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