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authorRoel Janssen2016-02-17 11:15:14 +0100
committerRoel Janssen2016-02-17 11:15:14 +0100
commitb3145ffd290341ec726c907ce329219caa3c99a7 (patch)
treeb805cacc6d749c545fa82ec74da3d04b80b023e7 /gn/packages
parent60a90630fce9249b76be6674bd98e1a36dcd319c (diff)
downloadguix-bioinformatics-b3145ffd290341ec726c907ce329219caa3c99a7.tar.gz
Some more progress on Sambamba package.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm52
1 files changed, 30 insertions, 22 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index bb5c0fd..628e656 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -426,9 +426,10 @@ association studies (GWAS).")
(method url-fetch)
(uri (string-append
"https://github.com/lomereiter/sambamba/archive/v"
- version "tar.gz"))
+ version ".tar.gz"))
+ (file-name (string-append "sambamba-" version ".tar.gz"))
(sha256
- (base32 ""))))
+ (base32 "152zbg4m10ikr7xgk20c0nwqwrqvydmpc73p2c1fqmbhpk0l0ws6"))))
(build-system gnu-build-system)
(inputs
`(("ldc" ,ldc)
@@ -443,15 +444,13 @@ association studies (GWAS).")
("lz4" ,lz4)
("gcc" ,gcc)
("htslib-src"
- (let ((version "0.2.0-rc10"))
- ,(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/lomereiter/htslib/archive/"
- version ".tar.gz"))
- (file-name (string-append "htslib-" version ".tar.gz"))
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz"))
+ (file-name (string-append "htslib-0.2.0-rc10.tar.gz"))
(sha256
- (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs")))))
+ (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
("biod-src"
,(origin
(method git-fetch)
@@ -462,17 +461,26 @@ association studies (GWAS).")
(base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))
(file-name "biod")))))
(arguments
- `(#:make-flags "sambamba-ldmd2-64" ; This target is used for releases.
- #:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (add-after 'unpack 'unpack-htslib-sources
- (lambda* (#:key inputs #:allow-other-keys)
- (with-directory-excursion "htslib"
- (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
- "--strip-components=1")))))
- (add-after 'unpack 'move-biod-sources
- '()))) ; TODO: Figure out how to move or symlink the BioD sources to the right place.
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'unpack-htslib-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; Unfortunately, the current build compiles htslib statically
+ ;; into the executable. Instead of patching the build files
+ ;; for Guix, this should be resolved on Sambamba upstream. For
+ ;; now, just extract the source code to the desired directory.
+ (and (with-directory-excursion "htslib"
+ (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
+ "--strip-components=1")))
+ (zero? (system* "cp" "-R" (assoc-ref inputs "biod-src") "BioD")))))
+ ;; Building a production-quality executable is done with a
+ ;; non-default make target. Adding it with #:make-flags breaks
+ ;; building tests. Therefore, the default make got replaced by this.
+ (replace
+ 'build
+ (lambda* (#:key (make-flags '()) #:allow-other-keys)
+ (zero? (system* "make" "sambamba-ldmd2-64" make-flags)))))))
(home-page "https://github.com/lomereiter/sambamba")
(synopsis "A tool for working with SAM and BAM files written in D.")
(description
@@ -481,4 +489,4 @@ library), written in the D programming language, for working with SAM
and BAM files. Current parallelised functionality is an important
subset of samtools functionality, including view, index, sort,
markdup, and depth.")
- (license license:gpl2+))))
+ (license license:gpl2+)))