guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 03732b485b789641773defca43d1d630fbdf9bbb
Author: Andreas Enge <[email protected]>
AuthorDate: Tue Feb 17 11:37:58 2026 +0100
gnu: Remove tophat.
* gnu/packages/bioinformatics.scm (tophat): Delete variable.
Fixes: guix/guix#5660
Change-Id: I57eb5355b1eb3da2acbd539e5f795c66f3e1fae6
---
gnu/packages/bioinformatics.scm | 76 -----------------------------------------
1 file changed, 76 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1b7b848d3f..1e7cd45124 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")
