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authorpjotrp2017-03-14 15:40:55 +0000
committerpjotrp2017-03-14 15:40:55 +0000
commit0062de95882c896c0379f90fcfb11e2d249fccad (patch)
treef158b16e3a0fcb78208f5744852d244b65e34a9e /gn/packages
parentb2f7f57f84a3a123e6cc86639c32f46554e22f55 (diff)
downloadguix-bioinformatics-0062de95882c896c0379f90fcfb11e2d249fccad.tar.gz
sambamba: update build to release
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/sambamba.scm22
1 files changed, 12 insertions, 10 deletions
diff --git a/gn/packages/sambamba.scm b/gn/packages/sambamba.scm
index 6463689..f5a384f 100644
--- a/gn/packages/sambamba.scm
+++ b/gn/packages/sambamba.scm
@@ -19,10 +19,10 @@
#:use-module (srfi srfi-1))
(define-public sambamba
- (let ((commit "54778aea4c054702d34740d229bbf03e5b907482"))
+ (let ((commit "52ab1eff7070cd3dafad94a15c9fd6e243a45a4d"))
(package
(name "sambamba")
- (version (string-append "0.6.6-pre4-" (string-take commit 7)))
+ (version (string-append "0.6.6-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -31,9 +31,9 @@
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "131311h0ccz3r74yvw20f96pc86s760cvvnzgxin0kks7wgixmmz"))))
+ "16nfvmipa1gj7f8c9lqhh5yffdmaic1pzcrm9281dqwywl9w8hsg"))))
(build-system gnu-build-system)
- (outputs '("out"
+ (outputs '("out" ; disable all checks for speed
"debug"))
(inputs
`(("samtools" ,samtools) ; for pileup
@@ -87,7 +87,7 @@
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "sambamba/pileup.d"
(("string samtoolsBin = null;") (string-append "string samtoolsBin = \"" (which "samtools") "\";"))
- (("string samtoolsBin = null;") (string-append "string samtoolsBin = \"" (which "samtools") "\";"))
+ (("string bcftoolsBin = null;") (string-append "string bcftoolsBin = \"" (which "bcftools") "\";"))
((" this_app = args[0];") (string-append " this_app = \"" (which "sambamba") "\";")))))
(add-after 'unpack 'unpack-htslib-sources
(lambda* (#:key inputs #:allow-other-keys)
@@ -101,11 +101,13 @@
(copy-recursively (assoc-ref inputs "biod-src") "BioD"))))
(replace
'build
- (lambda* (#:key inputs make-flags #:allow-other-keys)
- (zero? (system* "make" "-f" "Makefile.guix" "guix-debug"
- (string-append "LDC_LIB_PATH="
- (assoc-ref inputs "ldc")
- "/lib")))))
+ (lambda* (#:key inputs outputs make-flags #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (debug-out (assoc-ref outputs "debug")))
+ (zero? (system* "make" "-f" "Makefile.guix" "guix"
+ (string-append "LDC_LIB_PATH="
+ (assoc-ref inputs "ldc")
+ "/lib"))))))
(replace
'install
(lambda* (#:key outputs #:allow-other-keys)