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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 55 |
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") |