From c5f83ff606c629a888d2f69aace076aff1417823 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 18 Feb 2016 10:47:35 +0100 Subject: Added rdmd. --- gn/packages/bioinformatics.scm | 44 ++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 42 insertions(+), 2 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 94e1839..e243db3 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -418,6 +418,45 @@ 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") @@ -443,6 +482,7 @@ association studies (GWAS).") ;;("phobos2-ldc" ,phobos2-ldc) ("lz4" ,lz4) ("gcc" ,gcc) + ("rdmd" ,rdmd) ("htslib-src" ,(origin (method url-fetch) @@ -451,7 +491,7 @@ 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 @@ -459,7 +499,7 @@ association studies (GWAS).") (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b"))) (sha256 (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf")) - (file-name "biod"))))) + (file-name "biod-src"))))) (arguments '(#:phases (modify-phases %standard-phases -- cgit v1.2.3 From 8d7549806cb58e14a9432211ebc83f944f8fee1a Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 18 Feb 2016 10:48:24 +0100 Subject: Fix for compilation. --- gn/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index e243db3..d840875 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -543,6 +543,7 @@ 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") -- cgit v1.2.3 From 5dbfda7d08ca718712a4c86bc3b7a6219843527a Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 18 Feb 2016 10:56:00 +0100 Subject: Fix migration inconsistencies. --- gn/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a2da94b..b7384ef 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -490,7 +490,7 @@ internally during various build tasks.") (file-name (string-append "htslib-0.2.0-rc10.tar.gz")) (sha256 (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs")))) - ("biod" + ("biod-src" ,(origin (method git-fetch) (uri (git-reference @@ -498,7 +498,7 @@ internally during various build tasks.") (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b"))) (sha256 (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf")) - (file-name "biod-src"))))) + (file-name "biod"))))) (arguments '(#:phases (modify-phases %standard-phases -- cgit v1.2.3