[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
[PATCH] Add GenomicFeatures.
|
From: |
Ricardo Wurmus |
|
Subject: |
[PATCH] Add GenomicFeatures. |
|
Date: |
Fri, 18 Dec 2015 14:19:55 +0100 |
Hi Guix,
Here’s another batch of R packages leading to GenomicFeatures, a popular
and well-featured package to derive all sorts of interesting features
from genomic data.
Some of the packages needed to be patched to remove the dependency on
zlibbioc (which is only needed for Windows users).
~~ Ricardo
PS: If reviewing these patch sets is uncomfortable in this format and
you’d prefer separate emails or some other approach, please let me
know. I appreciate your reviews a lot!
>From 7c72ac485149a9fe0128f2af2202d0f489ce8b3b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:02:40 +0100
Subject: [PATCH 01/17] gnu: Add RSQLite.
* gnu/packages/statistics.scm (r-rsqlite): New variable.
---
gnu/packages/statistics.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e62924b..efd1967 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1482,3 +1482,25 @@ grobs.")
and draw tables.")
(license license:gpl2+)))
+(define-public r-rsqlite
+ (package
+ (name "r-rsqlite")
+ (version "1.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "RSQLite" version))
+ (sha256
+ (base32
+ "08b1syv8z887gxiw8i09dpqh0zisfb6ihq6qqr01zipvkahzq34f"))))
+ (properties `((upstream-name . "RSQLite")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dbi" ,r-dbi)))
+ (home-page "https://github.com/rstats-db/RSQLite";)
+ (synopsis "SQLite interface for R")
+ (description
+ "This package embeds the SQLite database engine in R and provides an
+interface compliant with the DBI package. The source for the SQLite
+engine (version 3.8.6) is included.")
+ (license license:lgpl2.0+)))
+
--
2.1.0
>From 16a29872438e3e22cdfe822496a0ddd87da0aed9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:03:08 +0100
Subject: [PATCH 02/17] gnu: Add RCurl.
* gnu/packages/statistics.scm (r-rcurl): New variable.
---
gnu/packages/statistics.scm | 32 ++++++++++++++++++++++++++++++++
1 file changed, 32 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index efd1967..95aebdf 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -27,6 +27,7 @@
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages curl)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gtk)
#:use-module (gnu packages haskell)
@@ -1504,3 +1505,34 @@ interface compliant with the DBI package. The source
for the SQLite
engine (version 3.8.6) is included.")
(license license:lgpl2.0+)))
+(define-public r-rcurl
+ (package
+ (name "r-rcurl")
+ (version "1.95-0.1.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://www.bioconductor.org/packages/";
+ "release/extra/src/"
+ "contrib/RCurl_" version ".tar.gz"))
+ (sha256
+ (base32
+ "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
+ (properties `((upstream-name . "RCurl")))
+ (build-system r-build-system)
+ (inputs
+ `(("libcurl" ,curl)))
+ (propagated-inputs
+ `(("r-bitops" ,r-bitops)))
+ (home-page "http://www.omegahat.org/RCurl";)
+ (synopsis "General network client interface for R")
+ (description
+ "The package allows one to compose general HTTP requests and provides
+convenient functions to fetch URIs, GET and POST forms, etc. and process the
+results returned by the Web server. This provides a great deal of control
+over the HTTP/FTP/... connection and the form of the request while providing a
+higher-level interface than is available just using R socket connections.
+Additionally, the underlying implementation is robust and extensive,
+supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
+ldap, and also supports cookies, redirects, authentication, etc.")
+ (license license:bsd-3)))
+
--
2.1.0
>From 79ab2e73343fa3e3135bd13a6fdbcc8654f9ac79 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:03:26 +0100
Subject: [PATCH 03/17] gnu: Add r-xml.
* gnu/packages/statistics.scm (r-xml): New variable.
---
gnu/packages/statistics.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 95aebdf..03fe218 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1536,3 +1536,28 @@ supporting FTP/FTPS/TFTP (uploads and downloads),
SSL/HTTPS, telnet, dict,
ldap, and also supports cookies, redirects, authentication, etc.")
(license license:bsd-3)))
+(define-public r-xml
+ (package
+ (name "r-xml")
+ (version "3.98-1.3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "XML" version))
+ (sha256
+ (base32
+ "0j9ayp8a35g0227a4zd8nbmvnbfnj5w687jal6qvj4lbhi3va7sy"))))
+ (properties
+ `((upstream-name . "XML")))
+ (build-system r-build-system)
+ (inputs
+ `(("libxml2" ,libxml2)))
+ (propagated-inputs
+ `(("r-rcurl" ,r-rcurl)))
+ (home-page "http://www.omegahat.org/RSXML";)
+ (synopsis "Tools for parsing and generating XML within R")
+ (description
+ "Many approaches for both reading and creating XML (and HTML)
+documents (including DTDs), both local and accessible via HTTP or FTP. Also
+offers access to an XPath \"interpreter\".")
+ (license license:bsd-2)))
+
--
2.1.0
>From 6d2b8e800765659f8ae291159fc96b57bae93465 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:03:47 +0100
Subject: [PATCH 04/17] gnu: Add lambda.r.
* gnu/packages/statistics.scm (r-lambda-r): New variable.
---
gnu/packages/statistics.scm | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 03fe218..01f1f43 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1561,3 +1561,24 @@ documents (including DTDs), both local and accessible
via HTTP or FTP. Also
offers access to an XPath \"interpreter\".")
(license license:bsd-2)))
+(define-public r-lambda-r
+ (package
+ (name "r-lambda-r")
+ (version "1.1.7")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "lambda.r" version))
+ (sha256
+ (base32
+ "1lxzrwyminc3dfb07pbn1rmj45kplxgsb17b06pzflj728knbqwa"))))
+ (properties `((upstream-name . "lambda.r")))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/lambda.r";)
+ (synopsis "Functional programming extension for R")
+ (description
+ "This package provides a language extension to efficiently write
+functional programs in R. Syntax extensions include multi-part function
+definitions, pattern matching, guard statements, built-in (optional) type
+safety.")
+ (license license:lgpl3+)))
+
--
2.1.0
>From 5cfc72bc048490d5ab5709ca8d4b15f53d58d40f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:04:49 +0100
Subject: [PATCH 05/17] gnu: Add futile.options.
* gnu/packages/statistics.scm (r-futile-options): New variable.
---
gnu/packages/statistics.scm | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 01f1f43..70f9cbb 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1582,3 +1582,22 @@ definitions, pattern matching, guard statements,
built-in (optional) type
safety.")
(license license:lgpl3+)))
+(define-public r-futile-options
+ (package
+ (name "r-futile-options")
+ (version "1.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "futile.options" version))
+ (sha256
+ (base32
+ "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f"))))
+ (properties
+ `((upstream-name . "futile.options")))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/futile.options";)
+ (synopsis "Options management framework")
+ (description
+ "This package provides a scoped options management framework.")
+ (license license:lgpl3+)))
+
--
2.1.0
>From 51e0306453052e938426a2ec6cbfd93f123ea3f3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:05:07 +0100
Subject: [PATCH 06/17] gnu: Add futile.logger.
* gnu/packages/statistics.scm (r-futile-logger): New variable.
---
gnu/packages/statistics.scm | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 70f9cbb..e1c1fab 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1601,3 +1601,27 @@ safety.")
"This package provides a scoped options management framework.")
(license license:lgpl3+)))
+(define-public r-futile-logger
+ (package
+ (name "r-futile-logger")
+ (version "1.4.1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "futile.logger" version))
+ (sha256
+ (base32
+ "1plld1icxrcay7llplbd4i8inpg97crpnczk58mbk26j8glqbr51"))))
+ (properties `((upstream-name . "futile.logger")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-futile-options" ,r-futile-options)
+ ("r-lambda-r" ,r-lambda-r)))
+ (home-page "http://cran.r-project.org/web/packages/futile.logger";)
+ (synopsis "Logging utility for R")
+ (description
+ "This package provides a simple yet powerful logging utility. Based
+loosely on log4j, futile.logger takes advantage of R idioms to make logging a
+convenient and easy to use replacement for @code{cat} and @code{print}
+statements.")
+ (license license:lgpl3+)))
+
--
2.1.0
>From 44a3cac8e7bbd0af9aff2adf637363f65397e1a0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:05:29 +0100
Subject: [PATCH 07/17] gnu: Add snow.
* gnu/packages/statistics.scm (r-snow): New variable.
---
gnu/packages/statistics.scm | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e1c1fab..fd500de 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1625,3 +1625,21 @@ convenient and easy to use replacement for @code{cat}
and @code{print}
statements.")
(license license:lgpl3+)))
+(define-public r-snow
+ (package
+ (name "r-snow")
+ (version "0.4-1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "snow" version))
+ (sha256
+ (base32
+ "19r2yq8aqw99vwyx81p6ay4afsfqffal1wzvizk3dj882s2n4j8w"))))
+ (properties `((upstream-name . "snow")))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/snow";)
+ (synopsis "Support for simple parallel computing in R")
+ (description
+ "This package provides support for simple parallel computing in R.")
+ (license (list license:gpl2+ license:gpl3+))))
+
--
2.1.0
>From fb79596b106081d8fabff9b0e3d5a2869057a8bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:06:09 +0100
Subject: [PATCH 08/17] gnu: Add Biobase.
* gnu/packages/bioinformatics.scm (r-biobase): New variable.
---
gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 142b29a..263bcc0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3495,6 +3495,29 @@ GenomicRanges package defines general purpose containers
for storing and
manipulating genomic intervals and variables defined along a genome.")
(license license:artistic2.0)))
+(define-public r-biobase
+ (package
+ (name "r-biobase")
+ (version "2.30.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Biobase" version))
+ (sha256
+ (base32
+ "1qasjpq3kw8h7qw8cin3bjvv1256hqr1mm24fq3v0ymxzlb66szi"))))
+ (properties
+ `((upstream-name . "Biobase")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)))
+ (home-page "http://bioconductor.org/packages/Biobase";)
+ (synopsis "Base functions for Bioconductor")
+ (description
+ "This package provides functions that are needed by many other packages
+on Bioconductor or which replace R functions.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From 889b7cc64444e3c6c160bca49800a375a3f94537 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:06:28 +0100
Subject: [PATCH 09/17] gnu: Add AnnotationDbi.
* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
---
gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 263bcc0..ea78798 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3518,6 +3518,34 @@ manipulating genomic intervals and variables defined
along a genome.")
on Bioconductor or which replace R functions.")
(license license:artistic2.0)))
+(define-public r-annotationdbi
+ (package
+ (name "r-annotationdbi")
+ (version "1.32.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationDbi" version))
+ (sha256
+ (base32
+ "08ncdjvq0l44kqyiv32kn9wnbw1xgfb6qjfzfbjpqrcfp1jygz9j"))))
+ (properties
+ `((upstream-name . "AnnotationDbi")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-dbi" ,r-dbi)
+ ("r-iranges" ,r-iranges)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "http://bioconductor.org/packages/AnnotationDbi";)
+ (synopsis "Annotation database interface")
+ (description
+ "This package provides user interface and database connection code for
+annotation data packages using SQLite data storage.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From b4569f95fc2610382206c8dc592df7c45f1ff6fb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:06:52 +0100
Subject: [PATCH 10/17] gnu: Add biomaRt.
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
---
gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ea78798..4e4bc54 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3546,6 +3546,37 @@ on Bioconductor or which replace R functions.")
annotation data packages using SQLite data storage.")
(license license:artistic2.0)))
+(define-public r-biomart
+ (package
+ (name "r-biomart")
+ (version "2.26.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "biomaRt" version))
+ (sha256
+ (base32
+ "1s709055abj2gd35g6nnk5d2ai5ii09iir270l2xika6pi62gj3f"))))
+ (properties
+ `((upstream-name . "biomaRt")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-rcurl" ,r-rcurl)
+ ("r-xml" ,r-xml)))
+ (home-page "http://bioconductor.org/packages/biomaRt";)
+ (synopsis "Interface to BioMart databases")
+ (description
+ "biomaRt provides an interface to a growing collection of databases
+implementing the @url{BioMart software suite, http://www.biomart.org}. The
+package enables retrieval of large amounts of data in a uniform way without
+the need to know the underlying database schemas or write complex SQL queries.
+Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
+Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
+users direct access to a diverse set of data and enable a wide range of
+powerful online queries from gene annotation to database mining.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From f2b5410c3c118f3282dbaf6c0c7dd231cf6f57ee Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:07:08 +0100
Subject: [PATCH 11/17] gnu: Add BiocParallel.
* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
---
gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4e4bc54..71e47de 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3577,6 +3577,31 @@ users direct access to a diverse set of data and enable
a wide range of
powerful online queries from gene annotation to database mining.")
(license license:artistic2.0)))
+(define-public r-biocparallel
+ (package
+ (name "r-biocparallel")
+ (version "1.4.3")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocParallel" version))
+ (sha256
+ (base32
+ "1f5mndx66vampcsq0n66afg6x851crl0h3nyv2nyp9bsgzj9cdzq"))))
+ (properties
+ `((upstream-name . "BiocParallel")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-futile-logger" ,r-futile-logger)
+ ("r-snow" ,r-snow)))
+ (home-page "http://bioconductor.org/packages/BiocParallel";)
+ (synopsis "Bioconductor facilities for parallel evaluation")
+ (description
+ "This package provides modified versions and novel implementation of
+functions for parallel evaluation, tailored to use with Bioconductor
+objects.")
+ (license (list license:gpl2+ license:gpl3+))))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From 5c61e39898523f0479f47a2317bff4e2cd3a5ec8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:07:32 +0100
Subject: [PATCH 12/17] gnu: Add Biostrings.
* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
---
gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 71e47de..a9fa6cd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3602,6 +3602,33 @@ functions for parallel evaluation, tailored to use with
Bioconductor
objects.")
(license (list license:gpl2+ license:gpl3+))))
+(define-public r-biostrings
+ (package
+ (name "r-biostrings")
+ (version "2.38.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Biostrings" version))
+ (sha256
+ (base32
+ "1afp9szc8ci6jn0m3hrrqh6df65cpw3v1dcnl6xir3d3m3lwwmk4"))))
+ (properties
+ `((upstream-name . "Biostrings")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (home-page "http://bioconductor.org/packages/Biostrings";)
+ (synopsis "String objects and algorithms for biological sequences")
+ (description
+ "This package provides memory efficient string containers, string
+matching algorithms, and other utilities, for fast manipulation of large
+biological sequences or sets of sequences.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From b1a8cfeecc2cc296365df1ced5dec47a553cfd6d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:07:56 +0100
Subject: [PATCH 13/17] gnu: Add Rsamtools.
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
---
gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a9fa6cd..1582d32 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3629,6 +3629,51 @@ matching algorithms, and other utilities, for fast
manipulation of large
biological sequences or sets of sequences.")
(license license:artistic2.0)))
+(define-public r-rsamtools
+ (package
+ (name "r-rsamtools")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rsamtools" version))
+ (sha256
+ (base32
+ "1yc3nzzms3igjwr4l9yd3wdac95glcs08b4cfp7disyly0wcskjd"))))
+ (properties
+ `((upstream-name . "Rsamtools")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-system-zlib
+ (lambda _
+ (substitute* "DESCRIPTION"
+ (("zlibbioc, ") ""))
+ (substitute* "NAMESPACE"
+ (("import\\(zlibbioc\\)") ""))
+ #t)))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bitops" ,r-bitops)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (home-page
"http://bioconductor.org/packages/release/bioc/html/Rsamtools.html";)
+ (synopsis "Interface to samtools, bcftools, and tabix")
+ (description
+ "This package provides an interface to the 'samtools', 'bcftools', and
+'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA,
+binary variant call (BCF) and compressed indexed tab-delimited (tabix)
+files.")
+ (license license:expat)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From cb9db0a2094c121566ad6e0739bdd9e470b30187 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:08:17 +0100
Subject: [PATCH 14/17] gnu: Add SummarizedExperiment.
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
---
gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1582d32..2d80d78 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3674,6 +3674,36 @@ binary variant call (BCF) and compressed indexed
tab-delimited (tabix)
files.")
(license license:expat)))
+(define-public r-summarizedexperiment
+ (package
+ (name "r-summarizedexperiment")
+ (version "1.0.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "SummarizedExperiment" version))
+ (sha256
+ (base32
+ "0w1dwp99p6i7sc3cn0ir3dr8ksgxwjf16675h5i8n6gbv4rl9lz6"))))
+ (properties
+ `((upstream-name . "SummarizedExperiment")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "http://bioconductor.org/packages/SummarizedExperiment";)
+ (synopsis "Container for representing genomic ranges by sample")
+ (description
+ "The SummarizedExperiment container contains one or more assays, each
+represented by a matrix-like object of numeric or other mode. The rows
+typically represent genomic ranges of interest and the columns represent
+samples.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From ce941d077d87ffc8e118c8e97d45e0988524819a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:08:36 +0100
Subject: [PATCH 15/17] gnu: Add GenomicAlignments.
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
---
gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2d80d78..2142982 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3704,6 +3704,40 @@ typically represent genomic ranges of interest and the
columns represent
samples.")
(license license:artistic2.0)))
+(define-public r-genomicalignments
+ (package
+ (name "r-genomicalignments")
+ (version "1.6.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicAlignments" version))
+ (sha256
+ (base32
+ "03pxzkmwcpl0d7a09ahan0nllfv7qw2i7w361w6af2s4n3xwrniz"))))
+ (properties
+ `((upstream-name . "GenomicAlignments")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "http://bioconductor.org/packages/GenomicAlignments";)
+ (synopsis "Representation and manipulation of short genomic alignments")
+ (description
+ "This package provides efficient containers for storing and manipulating
+short genomic alignments (typically obtained by aligning short reads to a
+reference genome). This includes read counting, computing the coverage,
+junction detection, and working with the nucleotide content of the
+alignments.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From e76490679e3fe0775b499dab02770446a714bf93 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:09:00 +0100
Subject: [PATCH 16/17] gnu: Add rtracklayer.
* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
---
gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 48 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2142982..a5a0bdc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3738,6 +3738,54 @@ junction detection, and working with the nucleotide
content of the
alignments.")
(license license:artistic2.0)))
+(define-public r-rtracklayer
+ (package
+ (name "r-rtracklayer")
+ (version "1.30.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rtracklayer" version))
+ (sha256
+ (base32
+ "1if31hg56islx5vwydpgs5gkyas26kyvv2ljv1c7jikpm62w14qv"))))
+ (properties
+ `((upstream-name . "rtracklayer")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-system-zlib
+ (lambda _
+ (substitute* "DESCRIPTION"
+ (("zlibbioc, ") ""))
+ (substitute* "NAMESPACE"
+ (("import\\(zlibbioc\\)") ""))
+ #t)))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rcurl" ,r-rcurl)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xml" ,r-xml)
+ ("r-xvector" ,r-xvector)))
+ (home-page "http://bioconductor.org/packages/rtracklayer";)
+ (synopsis "R interface to genome browsers and their annotation tracks")
+ (description
+ "rtracklayer is an extensible framework for interacting with multiple
+genome browsers (currently UCSC built-in) and manipulating annotation tracks
+in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
+built-in). The user may export/import tracks to/from the supported browsers,
+as well as query and modify the browser state, such as the current viewport.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From ba531647302af1fe3d11990bb599c03c6cb880ea Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 18 Dec 2015 14:09:18 +0100
Subject: [PATCH 17/17] gnu: Add GenomicFeatures.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
---
gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a5a0bdc..4c350ff 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3786,6 +3786,48 @@ built-in). The user may export/import tracks to/from
the supported browsers,
as well as query and modify the browser state, such as the current viewport.")
(license license:artistic2.0)))
+(define-public r-genomicfeatures
+ (package
+ (name "r-genomicfeatures")
+ (version "1.22.7")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicFeatures" version))
+ (sha256
+ (base32
+ "1jb4s49ar5j9qslpd3kfdg2wrl4q7ciysd55h9a7zvspymxcngq8"))))
+ (properties
+ `((upstream-name . "GenomicFeatures")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biomart" ,r-biomart)
+ ("r-biostrings" ,r-biostrings)
+ ("r-dbi" ,r-dbi)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rcurl" ,r-rcurl)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (home-page "http://bioconductor.org/packages/GenomicFeatures";)
+ (synopsis "Tools for working with transcript centric annotations")
+ (description
+ "This package provides a set of tools and methods for making and
+manipulating transcript centric annotations. With these tools the user can
+easily download the genomic locations of the transcripts, exons and cds of a
+given organism, from either the UCSC Genome Browser or a BioMart
+database (more sources will be supported in the future). This information is
+then stored in a local database that keeps track of the relationship between
+transcripts, exons, cds and genes. Flexible methods are provided for
+extracting the desired features in a convenient format.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
- [PATCH] Add GenomicFeatures.,
Ricardo Wurmus <=