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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
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") |