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authorpjotrp2016-02-25 11:02:36 +0000
committerpjotrp2016-02-25 11:02:36 +0000
commite4f68f18630702686307977a159c1b23f755d576 (patch)
treeb4bf84726a4b5564e8c3557d59b4b9bb36701cb1 /gn/packages/bioinformatics.scm
parent8c2f2f7f65441a3b66bc2d9b145cd9065461d0cc (diff)
parent99eaee3ee57ab8ba6ef8d333778c472c0ab61cc6 (diff)
downloadguix-bioinformatics-e4f68f18630702686307977a159c1b23f755d576.tar.gz
Merge branch 'master' of github.com:genenetwork/guix-bioinformatics
Diffstat (limited to 'gn/packages/bioinformatics.scm')
-rw-r--r--gn/packages/bioinformatics.scm61
1 files changed, 23 insertions, 38 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 3363ea2..bf39935 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -325,39 +325,23 @@ and freshness without requiring additional information from the user.")
(base32
"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"))))
(build-system gnu-build-system)
- ;; (inputs
- ;; `(("ldc" ,ldc)
- ;; ;; These are currently included in "ldc".
- ;; ;;("druntime-ldc" ,druntime-ldc)
- ;; ;;("phobos2-ldc" ,phobos2-ldc)
- ;; ("lz4" ,lz4)))
(native-inputs
`(("ldc" ,ldc)
- ;;("druntime-ldc" ,druntime-ldc)
- ;;("phobos2-ldc" ,phobos2-ldc)
("lz4" ,lz4)
("rdmd" ,rdmd)
("zlib" ,zlib)
- ("perl" ,perl) ; Needed for htslib
- ("ruby" ,ruby) ; Needed for htslib
- ("python" ,python) ; Needed for htslib
+ ("perl" ,perl) ; Needed for htslib tests?
+ ("ruby" ,ruby) ; Needed for htslib tests?
+ ("python" ,python) ; Needed for htslib tests?
("gcc" ,gcc)
- ("lz4-src"
- ,(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/Cyan4973/lz4/archive/r131.tar.gz"))
- (file-name "lz4-r131.tar.gz")
- (sha256
- (base32 "1vfg305zvj50hwscad24wan9jar6nqj14gdk2hqyr7bb9mhh0kcx"))))
("htslib-src"
,(origin
(method url-fetch)
- (uri (string-append
- "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz"))
- (file-name "htslib-0.2.0-rc10.tar.gz")
+ (uri "https://github.com/samtools/htslib/archive/1.3.tar.gz")
+ (file-name "htslib-1.3.tar.gz")
(sha256
- (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
+ (base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9"))
+ (patches (list (search-patch "htslib-add-cram_to_bam.patch")))))
("biod-src"
,(origin
(method git-fetch)
@@ -369,33 +353,34 @@ and freshness without requiring additional information from the user.")
(base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))))))
(arguments
`(#:tests? #f
- ;;#:make-flags
+ #:make-flags (list "-f" "Makefile.guix")
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'check)
(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.
+ ;; 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")))
- (with-directory-excursion "lz4"
- (zero? (system* "tar" "xvf" (assoc-ref inputs "lz4-src")
- "--strip-components=1")))
- (and (zero? (system* "rm" "-r" "BioD"))
- (zero? (system* "ln" "--symbolic" "--no-target-directory"
- (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.
+ (zero? (system* "rm" "-r" "BioD"))
+ (zero? (system* "ln" "--symbolic" "--no-target-directory"
+ (assoc-ref inputs "biod-src") "BioD")))))
(replace
'build
(lambda* (#:key inputs make-flags #:allow-other-keys)
- (zero? (system* "make" "-f" "Makefile.guix" "CC=gcc" "D_COMPILER=ldc2")))))))
+ (zero? (system* "make" "-f" "Makefile.guix"
+ (string-append "LDC_LIB_PATH="
+ (assoc-ref inputs "ldc")
+ "/lib")))))
+ (replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "build/sambamba" bin)))))))
(home-page "https://github.com/lomereiter/sambamba")
(synopsis "A tool for working with SAM and BAM files written in D.")
(description