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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-01-19 14:29:19 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-01-23 08:53:10 +0100 |
| commit | 94ce537eacaa443df57bef14ceaa0d7fdad86071 (patch) | |
| tree | 1100bd70d046ab787e4730b6a00e8e77d43e4b2f /gnu/packages/bioinformatics.scm | |
| parent | 3062d750b4f8e16c979629360bf2dc411b71b04c (diff) | |
| download | patches-94ce537eacaa443df57bef14ceaa0d7fdad86071.tar patches-94ce537eacaa443df57bef14ceaa0d7fdad86071.tar.gz | |
gnu: Add TopHat.
* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 67 |
1 files changed, 67 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa2bea732c..f9b0d75613 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -654,6 +654,73 @@ gapped, local, and paired-end alignment modes.") (supported-systems '("x86_64-linux")) (license license:gpl3+))) +(define-public tophat + (package + (name "tophat") + (version "2.1.0") + (source (origin + (method url-fetch) + (uri (string-append + "http://ccb.jhu.edu/software/tophat/downloads/tophat-" + version ".tar.gz")) + (sha256 + (base32 + "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7")) + (patches (list (search-patch "tophat-build-with-later-seqan.patch"))) + (modules '((guix build utils))) + (snippet + '(begin + ;; Remove bundled SeqAn and samtools + (delete-file-recursively "src/SeqAn-1.3") + (delete-file-recursively "src/samtools-0.1.18") + #t)))) + (build-system gnu-build-system) + (arguments + '(#:parallel-build? #f ; not supported + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-samtools + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/Makefile.in" + (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix) + (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "") + (("SAMPROG = samtools_0\\.1\\.18") "") + (("\\$\\(samtools_0_1_18_SOURCES\\)") "") + (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") "")) + (substitute* '("src/common.cpp" + "src/tophat.py") + (("samtools_0.1.18") (which "samtools"))) + (substitute* '("src/common.h" + "src/bam2fastx.cpp") + (("#include \"bam.h\"") "#include <samtools/bam.h>") + (("#include \"sam.h\"") "#include <samtools/sam.h>")) + (substitute* '("src/bwt_map.h" + "src/map2gtf.h" + "src/align_status.h") + (("#include <bam.h>") "#include <samtools/bam.h>") + (("#include <sam.h>") "#include <samtools/sam.h>")) + #t))))) + (inputs + `(("boost" ,boost) + ("bowtie" ,bowtie) + ("samtools" ,samtools-0.1) + ("ncurses" ,ncurses) + ("python" ,python-2) + ("perl" ,perl) + ("zlib" ,zlib) + ("seqan" ,seqan))) + (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") + (synopsis "Spliced read mapper for RNA-Seq data") + (description + "TopHat is a fast splice junction mapper for nucleotide sequence +reads produced by the RNA-Seq method. It aligns RNA-Seq reads to +mammalian-sized genomes using the ultra high-throughput short read +aligner Bowtie, and then analyzes the mapping results to identify +splice junctions between exons.") + ;; TopHat is released under the Boost Software License, Version 1.0 + ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893 + (license license:boost1.0))) + (define-public bwa (package (name "bwa") |