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authorpjotrp2017-11-08 10:32:15 +0000
committerpjotrp2017-11-08 10:32:15 +0000
commit6b78041ea076507be5999cb7c12bee982b371710 (patch)
treeafbae459bd09ea35f02ebccb30619c85732ffbf4 /gn/packages
parent56ea80b33b6715d07a46b603aed5033d4fd8d9b0 (diff)
downloadguix-bioinformatics-6b78041ea076507be5999cb7c12bee982b371710.tar.gz
Sambamba test release
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/sambamba.scm46
1 files changed, 26 insertions, 20 deletions
diff --git a/gn/packages/sambamba.scm b/gn/packages/sambamba.scm
index 261e325..c2759fa 100644
--- a/gn/packages/sambamba.scm
+++ b/gn/packages/sambamba.scm
@@ -19,10 +19,10 @@
#:use-module (srfi srfi-1))
(define-public sambamba
- (let ((commit "52ab1eff7070cd3dafad94a15c9fd6e243a45a4d"))
+ (let ((commit "7cff06533b539a99b4e0db681fb573214d63aae2"))
(package
(name "sambamba")
- (version (string-append "0.6.6-" (string-take commit 7)))
+ (version (string-append "0.6.7-pre1-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -31,7 +31,7 @@
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "16nfvmipa1gj7f8c9lqhh5yffdmaic1pzcrm9281dqwywl9w8hsg"))))
+ "11k2xqgmbvxwki569439kvzf2b0cqy2x21kbgjijwvpqk9j8czx4"))))
(build-system gnu-build-system)
(outputs '("out" ; disable all checks for speed
"debug"))
@@ -52,37 +52,35 @@
("which" ,which)
("htslib-src"
,(origin
- (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-0.2.0-rc10-271-g2f3c3ea-dirty.tar.gz")
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pjotrp/htslib.git")
+ (commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")))
+ (file-name (string-append "htslib-src-" (string-take commit 7) "-checkout"))
(sha256
- (base32 "0bl6w856afnbgdsw8bybsxpqsyf2ba3f12rqh47hhpxvv866g08w"))))
- ;;(base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9"))
- ;;(patches (list (search-patch "htslib-add-cram_to_bam.patch")))))
+ (base32 "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
("biod-src"
,(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/pjotrp/BioD.git")
- (commit "b7f1db860d212ee5fb6f9adfb36c6e783aaeb6f5")))
+ (url "https://github.com/biod/BioD.git")
+ (commit "c778e4f2d8bacea7499283ce39f5577b232732c6")))
(file-name (string-append "biod-src-" (string-take commit 7) "-checkout"))
(sha256
- (base32 "01xkdjdn9lb2b4b5ykzhnrk2rjikagav8b3fyac3zafcfq600cr4"))))
+ (base32 "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37"))))
("dlang-undeaD-src"
,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/dlang/undeaD.git")
- (commit "610234f159132f91046d4fb893889fb8ee14cd2f")))
+ (commit "92803d25c88657e945511f0976a0c79d8da46e89")))
(file-name (string-append "dlang-undeaD-src-" (string-take commit 7) "-checkout"))
(sha256
- (base32 "12zxsgvka4a82ghp2gaviph6kz13jzjb5pbc8v6i3rmcnifzpbrl"))))))
+ (base32 "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138"))))))
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'configure)
- (delete 'check)
(add-after 'unpack 'patch-pileup-d
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "sambamba/pileup.d"
@@ -94,9 +92,8 @@
;; The current build compiles htslib statically into the
;; executable. On top of that, we need to patch the latest
;; version of htslib to have it working with Sambamba.
- (and (with-directory-excursion "htslib"
- (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
- "--strip-components=1")))
+ (and
+ (copy-recursively (assoc-ref inputs "htslib-src") "htslib")
(copy-recursively (assoc-ref inputs "dlang-undeaD-src") "undeaD")
(copy-recursively (assoc-ref inputs "biod-src") "BioD"))))
(replace
@@ -104,7 +101,16 @@
(lambda* (#:key inputs outputs make-flags #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(debug-out (assoc-ref outputs "debug")))
- (zero? (system* "make" "-f" "Makefile.guix" "guix"
+ (zero? (system* "make" "-f" "Makefile.guix" "guix" "-j" "8"
+ (string-append "LDC_LIB_PATH="
+ (assoc-ref inputs "ldc")
+ "/lib"))))))
+ (replace
+ 'check
+ (lambda* (#:key inputs outputs make-flags #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (debug-out (assoc-ref outputs "debug")))
+ (zero? (system* "make" "-f" "Makefile.guix" "check"
(string-append "LDC_LIB_PATH="
(assoc-ref inputs "ldc")
"/lib"))))))