diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2018-10-21 14:00:07 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-10-21 23:06:46 +0200 |
| commit | 7a1e62ca67849f9ca19ded4d26c542021db71e38 (patch) | |
| tree | 0b2d20288c9988592bb6fa9a6e1e027a048bc80c /gnu/packages/bioinformatics.scm | |
| parent | 4d494a4fa3ebb2d1deacede405d0b0d8e5dbc32b (diff) | |
gnu: delly: Update to 0.7.9.
* gnu/packages/bioinformatics.scm (delly): Update to 0.7.9.
[source]: Fetch from git.
[arguments]: Add phase install-templates; use default install phase.
[native-inputs]: Remove python-2.
[home-page]: Use new home page.
* gnu/packages/patches/delly-use-system-libraries.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 40 |
1 files changed, 20 insertions, 20 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bc21848367..78debbc873 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2155,42 +2155,42 @@ identify enrichments with functional annotations of the genome.") (define-public delly (package (name "delly") - (version "0.7.7") + (version "0.7.9") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/tobiasrausch/delly/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dellytools/delly.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj")) - (patches (search-patches "delly-use-system-libraries.patch")))) + (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/htslib") + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests to run. - #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time. + #:make-flags + (list "PARALLEL=1" ; Allow parallel execution at run-time. + (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda _ - (let ((bin (string-append (assoc-ref %outputs "out") "/bin")) - (templates (string-append (assoc-ref %outputs "out") + (add-after 'install 'install-templates + (lambda* (#:key outputs #:allow-other-keys) + (let ((templates (string-append (assoc-ref outputs "out") "/share/delly/templates"))) - (mkdir-p bin) (mkdir-p templates) (copy-recursively "excludeTemplates" templates) - (install-file "src/cov" bin) - (install-file "src/delly" bin) - (install-file "src/dpe" bin))))))) - (native-inputs - `(("python" ,python-2))) + #t)))))) (inputs `(("boost" ,boost) ("htslib" ,htslib) ("zlib" ,zlib) ("bzip2" ,bzip2))) - (home-page "https://github.com/tobiasrausch/delly") + (home-page "https://github.com/dellytools/delly") (synopsis "Integrated structural variant prediction method") (description "Delly is an integrated structural variant prediction method that can discover and genotype deletions, tandem duplications, inversions and |