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authorpjotrp2017-01-24 09:27:32 +0000
committerpjotrp2017-01-24 09:27:32 +0000
commitf8c952c5ae8594fcbd95c680ce3b6bcbfe563a6f (patch)
tree77c54ff01d8e3cab80279a4cd19661b692f129d4 /gn
parentf0d73d5582d225b997eb8407cce2e5e8b161ade5 (diff)
downloadguix-bioinformatics-f8c952c5ae8594fcbd95c680ce3b6bcbfe563a6f.tar.gz
Sambamba uses lz4.so, so the source download is no longer needed.
Tested view of both BAM and CRAM works.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm24
1 files changed, 12 insertions, 12 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index c920d30..701ac1d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -936,25 +936,25 @@ association studies (GWAS).")
"05nlhwjw17igcwiz4pq0r4f8flrqcy4065fhx4nhpc0g65p70mi5"))))
(build-system gnu-build-system)
(outputs '("out"
- "debug")) ;retain debug symbols
+ "debug")) ;retain debug symbols - note that -O2 is used
(native-inputs
`(("ldc" ,ldc)
("lz4" ,lz4)
("coreutils" ,coreutils) ; for env
- ("rdmd" ,rdmd)
+ ;; ("rdmd" ,rdmd)
("zlib" ,zlib)
("perl" ,perl) ; Needed for htslib
("ruby" ,ruby) ; Needed for htslib
("python" ,python-2) ; Needed for htslib
("gcc" ,gcc)
("which" ,which)
- ("lz4-src"
- ,(origin
- (method url-fetch)
- (uri "https://github.com/Cyan4973/lz4/archive/160661c7a4cbf805f4af74d2e3932a17a66e6ce7.tar.gz")
- (file-name (string-append "lz4-" (string-take commit 7) ".tar.gz" ))
- (sha256
- (base32 "131nnbsd5dh7c8sdqzc9kawh3mi0qi4qxznv7zhzfszlx4g2fd20"))))
+ ; ("lz4-src"
+ ; ,(origin
+ ; (method url-fetch)
+ ; (uri "https://github.com/Cyan4973/lz4/archive/160661c7a4cbf805f4af74d2e3932a17a66e6ce7.tar.gz")
+ ; (file-name (string-append "lz4-" (string-take commit 7) ".tar.gz" ))
+ ; (sha256
+ ; (base32 "131nnbsd5dh7c8sdqzc9kawh3mi0qi4qxznv7zhzfszlx4g2fd20"))))
("htslib-src"
,(origin
(method url-fetch)
@@ -988,9 +988,9 @@ association studies (GWAS).")
(and (with-directory-excursion "htslib"
(zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
"--strip-components=1")))
- (with-directory-excursion "lz4"
- (zero? (system* "tar" "xvf" (assoc-ref inputs "lz4-src")
- "--strip-components=1")))
+ ; (with-directory-excursion "lz4"
+ ; (zero? (system* "tar" "xvf" (assoc-ref inputs "lz4-src")
+ ; "--strip-components=1")))
(zero? (system* "rm" "-r" "BioD"))
(zero? (system* "ln" "--symbolic" "--no-target-directory"
(assoc-ref inputs "biod-src") "BioD")))))