diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 7 | ||||
| -rw-r--r-- | gnu/packages/patches/tophat-build-with-later-seqan.patch | 24 |
3 files changed, 3 insertions, 29 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 1c48fd3d6e..c167e6753c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1177,7 +1177,6 @@ dist_patch_DATA = \ %D%/packages/patches/tk-find-library.patch \ %D%/packages/patches/ttf2eot-cstddef.patch \ %D%/packages/patches/ttfautohint-source-date-epoch.patch \ - %D%/packages/patches/tophat-build-with-later-seqan.patch \ %D%/packages/patches/totem-meson-easy-codec.patch \ %D%/packages/patches/tuxpaint-stamps-path.patch \ %D%/packages/patches/twinkle-include-qregexpvalidator.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1e04081ceb..0dc81c8f61 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1332,7 +1332,7 @@ gapped, local, and paired-end alignment modes.") (define-public tophat (package (name "tophat") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (string-append @@ -1340,13 +1340,12 @@ gapped, local, and paired-end alignment modes.") version ".tar.gz")) (sha256 (base32 - "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7")) - (patches (search-patches "tophat-build-with-later-seqan.patch")) + "19add02kv2xhd6ihd779dr7x35ggym3jqr0m5c4315i1yfb0p11p")) (modules '((guix build utils))) (snippet '(begin ;; Remove bundled SeqAn and samtools - (delete-file-recursively "src/SeqAn-1.3") + (delete-file-recursively "src/SeqAn-1.4.2") (delete-file-recursively "src/samtools-0.1.18") #t)))) (build-system gnu-build-system) diff --git a/gnu/packages/patches/tophat-build-with-later-seqan.patch b/gnu/packages/patches/tophat-build-with-later-seqan.patch deleted file mode 100644 index fc742e2a7d..0000000000 --- a/gnu/packages/patches/tophat-build-with-later-seqan.patch +++ /dev/null @@ -1,24 +0,0 @@ -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"); - |