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-rw-r--r--gn/packages/bioinformatics.scm23
1 files changed, 15 insertions, 8 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 12a4bcb..d37a287 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -489,20 +489,24 @@ association studies (GWAS).")
(build-system gnu-build-system)
(native-inputs
`(("ldc" ,ldc)
- ("lz4" ,lz4)
+ ;;("lz4" ,lz4)
("rdmd" ,rdmd)
("zlib" ,zlib)
- ("perl" ,perl) ; Needed for htslib tests?
- ("ruby" ,ruby) ; Needed for htslib tests?
- ("python" ,python) ; Needed for htslib tests?
+ ("perl" ,perl) ; Needed for htslib
+ ("ruby" ,ruby) ; Needed for htslib
+ ("python" ,python) ; Needed for htslib
("gcc" ,gcc)
+ ("lz4-src"
+ ,(origin
+ (method url-fetch)
+ (uri "https://github.com/Cyan4973/lz4/archive/160661c7a4cbf805f4af74d2e3932a17a66e6ce7.tar.gz")
+ (sha256
+ (base32 "131nnbsd5dh7c8sdqzc9kawh3mi0qi4qxznv7zhzfszlx4g2fd20"))))
("htslib-src"
,(origin
(method url-fetch)
- (uri (string-append "https://github.com/lomereiter/htslib/archive/"
- "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5" ".tar.gz"))
+ (uri "https://github.com/lomereiter/htslib/archive/2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5.tar.gz")
;;(uri "https://github.com/samtools/htslib/archive/1.3.tar.gz")
- (file-name "htslib-2f3c3ea7b.tar.gz")
;;(file-name "htslib-1.3.tar.gz")
(sha256
(base32 "0bl6w856afnbgdsw8bybsxpqsyf2ba3f12rqh47hhpxvv866g08w"))))
@@ -532,13 +536,16 @@ 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")))
(zero? (system* "rm" "-r" "BioD"))
(zero? (system* "ln" "--symbolic" "--no-target-directory"
(assoc-ref inputs "biod-src") "BioD")))))
(replace
'build
(lambda* (#:key inputs make-flags #:allow-other-keys)
- (zero? (system* "make" "-f" "Makefile.guix"
+ (zero? (system* "make" "sambamba-ldmd2-64" "CC=gcc" "D_COMPILER=ldc2"
(string-append "LDC_LIB_PATH="
(assoc-ref inputs "ldc")
"/lib")))))