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| author | Ricardo Wurmus <rekado@elephly.net> | 2018-10-20 22:03:02 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-10-20 23:37:34 +0200 |
| commit | c793f4d8fb25044994b2694632c6d6f3d40b49b7 (patch) | |
| tree | fb666887717ee68e81f6a568ea536e3bafa17f92 /gnu/packages | |
| parent | 95758e2faf7bb96d8df270d37bf71d52cbd4270c (diff) | |
| download | patches-c793f4d8fb25044994b2694632c6d6f3d40b49b7.tar patches-c793f4d8fb25044994b2694632c6d6f3d40b49b7.tar.gz | |
gnu: bamm: Fetch from git and use INVOKE.
* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git.
[arguments]: Use INVOKE and return #T unconditionally.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 21 |
1 files changed, 12 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 56a566f1ef..4192a6c61b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -167,15 +167,16 @@ structure of the predicted RNA.") (name "bamm") (version "1.7.3") (source (origin - (method url-fetch) + (method git-fetch) ;; BamM is not available on pypi. - (uri (string-append - "https://github.com/Ecogenomics/BamM/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (git-reference + (url "https://github.com/Ecogenomics/BamM.git") + (commit version) + (recursive? #t))) + (file-name (git-file-name name version)) (sha256 (base32 - "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s")) + "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5")) (modules '((guix build utils))) (snippet `(begin @@ -197,11 +198,12 @@ structure of the predicted RNA.") (lambda _ (with-directory-excursion "c" (let ((sh (which "sh"))) + (for-each make-file-writable (find-files "." ".*")) ;; Use autogen so that 'configure' works. (substitute* "autogen.sh" (("/bin/sh") sh)) (setenv "CONFIG_SHELL" sh) - (substitute* "configure" (("/bin/sh") sh)) - (zero? (system* "./autogen.sh")))))) + (invoke "./autogen.sh"))) + #t)) (delete 'build) ;; Run tests after installation so compilation only happens once. (delete 'check) @@ -229,7 +231,8 @@ structure of the predicted RNA.") ;; There are 2 errors printed, but they are safe to ignore: ;; 1) [E::hts_open_format] fail to open file ... ;; 2) samtools view: failed to open ... - (zero? (system* "nosetests"))))))) + (invoke "nosetests") + #t))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) |