diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 45 |
1 files changed, 43 insertions, 2 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 0c4436c..a2da94b 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -417,6 +417,45 @@ association studies (GWAS).") (description "Genenetwork installation sumo.") (license license:agpl3+)))) +(define-public rdmd + (package + (name "rdmd") + (version "20160217") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/D-Programming-Language/tools.git") + (commit "4dba6877c481c1a911a7d50714da8fbd80022f0e"))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45")))) + (build-system gnu-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'check) + (replace + 'build + (lambda* _ + (zero? (system* "ldc2" "rdmd.d")))) + (replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (mkdir-p bin) + (copy-file "rdmd" (string-append bin "/rdmd")))))))) + (native-inputs + `(("gcc" ,gcc) + ("ldc" ,ldc))) + (home-page "https://github.com/D-Programming-Language/tools/") + (synopsis "Extra tools for building D programs") + (description + "This repository hosts various tools redistributed with DMD or used +internally during various build tasks.") + (license license:boost1.0))) + (define-public sambamba (package (name "sambamba") @@ -442,6 +481,7 @@ association studies (GWAS).") ;;("phobos2-ldc" ,phobos2-ldc) ("lz4" ,lz4) ("gcc" ,gcc) + ("rdmd" ,rdmd) ("htslib-src" ,(origin (method url-fetch) @@ -450,7 +490,7 @@ association studies (GWAS).") (file-name (string-append "htslib-0.2.0-rc10.tar.gz")) (sha256 (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs")))) - ("biod-src" + ("biod" ,(origin (method git-fetch) (uri (git-reference @@ -458,7 +498,7 @@ association studies (GWAS).") (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b"))) (sha256 (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf")) - (file-name "biod"))))) + (file-name "biod-src"))))) (arguments '(#:phases (modify-phases %standard-phases @@ -502,6 +542,7 @@ markdup, and depth.") version ".tar.gz")) (sha256 (base32 "")))) + (build-system gnu-build-system) (home-page "http://broadinstitute.github.io/picard/") (synopsis "A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats") |