diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 31 |
1 files changed, 16 insertions, 15 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index b509fc3..d524ea2 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -37,7 +37,7 @@ #:use-module (gnu packages graphviz) #:use-module (gnu packages java) #:use-module (gnu packages linux) - #:use-module (gnu packages ldc) + #:use-module (gn packages ldc) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -921,36 +921,37 @@ association studies (GWAS).") (license license:gpl3)))) (define-public sambamba - (let ((commit "c810c7ef14957f16288c205fd7b9d25c4ae7005d")) - ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84")) + (let ((commit "c6f52cc7f71d2cdb0bafe3bb911042c6e2ef2475")) (package (name "sambamba") - (version (string-append "0.5.9-1." (string-take commit 7))) + (version (string-append "0.6.5-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/roelj/sambamba.git") - ;;(url "https://github.com/pjotrp/sambamba.git") + ;; (url "https://github.com/roelj/sambamba.git") + (url "https://github.com/pjotrp/sambamba.git") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0c4c13f021sl7mf5xc2v8dbwsz775n8dlsrrn7qa6qgbx05n54dv")))) - ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5")))) + "0ljpiamx4fabm1ha4swfdghl5slwg530y0vzvd9h170shj6gaj91")))) (build-system gnu-build-system) (native-inputs `(("ldc" ,ldc) - ;;("lz4" ,lz4) + ("lz4" ,lz4) + ("coreutils" ,coreutils) ; for env ("rdmd" ,rdmd) ("zlib" ,zlib) ("perl" ,perl) ; Needed for htslib ("ruby" ,ruby) ; Needed for htslib - ("python" ,python) ; 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")))) ("htslib-src" @@ -958,7 +959,7 @@ association studies (GWAS).") (method url-fetch) (uri "https://github.com/lomereiter/htslib/archive/2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5.tar.gz") ;;(uri "https://github.com/samtools/htslib/archive/1.3.tar.gz") - ;;(file-name "htslib-1.3.tar.gz") + (file-name "htslib-0.2.0-rc10-271-g2f3c3ea-dirty.tar.gz") (sha256 (base32 "0bl6w856afnbgdsw8bybsxpqsyf2ba3f12rqh47hhpxvv866g08w")))) ;;(base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9")) @@ -968,12 +969,12 @@ association studies (GWAS).") (method git-fetch) (uri (git-reference (url "https://github.com/biod/BioD.git") - (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b"))) - (file-name "biod-src") + (commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))) + (file-name (string-append "biod-src-" (string-take commit 7) ".tar.gz")) (sha256 - (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf")))))) + (base32 "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))) (arguments - `(#:tests? #f + `(#:tests? #f ; no tests available #:make-flags (list "-f" "Makefile.guix") #:phases (modify-phases %standard-phases |