diff options
| -rw-r--r-- | gnu-system.am | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 67 | ||||
| -rw-r--r-- | gnu/packages/patches/tophat-build-with-later-seqan.patch | 24 |
3 files changed, 92 insertions, 0 deletions
diff --git a/gnu-system.am b/gnu-system.am index aeb0d0f4dc..3426056925 100644 --- a/gnu-system.am +++ b/gnu-system.am @@ -681,6 +681,7 @@ dist_patch_DATA = \ gnu/packages/patches/tidy-CVE-2015-5522+5523.patch \ gnu/packages/patches/tinyxml-use-stl.patch \ gnu/packages/patches/tk-find-library.patch \ + gnu/packages/patches/tophat-build-with-later-seqan.patch \ gnu/packages/patches/torsocks-dns-test.patch \ gnu/packages/patches/tvtime-gcc41.patch \ gnu/packages/patches/tvtime-pngoutput.patch \ 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") diff --git a/gnu/packages/patches/tophat-build-with-later-seqan.patch b/gnu/packages/patches/tophat-build-with-later-seqan.patch new file mode 100644 index 0000000000..fc742e2a7d --- /dev/null +++ b/gnu/packages/patches/tophat-build-with-later-seqan.patch @@ -0,0 +1,24 @@ +This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4. +This is the relevant part of a patch originally posted here: +https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html + +--- a/src/segment_juncs.cpp ++++ b/src/segment_juncs.cpp +@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl + typedef map<uint32_t, IntronMotifs> MotifMap; + + MotifMap ims; +- +- seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc); +- seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc); +- ++ ++ typedef seqan::ModifiedString< ++ seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >, ++ seqan::ModReverse> ConstDnaStringReverseComplement; ++ ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc); ++ ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc); ++ + if (talkative) + fprintf(stderr, "Collecting potential splice sites in islands\n"); + |