diff options
| author | pjotrp | 2017-01-29 06:48:17 +0000 |
|---|---|---|
| committer | pjotrp | 2017-01-29 06:48:17 +0000 |
| commit | 0c6ee6e845def194d50021eec528059671e04cd3 (patch) | |
| tree | 76cd94880b9b96f831c84371a10788d54362801e /gn/packages/bioinformatics.scm | |
| parent | 0ed58051da02e1819e0c7cbb56a85d8b5ea713b0 (diff) | |
| download | guix-bioinformatics-0c6ee6e845def194d50021eec528059671e04cd3.tar.gz | |
Shipped sambamba
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 19 |
1 files changed, 9 insertions, 10 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index e16c28e..4ded90e 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -921,10 +921,10 @@ association studies (GWAS).") (license license:gpl3)))) (define-public sambamba - (let ((commit "5a33d571339c966477c1f70ed08f64051f7b41c1")) + (let ((commit "91096e78c81162f855b1044a4b2d41895bd27262")) (package (name "sambamba") - (version (string-append "0.6.5-" (string-take commit 7))) + (version (string-append "0.6.6-pre1-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference @@ -933,15 +933,15 @@ association studies (GWAS).") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "05nlhwjw17igcwiz4pq0r4f8flrqcy4065fhx4nhpc0g65p70mi5")))) + "0d7d0f3ri8qi5r9wq2wy9wzkr1wm68alfsn20q61lqzrfrfwm93k")))) (build-system gnu-build-system) (outputs '("out" - "debug")) ;retain debug symbols - note that -O2 is used + "debug")) (native-inputs `(("ldc" ,ldc) ("lz4" ,lz4) - ("coreutils" ,coreutils) ; for env ("zlib" ,zlib) + ("coreutils" ,coreutils) ; for env ("perl" ,perl) ; Needed for htslib ("ruby" ,ruby) ; Needed for htslib ("python" ,python-2) ; Needed for htslib @@ -963,7 +963,7 @@ association studies (GWAS).") (uri (git-reference (url "https://github.com/biod/BioD.git") (commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))) - (file-name (string-append "biod-src-" (string-take commit 7) ".tar.gz")) + (file-name (string-append "biod-src-" (string-take commit 7) "-checkout")) (sha256 (base32 "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))) (arguments @@ -980,13 +980,12 @@ association studies (GWAS).") (and (with-directory-excursion "htslib" (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src") "--strip-components=1"))) - (zero? (system* "rm" "-r" "BioD")) - (zero? (system* "ln" "--symbolic" "--no-target-directory" - (assoc-ref inputs "biod-src") "BioD"))))) + ;; (zero? (system* "cp" "--recursive" (string-append (assoc-ref inputs "biod-src") "/*") "BioD/"))))) + (copy-recursively (assoc-ref inputs "biod-src") "BioD")))) (replace 'build (lambda* (#:key inputs make-flags #:allow-other-keys) - (zero? (system* "make" "-f" "Makefile.guix" "sambamba-ldmd2" + (zero? (system* "make" "-f" "Makefile.guix" "guix-debug" (string-append "LDC_LIB_PATH=" (assoc-ref inputs "ldc") "/lib"))))) |