diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 86 |
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+)))) |