gnu: Remove tophat.

* gnu/packages/bioinformatics.scm (tophat): Delete variable.

Fixes: guix/guix#5660
Change-Id: I57eb5355b1eb3da2acbd539e5f795c66f3e1fae6

1 files changed, 0 insertions, 76 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1b7b848d3f8..1e7cd451247 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5757,82 +5757,6 @@ keep its memory footprint small: typically about 2.2 GB for the human
 genome (2.9 GB for paired-end).")
     (license license:artistic2.0)))
 
-(define-public tophat
-  (package
-    (name "tophat")
-    (version "2.1.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "http://ccb.jhu.edu/software/tophat/downloads/tophat-"
-                    version ".tar.gz"))
-              (sha256
-               (base32
-                "19add02kv2xhd6ihd779dr7x35ggym3jqr0m5c4315i1yfb0p11p"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; Remove bundled SeqAn and samtools
-                  (delete-file-recursively "src/SeqAn-1.4.2")
-                  (delete-file-recursively "src/samtools-0.1.18")))))
-    (build-system gnu-build-system)
-    (arguments
-     '(#:parallel-build? #f             ; not supported
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'set-paths 'hide-default-gcc
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((gcc (assoc-ref inputs "gcc")))
-               ;; Remove the default GCC from CPLUS_INCLUDE_PATH to prevent
-               ;; conflicts with the GCC 5 input.
-               (setenv "CPLUS_INCLUDE_PATH"
-                       (string-join
-                        (delete (string-append gcc "/include/c++")
-                                (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
-                        ":")))))
-         (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.cpp"
-                            "src/tophat.py")
-               (("samtools_0.1.18") (which "samtools")))
-             (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>")))))))
-    (native-inputs
-     `(("gcc@5" ,gcc-5))) ;; doesn't build with later versions
-    (inputs
-     `(("boost" ,boost)
-       ("bowtie" ,bowtie)
-       ("ncurses" ,ncurses)
-       ("perl" ,perl)
-       ("python" ,python-2)
-       ("samtools" ,samtools-0.1)
-       ("seqan" ,seqan-1)
-       ("zlib" ,zlib)))
-    (home-page "https://ccb.jhu.edu/software/tophat/index.shtml")
-    (synopsis "Spliced read mapper for RNA-Seq data")
-    (description
-     "TopHat is a fast splice junction mapper for nucleotide sequence
-reads produced by the RNA-Seq method.  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:boost1.0)))
-
 (define-public bwa
   (package
     (name "bwa")