[PATCH] gnu: Add TopHat.

[Ricardo Wurmus]

Hi Guix,

I’m happy to be able to submit a patch to add TopHat.  It’s a very
popular piece of bioinformatics software that I didn’t submit to Guix
upstream before as the license wasn’t clear.  The latest release at that
time contained a LICENSE file with the text of the Artistic license 1.0.

The new 2.1.0 release no longer contains this file; instead it declares
the license to be the Boost Software license 1.0.  Additionally, the
license has been clarified on a Github issue (which I linked to).  I
only just noticed this because a user asked me to package the latest
version and I was very happy to see the Artistic license removed.

The sources of TopHat bundle the SeqAn header library (version 1.3) and
the sources of samtools 0.1.18.  I’m patching the Makefile in a build
phase to use our packages for address@hidden and address@hidden  A
snippet removes the bundled sources.

An additional patch to the sources makes it possible to build TopHat
with SeqAn 1.4.2.

~~ Ricardo

>From 91f7bacd8657b4be6669a2e72a2ca74b2e44a62f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Tue, 19 Jan 2016 14:29:19 +0100
Subject: [PATCH] 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.
---
 gnu-system.am                                      |  1 +
 gnu/packages/bioinformatics.scm                    | 64 ++++++++++++++++++++++
 .../patches/tophat-build-with-later-seqan.patch    | 24 ++++++++
 3 files changed, 89 insertions(+)
 create mode 100644 gnu/packages/patches/tophat-build-with-later-seqan.patch

diff --git a/gnu-system.am b/gnu-system.am
index 543a825..c9d16d6 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -678,6 +678,7 @@ dist_patch_DATA =                                           
\
   gnu/packages/patches/tidy-CVE-2015-5522+5523.patch           \
   gnu/packages/patches/tinyxml-use-stl.patch                   \
   gnu/packages/patches/tk-find-library.patch                   \
+  gnu/packages/patches/tophat-build-with-later-seqan.patch     \
   gnu/packages/patches/torsocks-dns-test.patch                 \
   gnu/packages/patches/tvtime-gcc41.patch                      \
   gnu/packages/patches/tvtime-pngoutput.patch                  \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d7ff5e8..74cadff 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -654,6 +654,70 @@ gapped, local, and paired-end alignment modes.")
     (supported-systems '("x86_64-linux"))
     (license license:gpl3+)))
 
+(define-public tophat
+  (package
+    (name "tophat")
+    (version "2.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://ccb.jhu.edu/software/tophat/downloads/tophat-";
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
+              (patches (list (search-patch 
"tophat-build-with-later-seqan.patch")))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Remove bundled SeqAn and samtools
+                  (delete-file-recursively "src/SeqAn-1.3")
+                  (delete-file-recursively "src/samtools-0.1.18")
+                  #t))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:parallel-build? #f ; not supported
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-samtools
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "src/Makefile.in"
+               (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
+               (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
+               (("SAMPROG = samtools_0\\.1\\.18") "")
+               (("\\$\\(samtools_0_1_18_SOURCES\\)") "")
+               (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
+             (substitute* '("src/common.h"
+                            "src/bam2fastx.cpp")
+               (("#include \"bam.h\"") "#include <samtools/bam.h>")
+               (("#include \"sam.h\"") "#include <samtools/sam.h>"))
+             (substitute* '("src/bwt_map.h"
+                            "src/map2gtf.h"
+                            "src/align_status.h")
+               (("#include <bam.h>") "#include <samtools/bam.h>")
+               (("#include <sam.h>") "#include <samtools/sam.h>"))
+             #t)))))
+    (inputs
+     `(("boost" ,boost)
+       ("bowtie" ,bowtie)
+       ("samtools" ,samtools-0.1)
+       ("ncurses" ,ncurses)
+       ("python" ,python-2)
+       ("perl" ,perl)
+       ("zlib" ,zlib)
+       ("seqan" ,seqan)))
+    (home-page "http://ccb.jhu.edu/software/tophat/index.shtml";)
+    (synopsis "Spliced read mapper for RNA-Seq")
+    (description
+     "TopHat is a fast splice junction mapper for RNA-Seq reads.  It aligns
+RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short
+read aligner Bowtie, and then analyzes the mapping results to identify splice
+junctions between exons.")
+    ;; TopHat is released under the Boost Software License, Version 1.0
+    ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
+    (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt";
+                                "Some components have other similar 
licences."))))
+
 (define-public bwa
   (package
     (name "bwa")
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 0000000..fc742e2
--- /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");
+ 
-- 
2.1.0