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-rw-r--r--gn/packages/genenetwork.scm338
-rw-r--r--gn/packages/pangenome.scm51
-rw-r--r--gn/past/genenetwork1.scm289
3 files changed, 344 insertions, 334 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index da18c08..1b028fa 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -18,13 +18,13 @@
#: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 golang)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages parallel)
#:use-module (gnu packages python)
@@ -38,143 +38,20 @@
#: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 vim)
#:use-module (gnu packages web)
- #:use-module (gnu packages wget)
+ ; #: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 twint)
#: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+))))
-
-;; Reintroduced python2-gunicorn because we are running GN with python2
-;; right now. Please keep it until we migrate to Python3 fully!
-
-(define-public python-gunicorn-gn
- (package
- (name "python-gunicorn-gn")
- (version "19.9.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "gunicorn" version))
- (sha256
- (base32
- "1wzlf4xmn6qjirh5w81l6i6kqjnab1n1qqkh7zsj1yb6gh4n49ps"))))
- (build-system python-build-system)
- (inputs
- `(("python-mock" ,python-mock)))
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'loosen-verion-restrictions
- (lambda _
- (substitute* "requirements_test.txt"
- (("coverage.*") "coverage\n")
- (("pytest.*") "pytest\n")
- (("pytest-cov.*") "pytest-cov\n"))
- #t)))))
- (native-inputs
- `(("python-coverage" ,python-coverage)
- ("python-pytest" ,python-pytest)
- ("python-pytest-cov" ,python-pytest-cov)))
- (home-page "https://gunicorn.org")
- (synopsis "WSGI HTTP Server for UNIX")
- (description "Gunicorn 'Green Unicorn' is a Python WSGI HTTP Server for
-UNIX. It's a pre-fork worker model ported from Ruby's Unicorn project. The
-Gunicorn server is broadly compatible with various web frameworks, simply
-implemented, light on server resource usage, and fairly speedy.")
- (license license:expat)))
-
(define-public rust-qtlreaper
(let ((commit "2e7fed6d45b0b602d80fa2a55835f96ef1cba9e3")
(revision "1"))
@@ -219,35 +96,6 @@ implemented, light on server resource usage, and fairly speedy.")
(description "Reimplementation of genenetwork/QTLReaper in Rust")
(license #f))))
-(define-public gfautil
- (package
- (name "gfautil")
- (version "0.1.0")
- (source
- (origin
- (method url-fetch)
- (uri (crate-uri "gfautil" version))
- (file-name
- (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "0cgiis9v1nd4m7zxvgsz8jf8ijv4d8fa5wb7cpnjshksb8z7xh69"))))
- (build-system cargo-build-system)
- (arguments
- `(#:cargo-inputs
- (("rust-bstr" ,rust-bstr-0.2)
- ("rust-clap" ,rust-clap-2)
- ("rust-gfa" ,rust-gfa-0.6)
- ("rust-handlegraph" ,rust-handlegraph-0.3)
- ("rust-rayon" ,rust-rayon-1)
- ("rust-serde" ,rust-serde-1)
- ("rust-structopt" ,rust-structopt-0.3))))
- (home-page "https://github.com/chfi/rs-gfa-utils")
- (synopsis "Command line tools for working with GFA files")
- (description
- "This package provides command line tools for working with @acronym{GFA,
-Graphical Fragment Assembly} files and related formats.")
- (license license:expat)))
(define-public genenetwork3
(let ((commit "c9ee473ff7797f6bbd7507eb55c772a3a646acee"))
@@ -646,184 +494,6 @@ Graphical Fragment Assembly} files and related formats.")
-(define-public python-reaper
- (let ((commit "63391333a6619771277bfffa9bd9d33811fa0d28"))
- (package
- (name "python-reaper")
- (version (string-append "0.0.1-"
- (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/fredmanglis/reaper.git")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1rq2qn0vrqd8k676yy8drm0zxzkj065ywhxjl0j1n2r25zifay7r"))))
- (build-system python-build-system)
- (arguments
- `(#:tests? #f))
- (home-page "https://github.com/fredmanglis/reaper")
- (synopsis "Parser for .geno files")
- (description "Parser for .geno files. It replaces the Python2 library
-written in C")
- (license license:agpl3+))))
-
-
-(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+))))
-
(define (genenetwork-graph)
(with-imported-modules '((guix build utils))
(gexp->derivation "genenetwork-graph"
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
new file mode 100644
index 0000000..69e3d81
--- /dev/null
+++ b/gn/packages/pangenome.scm
@@ -0,0 +1,51 @@
+;; Bioinformatics module
+
+(define-module (gn packages pangenome)
+ #: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 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 crates-io)
+ #:use-module (gnu packages rust)
+ #:use-module (gnu packages version-control)
+ #:use-module (srfi srfi-1))
+
+
+(define-public gfautil
+ (package
+ (name "gfautil")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "gfautil" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0cgiis9v1nd4m7zxvgsz8jf8ijv4d8fa5wb7cpnjshksb8z7xh69"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-bstr" ,rust-bstr-0.2)
+ ("rust-clap" ,rust-clap-2)
+ ("rust-gfa" ,rust-gfa-0.6)
+ ("rust-handlegraph" ,rust-handlegraph-0.3)
+ ("rust-rayon" ,rust-rayon-1)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-structopt" ,rust-structopt-0.3))))
+ (home-page "https://github.com/chfi/rs-gfa-utils")
+ (synopsis "Command line tools for working with GFA files")
+ (description
+ "This package provides command line tools for working with @acronym{GFA,
+Graphical Fragment Assembly} files and related formats.")
+ (license license:expat)))
diff --git a/gn/past/genenetwork1.scm b/gn/past/genenetwork1.scm
new file mode 100644
index 0000000..b14d787
--- /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)
+ ("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+))))
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-01 14:28:40 +0000