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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-19 14:29:19 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-23 08:53:10 +0100
commit94ce537eacaa443df57bef14ceaa0d7fdad86071 (patch)
tree1100bd70d046ab787e4730b6a00e8e77d43e4b2f /gnu/packages/patches
parent3062d750b4f8e16c979629360bf2dc411b71b04c (diff)
downloadguix-94ce537eacaa443df57bef14ceaa0d7fdad86071.tar
guix-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/patches')
-rw-r--r--gnu/packages/patches/tophat-build-with-later-seqan.patch24
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");
+