diff options
| 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/patches | |
| parent | 3062d750b4f8e16c979629360bf2dc411b71b04c (diff) | |
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/patches')
| -rw-r--r-- | gnu/packages/patches/tophat-build-with-later-seqan.patch | 24 |
1 files changed, 24 insertions, 0 deletions
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"); + |