From 96706fd977738f6ca3eb981591ced6c7db833887 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 22 Feb 2016 08:50:37 +0000 Subject: Moving genenetwork stuff into its own module --- gn/packages/genenetwork.scm | 200 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 200 insertions(+) create mode 100644 gn/packages/genenetwork.scm (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm new file mode 100644 index 0000000..b2e7f00 --- /dev/null +++ b/gn/packages/genenetwork.scm @@ -0,0 +1,200 @@ +;; Bioinformatics module + +(define-module (gn packages genenetwork) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix utils) + #:use-module (guix download) + #:use-module (guix git-download) + #:use-module (guix build-system gnu) + #: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 r) + #:use-module (guix build-system trivial) + #:use-module (gnu packages) + #:use-module (gnu packages algebra) + #:use-module (gnu packages base) + #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages boost) + #:use-module (gnu packages compression) + #:use-module (gnu packages databases) + #:use-module (gnu packages cpio) + #:use-module (gnu packages file) + #:use-module (gnu packages gcc) + #: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) + #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages popt) + #:use-module (gnu packages protobuf) + #:use-module (gnu packages python) + #:use-module (gnu packages statistics) + #:use-module (gnu packages tbb) + #:use-module (gnu packages textutils) + #:use-module (gnu packages vim) + #:use-module (gnu packages web) + #:use-module (gnu packages xml) + #: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 + (package + (name "my-deploy") + (version "0.0.1") + (source #f) + (build-system trivial-build-system) + (arguments + `(#:guile ,%bootstrap-guile + #:modules ((guix build utils)) + #:builder + (let* ((out (assoc-ref %outputs "out")) + (bash (assoc-ref %build-inputs "bash")) + (foo (string-append out "/foo"))) + (begin + (use-modules (guix build utils)) + (mkdir out) + (call-with-output-file foo + (lambda (p) + (format p + "#!~a~%echo \"${GUIX_FOO} ${GUIX_BAR}\"~%" + bash))) + (chmod foo #o777) + ;; wrap-program uses `which' to find bash for the wrapper + ;; shebang, but it can't know about the bootstrap bash in + ;; the store, since it's not named "bash". Help it out a + ;; bit by providing a symlink it this package's output. + (symlink bash (string-append out "/bash")) + (setenv "PATH" out) + (wrap-program foo `("GUIX_FOO" prefix ("hello"))) + (wrap-program foo `("GUIX_BAR" prefix ("world"))) + #t)))) + (inputs `(("bash" ,(search-bootstrap-binary "bash" + (%current-system))))) + + (home-page #f) + (synopsis #f) + (description #f) + (license #f))) + + +(define-public genenetwork1 + (let ((commit "d622c803b")) + (package + (name "genenetwork1") + (version (string-append "1.0-" commit )) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/genenetwork.git") + ;; (url "https://github.com/pjotrp/genenetwork.git") + (commit commit))) + (file-name (string-append name "-" commit)) + (sha256 + (base32 + "14fzfcm4vl20mlhxjslfa01i1nmxpk8lbxmfvpq6dyfc22ir62py")))) + (propagated-inputs `( + ("python" ,python-2) ;; probably superfluous + ("r" ,r) + )) + (inputs `( + ;; http://spring211.uthsc.edu/gn/thirdparty.tbz + ;; graphviz-2.22.2 htmlgen json numarray-1.5.2 piddle PIL pp-1.5.7 pyx pyXLWriter svg + ("mysql" ,mysql) + ("nginx" ,nginx) + ("graphviz" ,graphviz) + ; ("python2-jinja2" ,python2-jinja2) + ; ("python2-sqlalchemy" ,python2-sqlalchemy) + ; ("python2-setuptools" ,python2-setuptools) + ; ("python2-scipy" ,python2-scipy) + ;; looks like python-numarray is not needed + ; ("python2-numpy" ,python2-numpy) + ; ("python2-pandas" ,python2-pandas) + ; ("python2-passlib" ,python2-passlib) + ; ("python2-redis" ,python2-redis) + ; ("python2-requests" ,python2-requests) + ; ("python2-simplejson" ,python2-simplejson) + ; ("python2-pyyaml" ,python2-pyyaml) + ;; python-yolk is not needed + ("python2-pil" ,python2-pil) + ("python2-numarray" ,python2-numarray) + ("plink" ,plink) ;; gn1 + ; ("r-qtl" ,r-qtl) + )) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:tests? #f)) ; no 'setup.py test' + (home-page "http://genenetwork.org/") + (synopsis "Full genenetwork services") + (description "Genenetwork installation sumo.") + (license license:agpl3+)))) + +(define-public genenetwork2 + (let ((commit "9e9475053")) + (package + (name "genenetwork2") + (version (string-append "2.0-" commit )) + (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)) + (sha256 + (base32 + "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd")))) + (propagated-inputs `( ;; propagated for development purposes + ("python" ,python-2) ;; probably superfluous + ("r" ,r) + ("redis" ,redis) + ("mysql" ,mysql) + ("gemma" ,gemma-git) + ("pylmm-gn2" ,pylmm-gn2) + ("plink2" ,plink-ng) + ("nginx" ,nginx) + ("python2-flask" ,python2-flask) + ("python2-htmlgen-gn" ,python2-htmlgen-gn) + ("python2-jinja2" ,python2-jinja2) + ("python2-sqlalchemy" ,python2-sqlalchemy) + ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) + ("python2-setuptools" ,python2-setuptools) + ("python2-scipy" ,python2-scipy) + ;; looks like python-numarray is not needed + ("python2-mysqlclient" ,python2-mysqlclient) + ("python2-numarray" ,python2-numarray) + ("python2-numpy" ,python2-numpy) + ("python2-pandas" ,python2-pandas) + ("python2-parallel" ,python2-parallel) + ("python2-passlib" ,python2-passlib) + ("python2-piddle" ,python2-piddle) + ("python2-redis" ,python2-redis) + ("python2-requests" ,python2-requests) + ("python2-rpy2" ,python2-rpy2) + ("python2-scipy" ,python2-scipy) + ("python2-simplejson" ,python2-simplejson) + ("python2-pyyaml" ,python2-pyyaml) + ("python2-xlsxwriter" ,python2-xlsxwriter) + ;; python-yolk is not needed + ("plink" ,plink) + ("qtlreaper" ,qtlreaper) + ("r-qtl" ,r-qtl) + )) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:tests? #f)) ; no 'setup.py test' + (home-page "http://genenetwork.org/") + (synopsis "Full genenetwork services") + (description "Genenetwork installation sumo.") + (license license:agpl3+)))) -- cgit v1.2.3 From 520b002306561ed81599ddfed18f9662b99d5846 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 22 Feb 2016 08:56:47 +0000 Subject: Missing module reference --- gn/packages/genenetwork.scm | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index b2e7f00..2f755a6 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -43,6 +43,7 @@ #:use-module (gnu packages xml) #:use-module (gnu packages zip) #:use-module (gnu packages bootstrap) + #:use-module (gn packages bioinformatics) #:use-module (gn packages python) #:use-module (gn packages statistics) #:use-module (srfi srfi-1)) @@ -198,3 +199,6 @@ (synopsis "Full genenetwork services") (description "Genenetwork installation sumo.") (license license:agpl3+)))) + +;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip +;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x -- cgit v1.2.3 From 0660647c4bf43114a087337fa11131313afc7b9a Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 25 Feb 2016 09:29:13 +0000 Subject: Small GN database --- gn/packages/genenetwork.scm | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 2f755a6..dea6eae 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -178,7 +178,7 @@ ("python2-pandas" ,python2-pandas) ("python2-parallel" ,python2-parallel) ("python2-passlib" ,python2-passlib) - ("python2-piddle" ,python2-piddle) + ("python2-piddle-gn2" ,python2-piddle-gn2) ("python2-redis" ,python2-redis) ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) @@ -202,3 +202,35 @@ ;; ./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+)))) + -- cgit v1.2.3 From 8c2f2f7f65441a3b66bc2d9b145cd9065461d0cc Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 25 Feb 2016 11:02:28 +0000 Subject: Fix python-piddle --- gn/packages/genenetwork.scm | 2 +- gn/packages/python.scm | 17 +++++++++-------- 2 files changed, 10 insertions(+), 9 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index dea6eae..b77ccb4 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -178,7 +178,7 @@ ("python2-pandas" ,python2-pandas) ("python2-parallel" ,python2-parallel) ("python2-passlib" ,python2-passlib) - ("python2-piddle-gn2" ,python2-piddle-gn2) + ("python2-piddle-gn" ,python2-piddle-gn) ("python2-redis" ,python2-redis) ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 61d186b..7781521 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -426,19 +426,20 @@ capabilities to the Python interpreter.") (method url-fetch) (uri (string-append "http://files.genenetwork.org/software/contrib/piddle-" -version "-gn.tgz")) +version ".tgz")) (sha256 (base32 - "0yl6frmhy94cmwzdks7ndc7nzh1ml2a4ch86gz2l7wcwpxjhwgmk")))) + "05gjnn31v7p0kh58qixrpcizcxqf3b7zv4a5kk8nsmqwgxh0c6gq")))) (build-system python-build-system) - ;; (native-inputs - ;; `(("python-setuptools" ,python-setuptools))) + (native-inputs + `(("python2-setuptools" ,python2-setuptools))) (arguments - `(#:python ,python-2 - #:tests? #f - )) ; no 'setup.py test' really! - (home-page "http://www.numpy.org/") + `( + #:python ,python-2 + #:tests? #f ; no 'setup.py test' really! + )) + (home-page #f) (synopsis "Canvas drawing library for python2 (old!)") (description #f) (license #f))) -- cgit v1.2.3 From f82b7c5b7ef5bdb9761e48761f683d62d3a05c48 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 28 Feb 2016 17:42:06 +0000 Subject: r-wgcna deps --- gn/packages/bioinformatics.scm | 24 +++++++++++++++++++++++- gn/packages/genenetwork.scm | 1 + 2 files changed, 24 insertions(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 92be2b4..b503e22 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -48,6 +48,28 @@ #:use-module (gn packages statistics) #:use-module (srfi srfi-1)) + +(define-public r-biocpreprocesscore + (package + (name "r-biocpreprocesscore") + (version "1.32.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "preprocessCore" version)) + (sha256 + (base32 + "07isghjkqm91rg37l1fzpjrbq36b7w4pbsi95wwh6a8qq7r69z1n")))) + (properties + `((upstream-name . "BiocpreprocessCore") + (r-repository . bioconductor))) + (build-system r-build-system) + (home-page "http://bioconductor.org/packages/preprocessCore") + (synopsis "Preprocess functions for Bioconductor") + (description + "A library of core preprocessing routines.") + (license license:lgpl2.0+))) + + (define-public r-wgcna (let ((commit "425bc170cc0873ddbd414675ac40f6d4d724c7cb")) (package @@ -78,7 +100,7 @@ ("r-impute" ,r-impute) ("r-matrixstats" ,r-matrixstats) ; ("r-parallel" ,r-parallel) - ; ("r-preprocesscore" ,r-preprocesscore) + ("r-biocpreprocesscore" ,r-biocpreprocesscore) ; ("r-splines" ,r-splines) ; ("r-stats" ,r-stats) ; ("r-survival" ,r-survival) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index b77ccb4..033bf94 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -158,6 +158,7 @@ (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) + ("r-wgcna" ,r-wgcna) ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-git) -- cgit v1.2.3 From 7d5d0e85fd8c241d186ceb33d200c26319a95ecf Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 1 Mar 2016 09:47:56 +0000 Subject: gn2 updated --- gn/packages/genenetwork.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 033bf94..e7ebf41 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -141,20 +141,20 @@ (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")))) + "1i8shsqci73z8gsswjack6l1wbph4x3d7vdg4ah8j6r2zsaf5782")))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) -- cgit v1.2.3 From c9c9ff5f70e0fbb08c6b15d9cfc7a541b34cc818 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 1 Mar 2016 09:53:12 +0000 Subject: gn2 updated --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index e7ebf41..aec305b 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -154,7 +154,7 @@ (file-name (string-append name "-" (string-take commit 7))) (sha256 (base32 - "1i8shsqci73z8gsswjack6l1wbph4x3d7vdg4ah8j6r2zsaf5782")))) + "1kgigzs4rs6zgbqbnm40rcljzz9prlwv7n2n9an57jk58bjgf6v8")))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) -- cgit v1.2.3