From 3a40a92c73a7c6b7e493f1961c90999697f71953 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 16 Sep 2015 17:42:41 +0200
Subject: gnu: Add cufflinks.

* gnu/packages/bioinformatics.scm (cufflinks): New variable.
---
 gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)

(limited to 'gnu/packages/bioinformatics.scm')

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")
-- 
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