From 15b6a4ac8c87592327ba953ea3912bf5a344d439 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 16 Jan 2020 02:07:47 -0600
Subject: gn: Add genenetwork1

---
 gn/packages/genenetwork.scm | 86 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 86 insertions(+)

(limited to 'gn/packages')

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+))))
-- 
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