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Re: [PATCH] Add preseq.
From: |
Ricardo Wurmus |
Subject: |
Re: [PATCH] Add preseq. |
Date: |
Tue, 7 Jul 2015 14:45:29 +0200 |
>>> Why leave the headers? Isn’t it risky to leave headers that may be
>>> different from the Samtools that we’re actually linking against?
>>
>> The problem is with our Samtools package(s). They don't install
>> headers. I'd better update them to install the headers; then I could
>> just delete the complete "samtools" directory.
>
> Yes that would be best, if that’s fine with you.
Attached is a patch to add a build phase to samtools to install the
headers into $out/include/samtools/.
The second patch is just the updated patch for adding preseq.
>From b1ba27153faca9bdf46d42046c43f8c60f945368 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Thu, 2 Jul 2015 15:53:47 +0200
Subject: [PATCH 1/2] gnu: samtools: Install headers.
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
"install-headers" to install header files.
---
gnu/packages/bioinformatics.scm | 17 ++++++++++++++++-
1 file changed, 16 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4a1804a..ce2f55b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1824,6 +1824,10 @@ distribution, coverage uniformity, strand specificity,
etc.")
;; systems.
#:tests? ,(string=? (or (%current-system) (%current-target-system))
"x86_64-linux")
+ #:modules ((ice-9 ftw)
+ (ice-9 regex)
+ (guix build gnu-build-system)
+ (guix build utils))
#:make-flags (list "LIBCURSES=-lncurses"
(string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
@@ -1848,7 +1852,18 @@ distribution, coverage uniformity, strand specificity,
etc.")
(let ((lib (string-append (assoc-ref outputs "out") "/lib")))
(mkdir-p lib)
(copy-file "libbam.a" (string-append lib "/libbam.a"))))
- (alist-delete 'configure %standard-phases)))))
+ (alist-cons-after
+ 'install 'install-headers
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((include (string-append (assoc-ref outputs "out")
+ "/include/samtools/")))
+ (mkdir-p include)
+ (for-each (lambda (file)
+ (copy-file file (string-append include
+ (basename file))))
+ (scandir "." (lambda (name) (string-match "\\.h$"
name))))
+ #t))
+ (alist-delete 'configure %standard-phases))))))
(native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("ncurses" ,ncurses)
("perl" ,perl)
--
2.1.0
>From e3bd0a861121c441b44d77d30f2aaddb766b49c2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Tue, 23 Jun 2015 10:54:00 +0200
Subject: [PATCH 2/2] gnu: Add preseq.
* gnu/packages/bioinformatics.scm (preseq): New variable.
---
gnu/packages/bioinformatics.scm | 56 ++++++++++++++++++++++
.../patches/preseq-1.0.2-install-to-PREFIX.patch | 37 ++++++++++++++
.../patches/preseq-1.0.2-link-with-libbam.patch | 33 +++++++++++++
3 files changed, 126 insertions(+)
create mode 100644 gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
create mode 100644 gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ce2f55b..27b847e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2137,6 +2137,62 @@ subsequent visualization, annotation and storage of
results.")
;; LGPLv2.1+
(license (list license:gpl2 license:lgpl2.1+))))
+(define-public preseq
+ (package
+ (name "preseq")
+ (version "1.0.2")
+ (source (origin
+ (method url-fetch)
+ (uri
+ (string-append "http://smithlabresearch.org/downloads/preseq-"
+ version ".tar.bz2"))
+ (sha256
+ (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
+ (patches (list (search-patch
"preseq-1.0.2-install-to-PREFIX.patch")
+ (search-patch
"preseq-1.0.2-link-with-libbam.patch")))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Remove bundled samtools.
+ '(delete-file-recursively "preseq-master/samtools"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no "check" target
+ #:phases
+ (modify-phases %standard-phases
+ (add-after
+ 'unpack 'enter-dir
+ (lambda _
+ (chdir "preseq-master")
+ #t))
+ (add-after
+ 'unpack 'use-samtools-headers
+ (lambda _
+ (substitute* '("smithlab_cpp/SAM.cpp"
+ "smithlab_cpp/SAM.hpp")
+ (("sam.h") "samtools/sam.h"))
+ #t))
+ (delete 'configure))
+ #:make-flags (list (string-append "PREFIX="
+ (assoc-ref %outputs "out"))
+ (string-append "LIBBAM="
+ (assoc-ref %build-inputs "samtools")
+ "/lib/libbam.a"))))
+ (inputs
+ `(("gsl" ,gsl)
+ ("samtools" ,samtools-0.1)
+ ("zlib" ,zlib)))
+ (home-page "http://smithlabresearch.org/software/preseq/")
+ (synopsis "Program for analyzing library complexity")
+ (description
+ "The preseq package is aimed at predicting and estimating the complexity
+of a genomic sequencing library, equivalent to predicting and estimating the
+number of redundant reads from a given sequencing depth and how many will be
+expected from additional sequencing using an initial sequencing experiment.
+The estimates can then be used to examine the utility of further sequencing,
+optimize the sequencing depth, or to screen multiple libraries to avoid low
+complexity samples.")
+ (license license:gpl3+)))
+
(define-public sra-tools
(package
(name "sra-tools")
diff --git a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
new file mode 100644
index 0000000..f8318ae
--- /dev/null
+++ b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
@@ -0,0 +1,37 @@
+This patch has been submitted upstream:
https://github.com/smithlabcode/preseq/pull/15
+
+From 65387b0d766e6c06a15cf8d8f9183d9a4ba644bb Mon Sep 17 00:00:00 2001
+From: Ricardo Wurmus <address@hidden>
+Date: Thu, 25 Jun 2015 15:01:53 +0200
+Subject: [PATCH] Install to PREFIX
+
+---
+ Makefile | 8 ++++++--
+ 1 file changed, 6 insertions(+), 2 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 4d0367a..e334f2f 100644
+--- a/preseq-master/Makefile
++++ b/preseq-master/Makefile
+@@ -22,6 +22,10 @@ ifndef ROOT
+ ROOT = $(shell pwd)
+ endif
+
++ifndef PREFIX
++PREFIX = $(ROOT)
++endif
++
+ ifndef SMITHLAB_CPP
+ SMITHLAB_CPP=$(ROOT)/smithlab_cpp/
+ endif
+@@ -91,8 +95,8 @@ endif
+ $(CXX) $(CXXFLAGS) -o $@ $^ $(INCLUDEARGS) $(LIBS)
+
+ install: $(PROGS)
+- @mkdir -p $(ROOT)/bin
+- @install -m 755 $(PROGS) $(ROOT)/bin
++ @mkdir -p $(PREFIX)/bin
++ @install -m 755 $(PROGS) $(PREFIX)/bin
+
+ clean:
+ @-rm -f $(PROGS) *.o *~
diff --git a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
new file mode 100644
index 0000000..035a3b1
--- /dev/null
+++ b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
@@ -0,0 +1,33 @@
+This patch has been submitted upstream:
https://github.com/smithlabcode/preseq/pull/15
+
+From a937a54d56e8a6ff06237471e568154d1fa5f267 Mon Sep 17 00:00:00 2001
+From: Ricardo Wurmus <address@hidden>
+Date: Thu, 25 Jun 2015 15:02:35 +0200
+Subject: [PATCH] Link with libbam.a if provided via LIBBAM
+
+---
+ Makefile | 7 +++++++
+ 1 file changed, 7 insertions(+)
+
+diff --git a/Makefile b/Makefile
+index e334f2f..de310e4 100644
+--- a/preseq-master/Makefile
++++ b/preseq-master/Makefile
+@@ -83,10 +83,17 @@ $(PROGS): $(addprefix $(SMITHLAB_CPP)/, \
+ preseq: continued_fraction.o load_data_for_complexity.o moment_sequence.o
+
+ ifdef SAMTOOLS_DIR
++ifdef LIBBAM
++LIBS += -pthread
++bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
++ $(LIBBAM)
++else
+ bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
+ $(addprefix $(SAMTOOLS_DIR)/, sam.o bam.o bam_import.o bam_pileup.o \
+ faidx.o bam_aux.o kstring.o knetfile.o sam_header.o razf.o bgzf.o)
+ endif
++endif # SAMTOOLS_DIR
++
+
+ %.o: %.cpp %.hpp
+ $(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDEARGS)
--
2.1.0
- Re: [PATCH] Add preseq., Ludovic Courtès, 2015/07/01
- Re: [PATCH] Add preseq., Ricardo Wurmus, 2015/07/01
- Re: [PATCH] Add preseq., Ludovic Courtès, 2015/07/01
- Re: [PATCH] Add preseq.,
Ricardo Wurmus <=
- Re: [PATCH] Add preseq., Ludovic Courtès, 2015/07/08
- Re: [PATCH] Add preseq., Mark H Weaver, 2015/07/08
- Re: [PATCH] Add preseq., Ricardo Wurmus, 2015/07/09
- Re: [PATCH] Add preseq., Mark H Weaver, 2015/07/09
- Re: [PATCH] Add preseq., Ricardo Wurmus, 2015/07/10