
+BUILDDEPS =
+LIBDEPS = gdbm
+
+######################################################################
+
+include ../../../gar/gar.lib/info.mk
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/other/zeptodb/gpg-keyring'
Binary files a/pkg/other/zeptodb/gpg-keyring 1970-01-01 00:00:00 +0000 and
b/pkg/other/zeptodb/gpg-keyring 2016-06-17 20:01:53 +0000 differ
=== added file 'pkg/other/zeptodb/sha256sums'
--- a/pkg/other/zeptodb/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/other/zeptodb/sha256sums 2016-06-17 20:01:53 +0000
@@ -0,0 +1,2 @@
+16fd4bbf39a1ce19cab768d9dbaac3bd6ae1b3974103644fb226a17db2e51239
download/zeptodb-3.0.1.tar.gz
+1bc1ba4e78c6ba86533d658c868ba11f53b5082c57e3ffdb017c4e28b6310f4f
download/zeptodb-3.0.1.tar.gz.sig
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- [Gsrc-commit] trunk r3733: big changes, added rest pkg from BioSrc,
Carl Hansen <=