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authorRoel Janssen2016-02-23 10:38:55 +0100
committerRoel Janssen2016-02-23 10:38:55 +0100
commit6c2c0499e817badf1cc41822dfdf813e065a34a3 (patch)
tree5a4a8d3e7b0deb5727363c9999d39485c513d37c /gn
parent9aea3e8744c11a2f108165260aa8a59a1f346cdc (diff)
downloadguix-bioinformatics-6c2c0499e817badf1cc41822dfdf813e065a34a3.tar.gz
Using my own fork of the Sambamba repository.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm155
1 files changed, 85 insertions, 70 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 098411e..cfc5dae 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -310,82 +310,97 @@ and freshness without requiring additional information from the user.")
(license license:boost1.0))))
(define-public sambamba
- (let ((commit "2ca5a2dba"))
- (package
- (name "sambamba")
- (version (string-append "0.5.9-" commit))
- (source (origin
+ (let ((commit "8fe1bda92423c7c97a52ef81c6871fd6569fd1da"))
+ ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
+ (package
+ (name "sambamba")
+ (version (string-append "0.5.9-" commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ ;; https://github.com/pjotrp/sambamba.git
+ (url "https://github.com/roelj/sambamba.git")
+ (commit commit)))
+ (file-name (string-append name "-" (string-take commit 7)))
+ (sha256
+ (base32
+ ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"
+ "14gx0hhn039xhgkf5hbvffn9d0ld4zn9ka2zvvdi16k441sc8wjh"))))
+ (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)
+ ("gcc" ,gcc)
+ ("lz4-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/Cyan4973/lz4/archive/r131.tar.gz"))
+ (file-name "lz4-131.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 (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
+ ("biod-src"
+ ,(origin
(method git-fetch)
- (uri (git-reference
- ;; https://github.com/pjotrp/sambamba.git
- (url "https://github.com/pjotrp/sambamba.git")
- (commit commit)))
- (file-name (string-append name "-" commit))
+ (uri (git-reference
+ (url "https://github.com/biod/BioD.git")
+ (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
(sha256
- (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)
- ("gcc" ,gcc)
- ("rdmd" ,rdmd)
- ("htslib-src"
- ,(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"))))
- ("biod-src"
- ,(origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/biod/BioD.git")
- (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
- (sha256
- (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))
- (file-name "biod")))))
- (arguments
- '(#: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" "-f" "Makefile.guix" make-flags)))))))
- (home-page "https://github.com/lomereiter/sambamba")
- (synopsis "A tool for working with SAM and BAM files written in D.")
- (description
- "Sambamba is a high performance modern robust and fast tool (and
+ (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))
+ (file-name "biod-src")))))
+ (arguments
+ `(#:tests? #f
+ #:make-flags (list "CC=gcc" "D_COMPILER=ldc2")
+ #: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")))
+ (with-directory-excursion "lz4"
+ (zero? (system* "tar" "xvf" (assoc-ref inputs "lz4-src")
+ "--strip-components=1")))
+ (zero? (system* "ln" "--symbolic" (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 inputs #:allow-other-keys)
+ (zero? (system* "make" "sambamba-ldmd2-64")))))))
+ (home-page "https://github.com/lomereiter/sambamba")
+ (synopsis "A tool for working with SAM and BAM files written in D.")
+ (description
+ "Sambamba is a high performance modern robust and fast tool (and
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+))))
(define-public picard
(package