diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/genenetwork.scm | 1 | ||||
| -rw-r--r-- | gn/packages/python24.scm | 122 | ||||
| -rw-r--r-- | gn/past/genenetwork1.scm | 289 |
3 files changed, 412 insertions, 0 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 0db7032..b60bd60 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -713,6 +713,7 @@ written in C") (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) diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm index cde8a02..4a26e1f 100644 --- a/gn/packages/python24.scm +++ b/gn/packages/python24.scm @@ -4,12 +4,18 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix build-system copy) #:use-module (guix build-system python) #:use-module (gn packages databases) #:use-module (gn packages python) #:use-module (past packages python) #:use-module (gnu packages compression) #:use-module (gnu packages databases) +<<<<<<< HEAD +======= + #:use-module (gnu packages elf) + #:use-module (gnu packages gcc) +>>>>>>> 0684b02... gn: Use known good binary version of direct.so for genenetwork1 #:use-module (gnu packages maths) #:use-module (gnu packages python-xyz) #:use-module (gnu packages tls) @@ -385,3 +391,119 @@ for Python. The design goals are: @item Compatibility with MySQL-3.23 and later @end itemize") (license license:gpl2+))) + +;; It seems this isn't the correct DIRECT binary +(define-public python24-direct + (package + (name "python24-direct") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "DIRECT" version)) + (sha256 + (base32 + "1d4cf9hynlr42hq0k8w7j4qi45rkrgil332sh0hymklxgmyi21h5")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Files are autogenerated using f2py. + (delete-file "src/direct-f2pywrappers.f") + (delete-file "src/directmodule.c") + #t)))) + (build-system python-build-system) + (arguments + `(#:python ,python-2.4 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "DIRECT/__init__.py" + (("\\.direct") "direct")) + #t)) + (replace 'check + (lambda* (#:key tests? inputs outputs #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "test" + (invoke "python" "test_direct.py"))) + #t)) + (add-after 'install 'copy-library + (lambda* (#:key outputs #:allow-other-keys) + (with-directory-excursion + (string-append (assoc-ref outputs "out") + "/lib/python2.4/site-packages") + (copy-file "DIRECT/direct.so" "direct.so")) + #t)) + (replace 'install-license-files + (lambda* (#:key outputs #:allow-other-keys) + (install-file "COPYRIGHT" + (string-append (assoc-ref outputs "out") + "/share/doc/" ,name "-" ,version)) + #t))))) + (propagated-inputs + `(("python24-numpy" ,python24-numpy-1.2))) + (inputs + `(("gfortran" ,gfortran))) + (native-inputs + `(("python24-nose" ,python24-nose) + ("python24-setuptools" ,python24-setuptools))) + ;; Also seems to be here: https://github.com/amitibo/pydirect + (home-page "http://code.google.com/p/pydirect/") + (synopsis "Python wrapper to the DIRECT algorithm") + (description + "DIRECT is a method to solve global bound constraint optimization problems +and was originally developed by D. R. Jones, C. D. Perttunen and B. E. Stuckmann. +@code{pydirect} is a python wrapper around DIRECT. It enables using DIRECT from +the comfort of the great Python scripting language. +The @code{pydirect} package uses the fortan implementation of DIRECT written by +Joerg.M.Gablonsky, DIRECT Version 2.0.4. More information on the DIRECT +algorithm can be found in Gablonsky's +@url{http://repository.lib.ncsu.edu/ir/bitstream/1840.16/3920/1/etd.pdf, +thesis}.") + (license license:expat))) + +; env IPFS_PATH=/export/ipfs/ ipfs add direct.so +; added QmYUZiuAP6DJeubu69JqvRWSsn53qCZCS3FkRWgTowtWkA direct.so +; penguin2:~/tmp$ env IPFS_PATH=/export/ipfs/ ipfs pin add QmYUZiuAP6DJeubu69JqvRWSsn53qCZCS3FkRWgTowtWkA +; pinned QmYUZiuAP6DJeubu69JqvRWSsn53qCZCS3FkRWgTowtWkA recursively + +(define-public python24-direct-gn + (package + (name "python24-direct-gn") + (version "GN") + (source (origin + (method url-fetch) + (uri "http://ipfs.genenetwork.org/ipfs/QmYUZiuAP6DJeubu69JqvRWSsn53qCZCS3FkRWgTowtWkA") + (file-name "direct.so") + (sha256 + (base32 + "0kj11dbi25k0wvyxxsylx7dsc7wm7rja799fymklkdd8h561la4i")))) + (build-system copy-build-system) + (arguments + `(#:install-plan + '(("direct.so" "lib/python2.4/site-packages/")) + #:phases + (modify-phases %standard-phases + (replace 'unpack + (lambda* (#:key inputs #:allow-other-keys) + (copy-file (assoc-ref inputs "source") "direct.so") + #t)) + (add-after 'unpack 'patchelf + (lambda* (#:key inputs #:allow-other-keys) + ;; Writable so we can use patchelf, executable so it is useful. + ;; After installation the writable bit is stripped off. + (chmod "direct.so" #o777) + (invoke "patchelf" + "--set-rpath" + (string-append (assoc-ref inputs "gcc:lib") "/lib") + "direct.so") + #t))))) + (inputs + `(("gcc:lib" ,gcc "lib"))) + (native-inputs + `(("patchelf" ,patchelf))) + (home-page "") + (synopsis "") + (description "") + (license #f))) diff --git a/gn/past/genenetwork1.scm b/gn/past/genenetwork1.scm new file mode 100644 index 0000000..c557ee7 --- /dev/null +++ b/gn/past/genenetwork1.scm @@ -0,0 +1,289 @@ +;; 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+)))) |