rekado pushed a commit to branch master
in repository guix.
commit 9a6808e0c00d6acb00b7be4aa573f252fa7d9635
Author: Ricardo Wurmus <rek...@elephly.net>
Date: Sun Oct 21 11:54:44 2018 +0200
gnu: tophat: Update to 2.1.1.
* gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
---
gnu/local.mk | 1 -
gnu/packages/bioinformatics.scm | 7 +++----
.../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 1c48fd3..c167e67 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 1e04081..0dc81c8 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 fc742e2..0000000
--- 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");
-
