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+;; Bioinformatics module
+
+(define-module (gn past genenetwork1)
+ #: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 cargo)
+ #:use-module (guix build-system gnu)
+ #:use-module (guix build-system python)
+ #:use-module (guix build-system trivial)
+ #:use-module (guix graph)
+ #:use-module (guix scripts graph)
+ #:use-module (guix store)
+ #:use-module (guix gexp)
+ #:use-module (gnu packages)
+ #:use-module (gnu packages base)
+ #:use-module (gnu packages bioconductor)
+ #:use-module (gnu packages bioinformatics)
+ #:use-module (gnu packages bootstrap)
+ #:use-module (gnu packages check)
+ #:use-module (gnu packages cran)
+ #: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 graphviz)
+ #:use-module (gnu packages parallel)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages python-check)
+ #:use-module (gnu packages python-crypto)
+ #:use-module (gnu packages python-science)
+ #:use-module (gnu packages python-web)
+ #:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages rdf)
+ #:use-module (gnu packages scheme)
+ #:use-module (gnu packages statistics)
+ #:use-module (gnu packages version-control)
+ #:use-module (gnu packages vim)
+ #:use-module (gnu packages web)
+ #:use-module (gnu packages wget)
+ #:use-module (gnu packages xml)
+ #:use-module (past packages python)
+ #:use-module (past packages web)
+ #:use-module (gn packages bioinformatics)
+ #:use-module (gn packages twint)
+ #:use-module (gn packages databases)
+ #:use-module (gn packages elixir)
+ #:use-module (gn packages gemma)
+ #:use-module (gn packages javascript)
+ #:use-module (gn packages phewas)
+ #:use-module (gn packages python)
+ #:use-module (gn packages python24)
+ #:use-module (gn packages statistics)
+ #:use-module (gn packages web)
+ #:use-module (srfi srfi-1))
+
+
+(define-public python2-qtlreaper
+ (let ((commit "442c217b90393380a8634ff8636b44992f5c53dd"))
+ (package
+ (name "python2-qtlreaper")
+ (version (string-append "1.11-gn2-" (string-take commit 7) ))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ ;; (url "https://github.com/genenetwork/genenetwork2.git")
+ (url "https://github.com/pjotrp/QTLreaper.git")
+ (commit commit)))
+ (file-name (string-append name "-" (string-take commit 7)))
+ (sha256
+ (base32
+ "1rrbm1ap2zzyjxmrs9aa1d18sgiba5dhj1fmkl7wmab06jv3j1hm"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:tests? #f)) ; no 'setup.py test' really!
+ (home-page "http://qtlreaper.sourceforge.net/")
+ (synopsis "Scan expression data for QTLs")
+ (description
+ "Batch-oriented version of WebQTL. It requires, as input,
+expression data from members of a set of recombinant inbred lines and
+genotype information for the same lines. It searches for an
+association between each expression trait and all genotypes and
+evaluates that association by a permutation test. For the permutation
+test, it performs only as many permutations as are necessary to define
+the empirical P-value to a reasonable precision. It also performs
+bootstrap resampling to estimate the confidence region for the
+location of a putative QTL.")
+ (license license:gpl2+))))
+
+(define-public python24-qtlreaper
+ (let ((commit "442c217b90393380a8634ff8636b44992f5c53dd"))
+ (package
+ (name "python24-qtlreaper")
+ (version (git-version "1.11" "gn1" commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ ;; (url "https://github.com/genenetwork/genenetwork2.git")
+ (url "https://github.com/pjotrp/QTLreaper.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1rrbm1ap2zzyjxmrs9aa1d18sgiba5dhj1fmkl7wmab06jv3j1hm"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2.4
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'make-max-markername-size-larger
+ (lambda _
+ (substitute* "Src/dataset.c"
+ (("512") "2048"))
+ #t))
+ (replace 'check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (add-installed-pythonpath inputs outputs)
+ (invoke "python" "test/runtest.py"))))))
+ (native-inputs
+ `(("python24-setuptools" ,python24-setuptools)))
+ (home-page "http://qtlreaper.sourceforge.net/")
+ (synopsis "Scan expression data for QTLs")
+ (description
+ "Batch-oriented version of WebQTL. It requires, as input,
+expression data from members of a set of recombinant inbred lines and
+genotype information for the same lines. It searches for an
+association between each expression trait and all genotypes and
+evaluates that association by a permutation test. For the permutation
+test, it performs only as many permutations as are necessary to define
+the empirical P-value to a reasonable precision. It also performs
+bootstrap resampling to estimate the confidence region for the
+location of a putative QTL.")
+ (license license:gpl2+))))
+
+(define-public genenetwork1
+ (let ((commit "acf65ac9ae4be395c07c1629758f7408bf4eab5f") ; June 3, 2020
+ (revision "2"))
+ (package
+ (name "genenetwork1")
+ (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
+ "0xmmmjyvh80yd8b0cjrwpdmxl8k9zj5ly65r2g9aygx74njsp4fi"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("ghostscript" ,ghostscript)
+ ("graphviz" ,graphviz)
+ ("wget" ,wget)))
+ (propagated-inputs
+ `(("python" ,python-2.4)
+ ("httpd-with-mod-python" ,httpd22-with-mod-python)
+ ("python-direct" ,python24-direct)
+ ("python-htmlgen-GN1" ,python24-htmlgen-GN1)
+ ("python-json-GN1" ,python24-json-GN1)
+ ("python-mysqlclient" ,python24-mysqlclient)
+ ("python-numarray" ,python24-numarray)
+ ("python-piddle" ,python24-piddle)
+ ("python-pp-GN1" ,python24-pp-GN1)
+ ("python-pyx" ,python24-pyx)
+ ("python-pyxlwriter" ,python24-pyxlwriter)
+ ("python-qtlreaper" ,python24-qtlreaper)
+ ("python-rpy2" ,python24-rpy2)
+ ("python-svg-GN1" ,python24-svg-GN1)))
+ (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/(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-after 'patch-generated-file-shebangs 'changes-for-deployed-service
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (substitute* "web/webqtl/base/webqtlConfigLocal.py"
+ ;; Where GN1 is located: (GNROOT)
+ (("/gnshare/gn") out)
+ ;; Where the database is located: (sql_host)
+ (("tux01.uthsc.edu") "127.0.0.1"))
+ (substitute* '("web/webqtl/maintainance/QTL_Reaper_cal_lrs.py")
+ (("128\\.169\\.5\\.59") "localhost"))
+ ;; This directory (TMPDIR) is expected to be writable by apache.
+ ;; /tmp is private inside the container.
+ (symlink "/tmp" "web/tmp")
+ ;; IMGDIR is expected to be writable.
+ (symlink "/tmp" "web/image")
+ (system "chmod 0777 web/tmp")
+ ;; More writable locations:
+ (substitute* (list "web/webqtl/collection/ExportSelectionDetailInfoPage.py"
+ "web/webqtl/pairScan/DirectPlotPage.py"
+ "web/webqtl/updateTrait/DataUpdatePage.py"
+ "web/webqtl/utility/Plot.py")
+ (("/gnshare/gn/web/debug_file.txt") "/tmp/debug_file.txt"))
+ ;; We mount the genotypes folder (GENODIR) in the OS-config and
+ ;; provide the symlink to that location from the package.
+ ;; And now the directory is magically available!
+ (symlink "/gnshare/gn/web/genotypes" "web/genotypes")
+ (substitute* "web/webqtl/base/webqtlConfig.py"
+ (("http://www.genenetwork.org") "http://gn1-test.genenetwork.org"))
+ ;; Inside the gn1 container, there's some conflict when
+ ;; importing the user module, therefore, as a hack, rename
+ ;; user to useralt
+ (mkdir "web/webqtl/useralt")
+ (copy-recursively "web/webqtl/user" "web/webqtl/useralt")
+ (substitute* '("web/webqtl/main.py")
+ (("from user import") "from useralt import"))
+ #t)))
+ (add-after 'unpack 'use-local-links
+ (lambda _
+ (substitute* '("web/javascript/menu_items.js"
+ "web/webqtl/maintainance/updateMenuJS.py")
+ (("http://(www|gn1).genenetwork.org") ""))
+
+ ;; Move this file out of the way while patching files.
+ (rename-file "web/infoshare/manager/MDB-Free/index.html"
+ "web/infoshare/manager/MDB-Free/index.htm")
+ (substitute* (cons*
+ "web/webqtl/base/indexBody.py"
+ "web/webqtl/submitTrait/BatchSubmitPage.py"
+ (find-files "web" "\\.html"))
+ ((".*base href.*") "")
+ (("(HREF|href)=\\\"http://(www.)?genenetwork.org")
+ "href=\""))
+ ;; Move this file back to its original location.
+ (rename-file "web/infoshare/manager/MDB-Free/index.htm"
+ "web/infoshare/manager/MDB-Free/index.html")
+
+ (substitute* (cons*
+ "web/humanCross.html"
+ "web/webqtl/base/indexBody.py"
+ "web/whats_new.html"
+ (find-files "web/dbdoc" "\\.html"))
+ (("src=\\\"http://www.genenetwork.org") "src=\""))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (copy-recursively "." (assoc-ref outputs "out"))
+ #t)))))
+ (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+))))