diff options
Diffstat (limited to 'gn/past')
| -rw-r--r-- | gn/past/genenetwork1.scm | 289 |
1 files changed, 0 insertions, 289 deletions
diff --git a/gn/past/genenetwork1.scm b/gn/past/genenetwork1.scm deleted file mode 100644 index c557ee7..0000000 --- a/gn/past/genenetwork1.scm +++ /dev/null @@ -1,289 +0,0 @@ -;; 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-gn) - ("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+)))) |