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authorpjotrp2017-02-24 16:03:16 +0000
committerpjotrp2017-02-24 16:03:16 +0000
commit2bef484b005f1fd18173ecde3da34bf9e67587f2 (patch)
tree7e035889d7e0090c6f29c79f12dd0ce9c5332f00 /gn/packages
parentac594bf9c0e2a95e9cd96a7e1d68c39a2ae7f82e (diff)
downloadguix-bioinformatics-2bef484b005f1fd18173ecde3da34bf9e67587f2.tar.gz
sambamba: now links in samtools and bcftools
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/sambamba.scm26
1 files changed, 18 insertions, 8 deletions
diff --git a/gn/packages/sambamba.scm b/gn/packages/sambamba.scm
index 46cf0e7..221aeb6 100644
--- a/gn/packages/sambamba.scm
+++ b/gn/packages/sambamba.scm
@@ -8,6 +8,7 @@
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (gnu packages base)
+ #:use-module (gnu packages bioinformatics) ; for samtools in sambamba
#:use-module (gnu packages compression)
#:use-module (gnu packages gcc)
#:use-module (gnu packages perl)
@@ -18,10 +19,10 @@
#:use-module (srfi srfi-1))
(define-public sambamba
- (let ((commit "6ae174bcb50d3a8f1b6dd10de9c68bbc4770e56a"))
+ (let ((commit "54778aea4c054702d34740d229bbf03e5b907482"))
(package
(name "sambamba")
- (version (string-append "0.6.6-pre3-" (string-take commit 7)))
+ (version (string-append "0.6.6-pre4-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -30,19 +31,23 @@
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "1m26i8icllclynqia4yi2mp7zfs2zajllva6bzxn188fhlyjwzqr"))))
+ "131311h0ccz3r74yvw20f96pc86s760cvvnzgxin0kks7wgixmmz"))))
(build-system gnu-build-system)
(outputs '("out"
"debug"))
+ (inputs
+ `(("samtools" ,samtools) ; for pileup
+ ("bcftools" ,bcftools) ; for pileup
+ ("lz4" ,lz4)
+ ("zlib" ,zlib)
+ ))
(native-inputs
`(("ldc" ,ldc)
- ("lz4" ,lz4)
("shunit2" ,shunit2)
- ("zlib" ,zlib)
("coreutils" ,coreutils) ; for env
- ("perl" ,perl) ; Needed for htslib
- ("ruby" ,ruby) ; Needed for htslib
- ("python" ,python-2) ; Needed for htslib
+ ("perl" ,perl) ; Needed for building htslib
+ ("ruby" ,ruby) ; Needed for building htslib
+ ("python" ,python-2) ; Needed for building htslib and sambamba
("gcc" ,gcc)
("which" ,which)
("htslib-src"
@@ -78,6 +83,11 @@
(modify-phases %standard-phases
(delete 'configure)
(delete 'check)
+ (add-after 'unpack 'patch-pileup-d
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "sambamba/pileup.d"
+ (("string samtoolsBin = null;") (string-append "string samtoolsBin = \"" (which "samtools") "\";"))
+ (("string bcftoolsBin = null;") (string-append "string bcftoolsBin = \"" (which "bcftools") "\";")))))
(add-after 'unpack 'unpack-htslib-sources
(lambda* (#:key inputs #:allow-other-keys)
;; The current build compiles htslib statically into the