From 9a6808e0c00d6acb00b7be4aa573f252fa7d9635 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 21 Oct 2018 11:54:44 +0200
Subject: 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(-)
 delete mode 100644 gnu/packages/patches/tophat-build-with-later-seqan.patch

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");
- 
-- 
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