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authorEfraim Flashner2020-01-16 02:07:47 -0600
committerEfraim Flashner2020-01-16 02:07:47 -0600
commit15b6a4ac8c87592327ba953ea3912bf5a344d439 (patch)
tree570b097f00220bee22cf78c02ee86ddd9fffcb94 /gn
parent586aeb8ece73707d858a1efb787f3876c821eef3 (diff)
downloadguix-bioinformatics-15b6a4ac8c87592327ba953ea3912bf5a344d439.tar.gz
gn: Add genenetwork1
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/genenetwork.scm86
1 files changed, 86 insertions, 0 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 489a88f..49f2935 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -7,6 +7,7 @@
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system cargo)
+ #:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
@@ -18,6 +19,7 @@
#:use-module (gnu packages crates-io)
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
+ #:use-module (gnu packages ghostscript)
#:use-module (gnu packages python)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-science)
@@ -27,10 +29,12 @@
#:use-module (gnu packages version-control)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
+ #:use-module (gnu packages wget)
#:use-module (gn packages bioinformatics)
#:use-module (gn packages crates-io)
#:use-module (gn packages elixir)
#:use-module (gn packages gemma)
+ #:use-module (gn packages graphviz)
#:use-module (gn packages javascript)
#:use-module (gn packages phewas)
#:use-module (gn packages python)
@@ -647,3 +651,85 @@ written in C")
(synopsis "Full genenetwork services")
(description "Genenetwork installation sumo.")
(license license:agpl3+))))
+
+(define-public genenetwork
+ (let ((commit "19791ce6b3c38be8cbf9bc9cd3e95dbee14116c2") ; Aug 23, 2018
+ (revision "1"))
+ (package
+ (name "genenetwork")
+ (version (git-version "0.0.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/genenetwork/genenetwork1.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1s735dj8kf98gf5w58p10zzyc5766gn27j4j5yh07ksadg7h1kdi"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (add-after 'patch-generated-file-shebangs 'patch-more-files
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((piddle (assoc-ref inputs "python-piddle")))
+ (substitute* "web/webqtl/networkGraph/networkGraphUtils.py"
+ (("/usr/local/bin/neato") (which "neato"))
+ (("/usr/local/bin/circo") (which "circo"))
+ (("/usr/local/bin/twopi") (which "twopi"))
+ (("/usr/local/bin/fdp") (which "fdp"))
+ (("ps2pdf") (which "ps2pdf")))
+ (substitute* "web/webqtl/maintainance/addRif.py"
+ (("rm ") (string-append (which "rm") " "))
+ (("wget ") (string-append (which "wget") " "))
+ (("gunzip") (which "gunzip")))
+ (substitute* "web/webqtl/misc/editHtmlPage.py"
+ (("/bin/cp") (which "cp")))
+ (substitute* "web/webqtl/geneWiki/AddGeneRIFPage.py"
+ (("touch") (which "touch")))
+ (substitute* '("web/webqtl/maintainance/addRif.py"
+ "web/webqtl/networkGraph/networkGraphPage.py"
+ "web/webqtl/utility/svg.py")
+ (("/usr/bin/python") (which "python"))
+ (("/usr/bin/env python") (which "python")))
+ (substitute* "web/webqtl/base/webqtlConfigLocal.py"
+ (("PythonPath.*")
+ (string-append "PythonPath = '" (which "python") "'\n"))
+ (("PIDDLE_FONT_PATH.*/lib")
+ (string-append "PIDDLE_FONT_PATH = '" piddle "/lib"))))
+ #t))
+ (add-before 'install 'replace-htaccess-file
+ (lambda _
+ (delete-file "web/webqtl/.htaccess")
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (copy-recursively "." (assoc-ref outputs "out"))
+ #t)))))
+ (inputs
+ `(("ghostscript" ,ghostscript)
+ ("graphviz" ,graphviz-2.26)
+ ("python24" ,python-2.4)
+ ("python-piddle" ,python24-piddle)
+ ("wget" ,wget)))
+ (home-page "http://www.genenetwork.org/webqtl/main.py")
+ (synopsis
+ "Combined database and data analysis software resource for systems genetics")
+ (description "GeneNetwork is a group of linked data sets and tools used to
+study complex networks of genes, molecules, and higher order gene function and
+phenotypes. GeneNetwork combines more than 25 years of legacy data generated by
+hundreds of scientists together with sequence data (SNPs) and massive
+transcriptome data sets (expression genetic or eQTL data sets). The
+@dfn{quantitative trait locus} (QTL) mapping module that is built into GN is
+optimized for fast on-line analysis of traits that are controlled by
+combinations of gene
+variants and environmental factors. GeneNetwork can be used to study humans,
+mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley
+and Arabidopsis). Most of these population data sets are linked with dense
+genetic maps (genotypes) that can be used to locate the genetic modifiers that
+cause differences in expression and phenotypes, including disease susceptibility.")
+ (license license:agpl3+))))