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| author | Ricardo Wurmus <rekado@elephly.net> | 2018-10-20 23:04:02 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-10-20 23:37:34 +0200 |
| commit | 21c837405a7d46590fbe1d9e45e16a56f182e451 (patch) | |
| tree | 4f012ea841984c2b0bd1e7c427c2594d69cddc0d /gnu/packages/bioinformatics.scm | |
| parent | f45093429c8319475b22c5478ea6b719b7c97cb8 (diff) | |
| download | patches-21c837405a7d46590fbe1d9e45e16a56f182e451.tar patches-21c837405a7d46590fbe1d9e45e16a56f182e451.tar.gz | |
gnu: bowtie: Update to 2.3.4.3.
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.4.3.
[source]: Fetch from git.
[inputs]: Replace python-2 with python-wrapper; move perl, perl-clone,
perl-test-deep, and perl-test-simple from here...
[native-inputs]: ...to here.
[arguments]: Simplify check phase.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 22 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 66e06869c4..7c58ab2455 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1273,15 +1273,16 @@ errors at the end of reads.") (define-public bowtie (package (name "bowtie") - (version "2.3.2") + (version "2.3.4.3") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/BenLangmead/bowtie2.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90")) + "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp")) (modules '((guix build utils))) (snippet '(begin @@ -1291,14 +1292,6 @@ errors at the end of reads.") (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) #t)))) (build-system gnu-build-system) - (inputs - `(("perl" ,perl) - ("perl-clone" ,perl-clone) - ("perl-test-deep" ,perl-test-deep) - ("perl-test-simple" ,perl-test-simple) - ("python" ,python-2) - ("tbb" ,tbb) - ("zlib" ,zlib))) (arguments '(#:make-flags (list "allall" @@ -1308,11 +1301,21 @@ errors at the end of reads.") (modify-phases %standard-phases (delete 'configure) (replace 'check - (lambda* (#:key outputs #:allow-other-keys) - (zero? (system* "perl" - "scripts/test/simple_tests.pl" - "--bowtie2=./bowtie2" - "--bowtie2-build=./bowtie2-build"))))))) + (lambda _ + (invoke "perl" + "scripts/test/simple_tests.pl" + "--bowtie2=./bowtie2" + "--bowtie2-build=./bowtie2-build") + #t))))) + (inputs + `(("tbb" ,tbb) + ("zlib" ,zlib) + ("python" ,python-wrapper))) + (native-inputs + `(("perl" ,perl) + ("perl-clone" ,perl-clone) + ("perl-test-deep" ,perl-test-deep) + ("perl-test-simple" ,perl-test-simple))) (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") (synopsis "Fast and sensitive nucleotide sequence read aligner") (description |