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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-02-02 15:45:38 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-02-16 14:51:10 +0100
commitd15d981ea29b17f880da3e17e2381750a759bba0 (patch)
tree7b924b25020ab47173c4b0f8f1faaf8b4f970362 /gnu
parent469d6589e35939c50b9ff04e6c7b77fad82389cf (diff)
gnu: Add StringTie.
* gnu/packages/bioinformatics.scm (stringtie): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm55
1 files changed, 55 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 899447d80f..81ec8f2cd2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3310,6 +3310,61 @@ features; exactSNP: a SNP caller that discovers SNPs by testing signals
against local background noises.")
(license license:gpl3+)))
+(define-public stringtie
+ (package
+ (name "stringtie")
+ (version "1.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
+ "stringtie-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file-recursively "samtools-0.1.18")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no test suite
+ #:phases
+ (modify-phases %standard-phases
+ ;; no configure script
+ (delete 'configure)
+ (add-before 'build 'use-system-samtools
+ (lambda _
+ (substitute* "Makefile"
+ (("stringtie: \\$\\{BAM\\}/libbam\\.a")
+ "stringtie: "))
+ (substitute* '("gclib/GBam.h"
+ "gclib/GBam.cpp")
+ (("#include \"(bam|sam|kstring).h\"" _ header)
+ (string-append "#include <samtools/" header ".h>")))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (install-file "stringtie" bin)
+ #t))))))
+ (inputs
+ `(("samtools" ,samtools-0.1)
+ ("zlib" ,zlib)))
+ (home-page "http://ccb.jhu.edu/software/stringtie/")
+ (synopsis "Transcript assembly and quantification for RNA-Seq data")
+ (description
+ "StringTie is a fast and efficient assembler of RNA-Seq sequence
+alignments into potential transcripts. It uses a novel network flow algorithm
+as well as an optional de novo assembly step to assemble and quantitate
+full-length transcripts representing multiple splice variants for each gene
+locus. Its input can include not only the alignments of raw reads used by
+other transcript assemblers, but also alignments of longer sequences that have
+been assembled from those reads. To identify differentially expressed genes
+between experiments, StringTie's output can be processed either by the
+Cuffdiff or Ballgown programs.")
+ (license license:artistic2.0)))
+
(define-public vcftools
(package
(name "vcftools")