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-rw-r--r--gn/packages/bioinformatics.scm31
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