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-rw-r--r--gn/packages/genenetwork.scm436
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.")