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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-12-03 13:53:54 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-12-03 13:56:02 +0100 |
| commit | 6d4f260166eb499564fa31ce487ecf301f445e4e (patch) | |
| tree | bf567799966d740c15942b4b9dc13d03b25c84b6 /gnu | |
| parent | 673cc2990807e36308cce4b20a8a6f1501b0f4b3 (diff) | |
| download | guix-patches-6d4f260166eb499564fa31ce487ecf301f445e4e.tar guix-patches-6d4f260166eb499564fa31ce487ecf301f445e4e.tar.gz | |
gnu: bamutils: Update to 1.0.14.
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.14.
[arguments]: Patch DATE for reproducibility; prepare sources of libstatgen.
[native-inputs]: Add sources of libstatgen.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 34 |
1 files changed, 25 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 27eccadd1e..be3fce6f70 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -324,27 +324,43 @@ BAM files.") (define-public bamutils (package (name "bamutils") - (version "1.0.13") + (version "1.0.14") (source (origin - (method url-fetch) - (uri - (string-append - "https://genome.sph.umich.edu/w/images/7/70/" - "BamUtilLibStatGen." version ".tgz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/statgen/bamUtil") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0asr1kmjbr3cyf4hkg865y8c2s30v87xvws4q6c8pyfi6wfd1h8n")))) + "0i2r332k1kz0jysyg89d858wqq59n16lw6dv5qmilcwshb77r9v7")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; There are no tests. + `(#:tests? #f ; Unclear how to run tests #:make-flags ,#~(list "USER_WARNINGS=-std=gnu++98" ; (string-append "INSTALLDIR=" #$output "/bin")) #:phases (modify-phases %standard-phases - (delete 'configure)))) + (replace 'configure + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/Makefile" ; + (("^DATE=.*") "DATE=\"1970-01-01\"\n")) + (copy-recursively (assoc-ref inputs "libstatgen") + "../libStatGen")))))) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("libstatgen" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/statgen/libStatGen/") + (commit (string-append "v" version)))) + (file-name (git-file-name "libstatgen" version)) + (sha256 + (base32 + "0q9iyk046r4m7qnav8c3f28zsar25lj9nydiklwaswmzdijhi4p1")))))) (home-page "https://genome.sph.umich.edu/wiki/BamUtil") (synopsis "Programs for working on SAM/BAM files") (description "This package provides several programs that perform |