diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 36 |
1 files changed, 20 insertions, 16 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index cfc5dae..3363ea2 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -35,6 +35,7 @@ #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages ruby) #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) #:use-module (gnu packages textutils) @@ -310,22 +311,19 @@ and freshness without requiring additional information from the user.") (license license:boost1.0)))) (define-public sambamba - (let ((commit "8fe1bda92423c7c97a52ef81c6871fd6569fd1da")) - ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84")) + (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84")) (package (name "sambamba") - (version (string-append "0.5.9-" commit)) + (version (string-append "0.5.9-1." (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference - ;; https://github.com/pjotrp/sambamba.git - (url "https://github.com/roelj/sambamba.git") + (url "https://github.com/pjotrp/sambamba.git") (commit commit))) - (file-name (string-append name "-" (string-take commit 7))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5" - "14gx0hhn039xhgkf5hbvffn9d0ld4zn9ka2zvvdi16k441sc8wjh")))) + "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5")))) (build-system gnu-build-system) ;; (inputs ;; `(("ldc" ,ldc) @@ -340,13 +338,16 @@ and freshness without requiring additional information from the user.") ("lz4" ,lz4) ("rdmd" ,rdmd) ("zlib" ,zlib) + ("perl" ,perl) ; Needed for htslib + ("ruby" ,ruby) ; Needed for htslib + ("python" ,python) ; Needed for htslib ("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") + (file-name "lz4-r131.tar.gz") (sha256 (base32 "1vfg305zvj50hwscad24wan9jar6nqj14gdk2hqyr7bb9mhh0kcx")))) ("htslib-src" @@ -354,7 +355,7 @@ and freshness without requiring additional information from the user.") (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")) + (file-name "htslib-0.2.0-rc10.tar.gz") (sha256 (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs")))) ("biod-src" @@ -363,15 +364,16 @@ and freshness without requiring additional information from the user.") (uri (git-reference (url "https://github.com/biod/BioD.git") (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b"))) + (file-name "biod-src") (sha256 - (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf")) - (file-name "biod-src"))))) + (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf")))))) (arguments `(#:tests? #f - #:make-flags (list "CC=gcc" "D_COMPILER=ldc2") + ;;#:make-flags #: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 @@ -384,14 +386,16 @@ and freshness without requiring additional information from the user.") (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"))))) + (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. (replace 'build - (lambda* (#:key inputs #:allow-other-keys) - (zero? (system* "make" "sambamba-ldmd2-64"))))))) + (lambda* (#:key inputs make-flags #:allow-other-keys) + (zero? (system* "make" "-f" "Makefile.guix" "CC=gcc" "D_COMPILER=ldc2"))))))) (home-page "https://github.com/lomereiter/sambamba") (synopsis "A tool for working with SAM and BAM files written in D.") (description |