summaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
diff options
context:
space:
mode:
authorRicardo Wurmus <rekado@elephly.net>2018-10-21 14:00:07 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-10-21 23:06:46 +0200
commit7a1e62ca67849f9ca19ded4d26c542021db71e38 (patch)
tree0b2d20288c9988592bb6fa9a6e1e027a048bc80c /gnu/packages/bioinformatics.scm
parent4d494a4fa3ebb2d1deacede405d0b0d8e5dbc32b (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.scm40
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