diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 36 | ||||
| -rw-r--r-- | gn/packages/statistics.scm | 40 |
2 files changed, 61 insertions, 15 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index b7384ef..896767b 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -10,7 +10,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system perl) #:use-module (guix build-system python) - #:use-module (guix build-system ruby) + ;; #:use-module (guix build-system ruby) #:use-module (guix build-system r) #:use-module (guix build-system trivial) #:use-module (gnu packages) @@ -26,6 +26,7 @@ #:use-module (gnu packages graphviz) #:use-module (gnu packages java) #:use-module (gnu packages linux) + #:use-module (gnu packages ldc) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages ncurses) @@ -34,7 +35,6 @@ #: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) @@ -44,6 +44,7 @@ #:use-module (gnu packages zip) #:use-module (gnu packages bootstrap) #:use-module (gn packages python) + #:use-module (gn packages statistics) #:use-module (srfi srfi-1)) (define-public my-deploy @@ -379,6 +380,7 @@ association studies (GWAS).") ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-git) + ("pylmm-gn2" ,pylmm-gn2) ("plink2" ,plink-ng) ("nginx" ,nginx) ("python2-flask" ,python2-flask) @@ -457,17 +459,20 @@ internally during various build tasks.") (license license:boost1.0))) (define-public sambamba + (let ((commit "2ca5a2dba")) (package (name "sambamba") - (version "0.5.9") + (version (string-append "0.5.9-" commit)) (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/lomereiter/sambamba/archive/v" - version ".tar.gz")) - (file-name (string-append "sambamba-" version ".tar.gz")) - (sha256 - (base32 "152zbg4m10ikr7xgk20c0nwqwrqvydmpc73p2c1fqmbhpk0l0ws6")))) + (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)) + (sha256 + (base32 + "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5")))) (build-system gnu-build-system) (inputs `(("ldc" ,ldc) @@ -510,16 +515,17 @@ internally during various build tasks.") ;; 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"))))) + (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" "sambamba-ldmd2-64" make-flags))))))) + (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 @@ -528,7 +534,7 @@ 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 diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm index 065826e..2d83816 100644 --- a/gn/packages/statistics.scm +++ b/gn/packages/statistics.scm @@ -148,3 +148,43 @@ "R/lmmlite") (home-page "https://github.com/kbroman/") (license license:asl2.0))) + +(define-public pylmm-gn2 + (let ((commit "3c6d1cac8")) + (package + (name "pylmm-gn2") + (version (string-append "1.0-" commit )) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/pylmm.git") + (commit commit))) + (file-name (string-append name "-" commit)) + (sha256 + (base32 + "0wryaadb36i275p9d2i1kzflahvbl9kj5wlk8jlbvjij8gpqg964")))) + (build-system python-build-system) + (inputs `( + ("python2-setuptools" ,python2-setuptools) + ("python2-scipy" ,python2-scipy) + ("python2-numpy" ,python2-numpy) + )) + (arguments + `(#:python ,python-2 + #:tests? #f ; no 'setup.py test' + #:phases + (modify-phases %standard-phases + (add-before + 'build 'change-paths + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* "scripts/pylmm_redis" + (("/usr/bin/python") (which "python")) + (("\\$PACKAGEDIR") (string-append out "/lib/python2.7/site-packages"))) + )))))) + + (home-page "http://genenetwork.org/") + (synopsis "LMM resolver") + (description "Fast and lightweight linear mixed-model (LMM) solver +for use in genome-wide association studies (GWAS).") + (license license:agpl3+)))) |