diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/genenetwork.scm | 436 |
1 files changed, 216 insertions, 220 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index dbd3abc..522e0c1 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -224,8 +224,7 @@ location of a putative QTL.") "1ldcvyk8y8w6f4ci04hzx85sknd5a3h424p5bfi4fz32sm2p7fja")))) (build-system python-build-system) (arguments - `( - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-tests @@ -292,62 +291,62 @@ location of a putative QTL.") (sha256 (base32 "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz")))) - (propagated-inputs `( ;; propagated for development purposes - ("python" ,python-2) ;; probably superfluous - ("coreutils" ,coreutils) - ("git" ,git) - ("vim" ,vim) - ("which" ,which) - ("grep" ,grep) - ("r" ,r) - ("r-ctl" ,r-ctl) - ("r-phewas" ,r-phewas) - ("r-qtl" ,r-qtl) - ("r-wgcna" ,r-wgcna) - ("redis" ,redis) - ("mysql" ,mysql) - ("gemma" ,gemma-gn2-git) - ("gemma-wrapper" ,gemma-wrapper) - ("genenetwork2-files-small" ,genenetwork2-files-small) - ("plink-ng-gn" ,plink-ng-gn) - ("pylmm-gn2" ,pylmm-gn2) - ("nginx" ,nginx) - ("python2-flask" ,python2-flask) - ("gunicorn" ,gunicorn) - ("python2-pillow" ,python2-pillow) - ("python2-cssselect" ,python2-cssselect) - ("python2-elasticsearch" ,python2-elasticsearch) - ("python2-htmlgen" ,python2-htmlgen) - ("python2-jinja2" ,python2-jinja2) - ("python2-sqlalchemy" ,python2-sqlalchemy) - ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) - ("python2-setuptools" ,python2-setuptools) - ("python2-scipy" ,python2-scipy) - ("python2-lxml" ,python2-lxml) - ("python2-mechanize" ,python2-mechanize) - ("python2-mysqlclient" ,python2-mysqlclient) - ("python2-numarray" ,python2-numarray) - ("python2-numpy" ,python2-numpy) - ("python2-pandas" ,python2-pandas) - ("python2-parallel" ,python2-parallel) - ("python2-parameterized" ,python2-parameterized) - ("python2-passlib" ,python2-passlib) - ("python2-redis" ,python2-redis) - ("python2-requests" ,python2-requests) - ("python2-requests" ,python2-requests) - ("python2-rpy2" ,python2-rpy2) - ("python2-scipy" ,python2-scipy) - ("python2-simplejson" ,python2-simplejson) - ("python2-pyyaml" ,python2-pyyaml) - ("python2-unittest2" ,python2-unittest2) - ("python2-xlsxwriter" ,python2-xlsxwriter) - ("python2-qtlreaper" ,python2-qtlreaper) - ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) - ("javascript-cytoscape" ,javascript-cytoscape) - ("javascript-panzoom" ,javascript-cytoscape-panzoom) - ("javascript-qtip" ,javascript-cytoscape-qtip) - - )) + (propagated-inputs + `(;; propagated for development purposes + ("python" ,python-2) ;; probably superfluous + ("coreutils" ,coreutils) + ("git" ,git) + ("vim" ,vim) + ("which" ,which) + ("grep" ,grep) + ("r" ,r) + ("r-ctl" ,r-ctl) + ("r-phewas" ,r-phewas) + ("r-qtl" ,r-qtl) + ("r-wgcna" ,r-wgcna) + ("redis" ,redis) + ("mysql" ,mysql) + ("gemma" ,gemma-gn2-git) + ("gemma-wrapper" ,gemma-wrapper) + ("genenetwork2-files-small" ,genenetwork2-files-small) + ("plink-ng-gn" ,plink-ng-gn) + ("pylmm-gn2" ,pylmm-gn2) + ("nginx" ,nginx) + ("python2-flask" ,python2-flask) + ("gunicorn" ,gunicorn) + ("python2-pillow" ,python2-pillow) + ("python2-cssselect" ,python2-cssselect) + ("python2-elasticsearch" ,python2-elasticsearch) + ("python2-htmlgen" ,python2-htmlgen) + ("python2-jinja2" ,python2-jinja2) + ("python2-sqlalchemy" ,python2-sqlalchemy) + ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) + ("python2-setuptools" ,python2-setuptools) + ("python2-scipy" ,python2-scipy) + ("python2-lxml" ,python2-lxml) + ("python2-mechanize" ,python2-mechanize) + ("python2-mysqlclient" ,python2-mysqlclient) + ("python2-numarray" ,python2-numarray) + ("python2-numpy" ,python2-numpy) + ("python2-pandas" ,python2-pandas) + ("python2-parallel" ,python2-parallel) + ("python2-parameterized" ,python2-parameterized) + ("python2-passlib" ,python2-passlib) + ("python2-redis" ,python2-redis) + ("python2-requests" ,python2-requests) + ("python2-requests" ,python2-requests) + ("python2-rpy2" ,python2-rpy2) + ("python2-scipy" ,python2-scipy) + ("python2-simplejson" ,python2-simplejson) + ("python2-pyyaml" ,python2-pyyaml) + ("python2-unittest2" ,python2-unittest2) + ("python2-xlsxwriter" ,python2-xlsxwriter) + ("python2-qtlreaper" ,python2-qtlreaper) + ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) + ("javascript-cytoscape" ,javascript-cytoscape) + ("javascript-panzoom" ,javascript-cytoscape-panzoom) + ("javascript-qtip" ,javascript-cytoscape-qtip) + )) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -355,37 +354,38 @@ location of a putative QTL.") (modify-phases %standard-phases (delete 'reset-gzip-timestamps) (add-after 'unpack 'fix-paths-scripts - (lambda* _ + (lambda _ (substitute* "bin/genenetwork2" - (("/usr/bin/env") (which "env")) - (("python ") (string-append (which "python2") " ")) - (("readlink") (which "readlink")) - (("dirname") (which "dirname")) - (("basename") (which "basename")) - (("cat") (which "cat")) - (("echo") (which "echo")) - (("redis-server") (which "redis-server")) - (("git") (which "git")) - (("grep") (which "grep")) - (("rm") (which "rm")) - (("which") (which "which")) ; three wiches in a row! - )#t)) + (("/usr/bin/env") (which "env")) + (("python ") (string-append (which "python2") " ")) + (("readlink") (which "readlink")) + (("dirname") (which "dirname")) + (("basename") (which "basename")) + (("cat") (which "cat")) + (("echo") (which "echo")) + (("redis-server") (which "redis-server")) + (("git") (which "git")) + (("grep") (which "grep")) + (("rm") (which "rm")) + (("which") (which "which")) ; three wiches in a row! + ) + #t)) (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 "plink-ng-gn") "/bin/plink2")) - (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) - ) + (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 "plink-ng-gn") "/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" )) - ) - )))) + (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") @@ -418,20 +418,17 @@ location of a putative QTL.") (let* ((out (assoc-ref %outputs "out")) (name "gn2_data_s") (tarfn (string-append name ".tar")) - (targetdir (string-append out "/share/genenetwork2/")) - ) + (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")) - ) + (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) - )))))) + (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.") @@ -458,8 +455,7 @@ location of a putative QTL.") #:builder (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source")) - (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")) - ) + (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip"))) (and (mkdir "db") (zero? (system* unzip source "-d" "db")) (chdir "db")))))) @@ -475,15 +471,16 @@ location of a putative QTL.") (package (name "python-reaper") (version (string-append "0.0.1-" - (string-take commit 7))) + (string-take commit 7))) (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/fredmanglis/reaper.git") - (commit commit))) - (sha256 - (base32 - "1rq2qn0vrqd8k676yy8drm0zxzkj065ywhxjl0j1n2r25zifay7r")))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/fredmanglis/reaper.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rq2qn0vrqd8k676yy8drm0zxzkj065ywhxjl0j1n2r25zifay7r")))) (build-system python-build-system) (arguments `(#:tests? #f)) @@ -495,133 +492,132 @@ written in C") (define-public genenetwork3 (let (;; (commit "1538ffd33af19e6ac922b4ee85fe701408968dfd") - (commit "5bff4f49dffb4ac982d36cd0d39e0a9ec6bc66e9")) + (commit "5bff4f49dffb4ac982d36cd0d39e0a9ec6bc66e9")) (package (name "genenetwork3") (version (string-append "2.10rc5-" (string-take commit 7) )) (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/fredmanglis/genenetwork2.git") - ;; (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git") - ;; (url "https://github.com/genenetwork/genenetwork2_diet.git") - (commit commit))) - (file-name (string-append name "-" version)) - (sha256 - (base32 - "0klgjra2qisfzs8mk0s8vzdr190l4n56xcm66dk0asqs7zswi8di" - ;; "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz" - )))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/fredmanglis/genenetwork2.git") + ;; (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git") + ;; (url "https://github.com/genenetwork/genenetwork2_diet.git") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "0klgjra2qisfzs8mk0s8vzdr190l4n56xcm66dk0asqs7zswi8di" + ;; "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz" + )))) (propagated-inputs ;; propagated for development purposes - `( ;; Agnostic to Python - ("r" ,r) - ("git" ,git) - ("vim" ,vim) - ("grep" ,grep) - ("which" ,which) - ("r-ctl" ,r-ctl) - ("r-qtl" ,r-qtl) - ("redis" ,redis) - ("mysql" ,mysql) - ("nginx" ,nginx) - ("r-wgcna" ,r-wgcna) - ;; ("r-phewas" ,r-phewas) - ("coreutils" ,coreutils) - ("gemma" ,gemma-gn2-git) - ("plink-ng-gn" ,plink-ng-gn) - ("python-lxml" ,python-lxml) ;; used for the tests - ("gemma-wrapper" ,gemma-wrapper) - ("python-unittest" ,python-unittest2) ;; used for the tests - ("python-parameterized" ,python-parameterized) ;; used for the tests - ("genenetwork2-files-small" ,genenetwork2-files-small) - ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) - ("javascript-cytoscape" ,javascript-cytoscape) - ("javascript-panzoom" ,javascript-cytoscape-panzoom) - ("javascript-qtip" ,javascript-cytoscape-qtip) - - ;; With Python3 support - ("gunicorn" ,gunicorn) - ("python-rpy2" ,python-rpy2) - ("python-flask" ,python-flask) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-redis" ,python-redis) - ("python-scipy" ,python-scipy) - ("python-pillow" ,python-pillow) - ("python-reaper" ,python-reaper) - ("python-pyyaml" ,python-pyyaml) - ("python-jinja2" ,python-jinja2) - ("python-pandas" ,python-pandas) - ("python-htmlgen" ,python-htmlgen) - ("python-passlib" ,python-passlib) - ("python-wrapper" ,python-wrapper) - ("python-requests" ,python-requests) - ("python-cssselect" ,python-cssselect) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-setuptools" ,python-setuptools) - ("python-simplejson" ,python-simplejson) - ("python-xlsxwriter" ,python-xlsxwriter) - ("python-mysqlclient" ,python-mysqlclient) - ("python-elasticsearch" ,python-elasticsearch) - ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) + `(;; Agnostic to Python + ("r" ,r) + ("git" ,git) + ("vim" ,vim) + ("grep" ,grep) + ("which" ,which) + ("r-ctl" ,r-ctl) + ("r-qtl" ,r-qtl) + ("redis" ,redis) + ("mysql" ,mysql) + ("nginx" ,nginx) + ("r-wgcna" ,r-wgcna) + ;; ("r-phewas" ,r-phewas) + ("coreutils" ,coreutils) + ("gemma" ,gemma-gn2-git) + ("plink-ng-gn" ,plink-ng-gn) + ("python-lxml" ,python-lxml) ;; used for the tests + ("gemma-wrapper" ,gemma-wrapper) + ("python-unittest" ,python-unittest2) ;; used for the tests + ("python-parameterized" ,python-parameterized) ;; used for the tests + ("genenetwork2-files-small" ,genenetwork2-files-small) + ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) + ("javascript-cytoscape" ,javascript-cytoscape) + ("javascript-panzoom" ,javascript-cytoscape-panzoom) + ("javascript-qtip" ,javascript-cytoscape-qtip) + ;; With Python3 support + ("gunicorn" ,gunicorn) + ("python-rpy2" ,python-rpy2) + ("python-flask" ,python-flask) + ("python-scipy" ,python-scipy) + ("python-numpy" ,python-numpy) + ("python-redis" ,python-redis) + ("python-scipy" ,python-scipy) + ("python-pillow" ,python-pillow) + ("python-reaper" ,python-reaper) + ("python-pyyaml" ,python-pyyaml) + ("python-jinja2" ,python-jinja2) + ("python-pandas" ,python-pandas) + ("python-htmlgen" ,python-htmlgen) + ("python-passlib" ,python-passlib) + ("python-wrapper" ,python-wrapper) + ("python-requests" ,python-requests) + ("python-cssselect" ,python-cssselect) + ("python-sqlalchemy" ,python-sqlalchemy) + ("python-setuptools" ,python-setuptools) + ("python-simplejson" ,python-simplejson) + ("python-xlsxwriter" ,python-xlsxwriter) + ("python-mysqlclient" ,python-mysqlclient) + ("python-elasticsearch" ,python-elasticsearch) + ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) - ;; Without Python3 support - ;; ("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program - ;; ("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program - ;; ("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT) - ;; ("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions - )) + ;; Without Python3 support + ;; ("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program + ;; ("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program + ;; ("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT) + ;; ("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions + )) (build-system python-build-system) (arguments `(#:phases - (modify-phases - %standard-phases - (delete 'reset-gzip-timestamps) - (add-after - 'unpack 'fix-paths-scripts - (lambda* _ - (substitute* "bin/genenetwork2" - (("/usr/bin/env") (which "env")) - (("python ") (string-append (which "python") " ")) - (("readlink") (which "readlink")) - (("dirname") (which "dirname")) - (("basename") (which "basename")) - (("cat") (which "cat")) - (("echo") (which "echo")) - (("redis-server") (which "redis-server")) - (("git") (which "git")) - (("grep") (which "grep")) - (("rm") (which "rm")) - (("which") (which "which"))) - #t)) - (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 "plink-ng-gn") "/bin/plink2")) - (gemmacmd - (string-append (assoc-ref inputs "gemma") "/bin/gemma"))) + (modify-phases + %standard-phases + (delete 'reset-gzip-timestamps) + (add-after + 'unpack 'fix-paths-scripts + (lambda _ + (substitute* "bin/genenetwork2" + (("/usr/bin/env") (which "env")) + (("python ") (string-append (which "python") " ")) + (("readlink") (which "readlink")) + (("dirname") (which "dirname")) + (("basename") (which "basename")) + (("cat") (which "cat")) + (("echo") (which "echo")) + (("redis-server") (which "redis-server")) + (("git") (which "git")) + (("grep") (which "grep")) + (("rm") (which "rm")) + (("which") (which "which"))) + #t)) + (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 "plink-ng-gn") "/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' + (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") (description "Genenetwork installation sumo.") |