aboutsummaryrefslogtreecommitdiff
path: root/gn/packages
diff options
context:
space:
mode:
authorpjotrp2017-01-24 09:04:07 +0000
committerpjotrp2017-01-24 09:04:07 +0000
commitf0d73d5582d225b997eb8407cce2e5e8b161ade5 (patch)
treefda8794ad4dcad260b179edca2342d9c0e73d04d /gn/packages
parent5fa0e726f7e76ebe7dc098fb3fc786f7ce67d540 (diff)
downloadguix-bioinformatics-f0d73d5582d225b997eb8407cce2e5e8b161ade5.tar.gz
sambamba: make file builds with symbols by default and O2
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm17
1 files changed, 9 insertions, 8 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 5d6f04d..c920d30 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -935,6 +935,8 @@ association studies (GWAS).")
(base32
"05nlhwjw17igcwiz4pq0r4f8flrqcy4065fhx4nhpc0g65p70mi5"))))
(build-system gnu-build-system)
+ (outputs '("out"
+ "debug")) ;retain debug symbols
(native-inputs
`(("ldc" ,ldc)
("lz4" ,lz4)
@@ -995,7 +997,7 @@ association studies (GWAS).")
(replace
'build
(lambda* (#:key inputs make-flags #:allow-other-keys)
- (zero? (system* "make" "-f" "Makefile.guix" "sambamba-ldmd2-debug" "CC=gcc" "D_COMPILER=ldc2"
+ (zero? (system* "make" "-f" "Makefile.guix" "sambamba-ldmd2"
(string-append "LDC_LIB_PATH="
(assoc-ref inputs "ldc")
"/lib")))))
@@ -1005,16 +1007,15 @@ association studies (GWAS).")
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "build/sambamba" bin)))))))
(home-page "https://github.com/lomereiter/sambamba")
- (synopsis "A tool for working with SAM and BAM files written in D.")
+ (synopsis "Fast tool for working with SAM, BAM and CRAM files written in D.")
(description
- "Sambamba is a high performance modern robust and fast tool (and
-library), written in the D programming language, for working with SAM
-and BAM files. Current parallelised functionality is an important
-subset of samtools functionality, including view, index, sort,
-markdup, and depth.")
+ "Sambamba is a high performance modern robust and fast
+tool (and library), written in the D programming language, for working
+with SAM, BAM and CRAM files. Current parallelised functionality is
+an important subset of samtools functionality, including view, index,
+sort, markdup, and depth.")
(license license:gpl2+))))
-
(define-public vcflib
(let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
(package