Hi Guix,
here’s a first batch of packages imported from Bioconductor. This patch
set adds the GenomicRanges package along with its dependencies. They
are all very simple.
Only XVector has a separate build phase to avoid a dependency on
zlibbioc, which is a version of zlib that’s frozen in time and only
provided for systems that don’t have a working version of zlib.
~~ Ricardo
>From 417d3f16b02a7295cf98a7f5fc365d87b06bb659 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Fri, 18 Dec 2015 12:06:55 +0100
Subject: [PATCH 1/6] gnu: Add BiocGenerics.
* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
---
gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5d93c52..7215fb9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3324,6 +3324,27 @@ use multiple corrections. Visualization of data can be done either by
barplots or heatmaps.")
(license license:gpl2+)))
+(define-public r-biocgenerics
+ (package
+ (name "r-biocgenerics")
+ (version "0.16.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocGenerics" version))
+ (sha256
+ (base32
+ "0f16ryy5f012hvksrwlmm33bcl7lw97i2jvhbnwfwl03j4w7nhc1"))))
+ (properties
+ `((upstream-name . "BiocGenerics")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (home-page "http://bioconductor.org/packages/BiocGenerics";)
+ (synopsis "S4 generic functions for Bioconductor")
+ (description
+ "This package provides S4 generic functions needed by many Bioconductor
+packages.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From 08ebe755038bbb4111d4d68192af790b6cd7b1dc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Fri, 18 Dec 2015 12:07:18 +0100
Subject: [PATCH 2/6] gnu: Add S4Vectors.
* gnu/packages/bioinformatics.scm (r-s4vectors): 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 7215fb9..83ba132 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3345,6 +3345,34 @@ barplots or heatmaps.")
packages.")
(license license:artistic2.0)))
+(define-public r-s4vectors
+ (package
+ (name "r-s4vectors")
+ (version "0.8.5")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "S4Vectors" version))
+ (sha256
+ (base32
+ "10f4jxwlwsiy7zhb3kgp6anid0d7wkvrrljl80r3nhx38yr24l5k"))))
+ (properties
+ `((upstream-name . "S4Vectors")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)))
+ (home-page "http://bioconductor.org/packages/S4Vectors";)
+ (synopsis "S4 implementation of vectors and lists")
+ (description
+ "The S4Vectors package defines the @code{Vector} and @code{List} virtual
+classes and a set of generic functions that extend the semantic of ordinary
+vectors and lists in R. Package developers can easily implement vector-like
+or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
+In addition, a few low-level concrete subclasses of general interest (e.g.
+@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
+S4Vectors package itself.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From ca719b062395d7fa5bc0bdd284a85b6573962f30 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Fri, 18 Dec 2015 12:07:39 +0100
Subject: [PATCH 3/6] gnu: Add IRanges.
* gnu/packages/bioinformatics.scm (r-iranges): 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 83ba132..1254d83 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3373,6 +3373,36 @@ In addition, a few low-level concrete subclasses of general interest (e.g.
S4Vectors package itself.")
(license license:artistic2.0)))
+(define-public r-iranges
+ (package
+ (name "r-iranges")
+ (version "2.4.6")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "IRanges" version))
+ (sha256
+ (base32
+ "00x0266sys1fc5ipa639y84p6m6mgspk2xb099vcwmd3w4hypj9d"))))
+ (properties
+ `((upstream-name . "IRanges")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "http://bioconductor.org/packages/IRanges";)
+ (synopsis "Infrastructure for manipulating intervals on sequences")
+ (description
+ "This package provides efficient low-level and highly reusable S4 classes
+for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
+generally, data that can be organized sequentially (formally defined as
+@code{Vector} objects), as well as views on these @code{Vector} objects.
+Efficient list-like classes are also provided for storing big collections of
+instances of the basic classes. All classes in the package use consistent
+naming and share the same rich and consistent \"Vector API\" as much as
+possible.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From 6300fdd91356ea73b019dc44455c6422954276de Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Fri, 18 Dec 2015 12:07:56 +0100
Subject: [PATCH 4/6] gnu: Add GenomeInfoDb.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): 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 1254d83..9a67c19 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3403,6 +3403,33 @@ naming and share the same rich and consistent \"Vector API\" as much as
possible.")
(license license:artistic2.0)))
+(define-public r-genomeinfodb
+ (package
+ (name "r-genomeinfodb")
+ (version "1.6.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomeInfoDb" version))
+ (sha256
+ (base32
+ "1j2n1v1mrw1fxn7cyffz112pm76wd6gy9q9qwlsfv3brbsqbvdbf"))))
+ (properties
+ `((upstream-name . "GenomeInfoDb")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "http://bioconductor.org/packages/GenomeInfoDb";)
+ (synopsis "Utilities for manipulating chromosome identifiers")
+ (description
+ "This package contains data and functions that define and allow
+translation between different chromosome sequence naming conventions (e.g.,
+\"chr1\" versus \"1\"), including a function that attempts to place sequence
+names in their natural, rather than lexicographic, order.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From cca6ffc0843d1043f55177d644e246472ab1a87e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Fri, 18 Dec 2015 12:08:22 +0100
Subject: [PATCH 5/6] gnu: Add XVector.
* gnu/packages/bioinformatics.scm (r-xvector): New variable.
---
gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9a67c19..1f00edc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3430,6 +3430,43 @@ translation between different chromosome sequence naming conventions (e.g.,
names in their natural, rather than lexicographic, order.")
(license license:artistic2.0)))
+(define-public r-xvector
+ (package
+ (name "r-xvector")
+ (version "0.10.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "XVector" version))
+ (sha256
+ (base32
+ "0havwyr6xqk7w0rmbwfj9jq1djz7wzdz7w39adhklwzwz9l4ih3a"))))
+ (properties
+ `((upstream-name . "XVector")
+ (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-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "http://bioconductor.org/packages/XVector";)
+ (synopsis "Representation and manpulation of external sequences")
+ (description
+ "This package provides memory efficient S4 classes for storing sequences
+\"externally\" (behind an R external pointer, or on disk).")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
>From 0cd8314f8163bc332eb2f365ed2beb528f2f245d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Fri, 18 Dec 2015 12:08:41 +0100
Subject: [PATCH 6/6] gnu: Add GenomicRanges.
* gnu/packages/bioinformatics.scm (r-genomicranges): 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 1f00edc..142b29a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3467,6 +3467,34 @@ names in their natural, rather than lexicographic, order.")
\"externally\" (behind an R external pointer, or on disk).")
(license license:artistic2.0)))
+(define-public r-genomicranges
+ (package
+ (name "r-genomicranges")
+ (version "1.22.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicRanges" version))
+ (sha256
+ (base32
+ "1jffvcs0jsi7q4l3pvjj6r73vll80csgkljvhqp0g2ixc43jjng9"))))
+ (properties
+ `((upstream-name . "GenomicRanges")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-xvector" ,r-xvector)))
+ (home-page "http://bioconductor.org/packages/GenomicRanges";)
+ (synopsis "Representation and manipulation of genomic intervals")
+ (description
+ "This package provides tools to efficiently represent and manipulate
+genomic annotations and alignments is playing a central role when it comes to
+analyzing high-throughput sequencing data (a.k.a. NGS data). The
+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-qtl
(package
(name "r-qtl")
--
2.1.0
