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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-09-16 17:42:41 +0200
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-23 09:15:11 +0100
commit3a40a92c73a7c6b7e493f1961c90999697f71953 (patch)
treef06508dfa8bfa7a1987266c6bc20ffba14197dc4
parent94ce537eacaa443df57bef14ceaa0d7fdad86071 (diff)
downloadpatches-3a40a92c73a7c6b7e493f1961c90999697f71953.tar
patches-3a40a92c73a7c6b7e493f1961c90999697f71953.tar.gz
gnu: Add cufflinks.
* gnu/packages/bioinformatics.scm (cufflinks): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm58
1 files changed, 58 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f9b0d75613..c8eb2b8ec4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -982,6 +982,64 @@ files between different genome assemblies. It supports most commonly used
file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
(license license:gpl2+)))
+(define-public cufflinks
+ (package
+ (name "cufflinks")
+ (version "2.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://cole-trapnell-lab.github.io/"
+ "cufflinks/assets/downloads/cufflinks-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:make-flags
+ (list
+ ;; The includes for "eigen" are located in a subdirectory.
+ (string-append "EIGEN_CPPFLAGS="
+ "-I" (assoc-ref %build-inputs "eigen")
+ "/include/eigen3/")
+ ;; Cufflinks must be linked with various boost libraries.
+ (string-append "LDFLAGS="
+ (string-join '("-lboost_system"
+ "-lboost_serialization"
+ "-lboost_thread"))))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-search-for-bam
+ (lambda _
+ (substitute* '("ax_bam.m4"
+ "configure"
+ "src/hits.h")
+ (("<bam/sam\\.h>") "<samtools/sam.h>")
+ (("<bam/bam\\.h>") "<samtools/bam.h>")
+ (("<bam/version\\.hpp>") "<samtools/version.h>"))
+ #t)))
+ #:configure-flags
+ (list (string-append "--with-bam="
+ (assoc-ref %build-inputs "samtools")))))
+ (inputs
+ `(("eigen" ,eigen)
+ ("samtools" ,samtools-0.1)
+ ("htslib" ,htslib)
+ ("boost" ,boost)
+ ("python" ,python-2)
+ ("zlib" ,zlib)))
+ (home-page "http://cole-trapnell-lab.github.io/cufflinks/")
+ (synopsis "Transcriptome assembly and RNA-Seq expression analysis")
+ (description
+ "Cufflinks assembles RNA transcripts, estimates their abundances,
+and tests for differential expression and regulation in RNA-Seq
+samples. It accepts aligned RNA-Seq reads and assembles the
+alignments into a parsimonious set of transcripts. Cufflinks then
+estimates the relative abundances of these transcripts based on how
+many reads support each one, taking into account biases in library
+preparation protocols.")
+ (license license:boost1.0)))
+
(define-public cutadapt
(package
(name "cutadapt")