[PATCH 1/3] gnu: Add r-chipseq.

[PATCH 1/3] gnu: Add r-chipseq.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-chipseq): New variable.
---
 gnu/packages/bioinformatics.scm | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6b363afe0..9c01c2436 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
@@ -7869,3 +7869,28 @@ replacement for strverscmp.")
 samples into a single report.  It contains modules for a large number of
 common bioinformatics tools.")
     (license license:gpl3)))
+
+(define-public r-chipseq
+  (package
+    (name "r-chipseq")
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "chipseq" version))
+       (sha256
+        (base32
+         "115ayp82rs99iaswrx45skw1i5iacgwzz5k8rzijbp5qic0554n0"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-shortread" ,r-shortread)))
+    (home-page "http://bioconductor.org/packages/chipseq")
+    (synopsis "Package for analyzing ChIPseq data")
+    (description
+     "This package provides tools for processing short read data from ChIPseq
+experiments.")
+    (license license:artistic2.0)))
-- 
2.11.0

[PATCH 2/3] gnu: Add r-copyhelper.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-copyhelper): New variable.
---
 gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9c01c2436..d4224115f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7894,3 +7894,29 @@ common bioinformatics tools.")
      "This package provides tools for processing short read data from ChIPseq
 experiments.")
     (license license:artistic2.0)))
+
+(define-public r-copyhelper
+  (package
+    (name "r-copyhelper")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://bioconductor.org/packages/release/"
+                           "data/experiment/src/contrib/CopyhelpeR_"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
+    (properties `((upstream-name . "CopyhelpeR")))
+    (build-system r-build-system)
+    (home-page "http://bioconductor.org/packages/CopyhelpeR/")
+    (synopsis "Helper files for CopywriteR")
+    (description
+     "This package contains the helper files that are required to run the
+Bioconductor package CopywriteR.  It contains pre-assembled 1kb bin GC-content
+and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
+mm10.  In addition, it contains a blacklist filter to remove regions that
+display copy number variation.  Files are stored as GRanges objects from the
+GenomicRanges Bioconductor package.")
+    (license license:gpl2)))
-- 
2.11.0

[PATCH 3/3] gnu: Add r-copywriter.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-copywriter): New variable.
---
 gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d4224115f..d963ded85 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7920,3 +7920,43 @@ mm10.  In addition, it contains a blacklist filter to remove regions that
 display copy number variation.  Files are stored as GRanges objects from the
 GenomicRanges Bioconductor package.")
     (license license:gpl2)))
+
+(define-public r-copywriter
+  (package
+    (name "r-copywriter")
+    (version "2.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "CopywriteR" version))
+       (sha256
+        (base32
+         "1bwwnsyk7cpgwkagsnn5mv6fv233b0rkhjvbadrh70h8m4anawfj"))))
+    (properties `((upstream-name . "CopywriteR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-chipseq" ,r-chipseq)
+       ("r-copyhelper" ,r-copyhelper)
+       ("r-data-table" ,r-data-table)
+       ("r-dnacopy" ,r-dnacopy)
+       ("r-futile-logger" ,r-futile-logger)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-gtools" ,r-gtools)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://github.com/PeeperLab/CopywriteR")
+    (synopsis "Copy number information from targeted sequencing")
+    (description
+     "CopywriteR extracts DNA copy number information from targeted sequencing
+by utilizing off-target reads.  It allows for extracting uniformly distributed
+copy number information, can be used without reference, and can be applied to
+sequencing data obtained from various techniques including chromatin
+immunoprecipitation and target enrichment on small gene panels.  Thereby,
+CopywriteR constitutes a widely applicable alternative to available copy
+number detection tools.")
+    (license license:gpl2)))
-- 
2.11.0

Re: [PATCH 1/3] gnu: Add r-chipseq.

[Ludovic Courtès]

All 3 packages look all right to me.

Thanks!

Ludo’.