diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 78 |
1 files changed, 70 insertions, 8 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 1b52a5d..79ad3fe 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -87,7 +87,6 @@ (description #f) (license #f))) - (define-public genenetwork1 (let ((commit "d622c803b")) (package @@ -141,26 +140,29 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "9e9475053")) + (let ((commit "a8fcff44d3bd768d02e7ed0c80b84d2516bdad2a")) (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") + (url "https://github.com/genenetwork/genenetwork2_diet.git") (commit commit))) - (file-name (string-append name "-" commit)) + (file-name (string-append name "-" (string-take commit 7))) (sha256 (base32 - "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd")))) + "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618")))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) + ("r-wgcna" ,r-wgcna) + ("r-qtl" ,r-qtl) ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-git) + ("genenetwork2-files-small" ,genenetwork2-files-small) ("pylmm-gn2" ,pylmm-gn2) ("plink2" ,plink-ng) ("nginx" ,nginx) @@ -178,8 +180,9 @@ ("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-pil" ,python2-pil) ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) ("python2-scipy" ,python2-scipy) @@ -189,11 +192,28 @@ ;; python-yolk is not needed ("plink" ,plink) ("qtlreaper" ,qtlreaper) - ("r-qtl" ,r-qtl) )) (build-system python-build-system) (arguments `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (add-before 'install 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (let* ( + (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" )) + (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) + (plink2cmd (string-append (assoc-ref inputs "plink2") "/bin/plink2")) + (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) + ) + + (substitute* '("etc/default_settings.py") + (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) + (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) + (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) + (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) + ) + )))) #:tests? #f)) ; no 'setup.py test' (home-page "http://genenetwork.org/") (synopsis "Full genenetwork services") @@ -203,6 +223,48 @@ ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x +(define-public genenetwork2-files-small1 + (let ((pfff "xx")) + (package + (name "genenetwork2-files-small") + (version "1.0") + (source + (origin + (method url-fetch) + (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") + (file-name (string-append name "-" pfff)) + (sha256 + (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) + (build-system trivial-build-system) + (native-inputs `(("lz4" ,lz4) + ("tar" ,tar) + ("source" ,source))) + + (arguments + `(#:modules ((guix build utils)) + #:builder + (let* ((out (assoc-ref %outputs "out")) + (name "gn2_data_s") + (tarfn (string-append name ".tar")) + (targetdir (string-append out "/share/genenetwork2/")) + ) + (begin + (use-modules (guix build utils)) + (let ((source (assoc-ref %build-inputs "source")) + (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4")) + (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")) + ) + (and + (zero? (system* lz4unpack source "-d" tarfn)) + (zero? (system* tar "xf" tarfn)) + (mkdir-p targetdir) + (copy-recursively name targetdir) + )))))) + (home-page "http://genenetwork.org/") + (synopsis "Small file archive to run on genenetwork") + (description "Genenetwork genotype and mapping files.") + (license license:agpl3+)))) + (define-public genenetwork2-database-small (let ((md5 "93e745e9c")) (package |