diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 43 |
1 files changed, 38 insertions, 5 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 2f755a6..aec305b 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -141,23 +141,24 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "9e9475053")) + (let ((commit "8c9de7e5a2016f1e5b7397be1a8e84396e3a25c5")) (package (name "genenetwork2") - (version (string-append "2.0-" commit )) + (version (string-append "2.0-" (string-take commit 7) )) (source (origin (method git-fetch) (uri (git-reference ;; (url "https://github.com/genenetwork/genenetwork2.git") (url "https://github.com/pjotrp/genenetwork2.git") (commit commit))) - (file-name (string-append name "-" commit)) + (file-name (string-append name "-" (string-take commit 7))) (sha256 (base32 - "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd")))) + "1kgigzs4rs6zgbqbnm40rcljzz9prlwv7n2n9an57jk58bjgf6v8")))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) + ("r-wgcna" ,r-wgcna) ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-git) @@ -178,7 +179,7 @@ ("python2-pandas" ,python2-pandas) ("python2-parallel" ,python2-parallel) ("python2-passlib" ,python2-passlib) - ("python2-piddle" ,python2-piddle) + ("python2-piddle-gn" ,python2-piddle-gn) ("python2-redis" ,python2-redis) ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) @@ -202,3 +203,35 @@ ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x + +(define-public genenetwork2-database-small + (let ((md5 "93e745e9c")) + (package + (name "genenetwork2-database-small") + (version "1.0") + (source + (origin + (method url-fetch) + (uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip") + (file-name (string-append name "-" md5)) + (sha256 + (base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x")))) + (build-system trivial-build-system) + (native-inputs `(("unzip" ,unzip) + ("source" ,source))) + + (arguments + `(#:modules ((guix build utils)) + #:builder (begin + (use-modules (guix build utils)) + (let ((source (assoc-ref %build-inputs "source")) + (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")) + ) + (and (mkdir "db") + (zero? (system* unzip source "-d" "db")) + (chdir "db")))))) + (home-page "http://genenetwork.org/") + (synopsis "Small database to run on genenetwork") + (description "Genenetwork installation + database.") + (license license:agpl3+)))) + |