diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 23 |
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"))))) |