From 06d9f9655d124803c911b8bcade0b97e08168c12 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Wed, 15 Jan 2020 04:42:43 -0600
Subject: gn: Add python2-htmlgen-2.2.
---
gn/packages/python.scm | 47 +++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 47 insertions(+)
(limited to 'gn')
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 2336cc9..c3e01fd 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -539,6 +539,53 @@ project)")
(description #f)
(license #f)))
+(define-public python2-htmlgen-2.2
+ (package
+ (name "python2-htmlgen-2.2")
+ (version "2.2.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://debian/pool/main/h/htmlgen/htmlgen_" version ".orig.tar.gz"))
+ (sha256
+ (base32
+ "186kb434q6z84g31ysvzi4kcfcvl3pmm57k4jlng4ccgls94x6wb"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'modernize-imports
+ (lambda _
+ (substitute* "HTMLgen.py"
+ (("whrandom") "random"))
+ (substitute* "HTMLcalendar.py"
+ (("import regex") "import re as regex"))
+ (substitute* "HTMLutil.py"
+ (("import string, regex") "import re as regex\nimport string"))
+ (substitute* "HTMLtest.py"
+ (("import string, regex, regsub") "import re as regex\nimport string")
+ (("regsub.split") "re.split"))
+ #t))
+ (replace 'build
+ (lambda _
+ (invoke "python" "-m" "compileall" ".")))
+ (replace 'check
+ (lambda _
+ (invoke "python" "HTMLtest.py")))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (lib (string-append out "/lib/python2.7/site-packages/htmlgen/")))
+ ;; Install libs and headers.
+ (for-each (lambda (file)
+ (install-file file lib))
+ (find-files "." "\\.py[c]?$"))
+ #t))))))
+ (home-page "https://packages.debian.org/unstable/python/python-htmlgen")
+ (synopsis "Genenetwork version of Python2 HTMLgen (defunkt project)")
+ (description #f)
+ (license #f)))
+
; penguin2:~/tmp$ env IPFS_PATH=/export/ipfs/ ipfs add -r Imaging/
; added QmV8Rew1re8gBTLsaqMU4bd7euFUPEpjiD572mtoz6KhPn Imaging/Imaging-1.1.6-gn.tar.gz
; added QmdkzQpVMLZVtywpYesynt9c7H8w7hHZRYKq8woN7stfpD Imaging
--
cgit v1.2.3
From 586aeb8ece73707d858a1efb787f3876c821eef3 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 16 Jan 2020 01:49:04 -0600
Subject: gn: python2-htmlgen-gn: Fixup package
Re-indented the whole package
Updated the package to work with python-2.7.
---
gn/packages/python.scm | 106 +++++++++++++++++++++++++------------------------
1 file changed, 54 insertions(+), 52 deletions(-)
(limited to 'gn')
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index c3e01fd..9c097e3 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -486,58 +486,60 @@ Python 3 support.")
; pinned QmZLWsPHLFTU3hWAfdTwj3RXFrS8Ma7KEixne1suWuYqeG recursively
(define-public python2-htmlgen-gn ; guix obsolete
-(package
- (name "python2-htmlgen-gn")
- (version "2.2.2")
- (source (origin
- (method url-fetch)
- ;; http://files.genenetwork.org/software/contrib/htmlgen-2.2.2-gn.tar.gz
- (uri (string-append
- "http://ipfs.genenetwork.org/ipfs/QmZLWsPHLFTU3hWAfdTwj3RXFrS8Ma7KEixne1suWuYqeG/htmlgen-" version "-gn.tar.gz"))
- (sha256
- (base32
- "1lwsk56rymhrma46cbyh3g64ksmq1vsih3qkrc2vh0lpba825y7r"))
- ;;(patches (list
- ;; (search-patch "python2-htmlgen-Applied-Deb-patch.patch")
- ;; (search-patch "python2-htmlgen-Fix-test-for-random.patch")
- ))
- (build-system python-build-system)
- (outputs '("out"))
- (native-inputs
- `(("make" ,gnu-make)
- ))
- (propagated-inputs
- `(("python2" ,python-2)))
- (arguments
- `(#:phases (modify-phases %standard-phases
- (replace 'build
- (lambda _
- (system* "python2" "-m" "compileall" ".")))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (include (string-append out "/include"))
- (lib2 (string-append out "/lib/htmlgen"))
- (lib (string-append (assoc-ref %outputs "out") "/lib/python2.7/site-packages/htmlgen"))
- (pkgconfig (string-append out "/lib/pkgconfig"))
- (doc (string-append out "/share/doc")))
- ;; Install libs and headers.
- ;; (copy-file "HTMLgen.pyc" "HTMLgen2.pyc")
- (install-file "HTMLgen.pyc" lib)
- (install-file "HTMLgen2.pyc" lib)
- (install-file "imgsize.pyc" lib)
- (install-file "ImageH.pyc" lib)
- (install-file "ImagePaletteH.pyc" lib)
- (install-file "__init__.pyc" lib)
- ))) ; install
- ) ; phases
- #:tests? #f))
- (home-page
- "https://packages.debian.org/unstable/python/python-htmlgen")
- (synopsis "Genenetwork version of Python2 HTMLgen (defunkt
-project)")
- (description #f)
- (license #f)))
+ (package
+ (name "python2-htmlgen-gn")
+ (version "2.2.2")
+ (source (origin
+ (method url-fetch)
+ ;; http://files.genenetwork.org/software/contrib/htmlgen-2.2.2-gn.tar.gz
+ (uri (string-append
+ "http://ipfs.genenetwork.org/ipfs/QmZLWsPHLFTU3hWAfdTwj3RXFrS8Ma7KEixne1suWuYqeG/htmlgen-" version "-gn.tar.gz"))
+ (sha256
+ (base32
+ "1lwsk56rymhrma46cbyh3g64ksmq1vsih3qkrc2vh0lpba825y7r"))
+ ;;(patches (list
+ ;; (search-patch "python2-htmlgen-Applied-Deb-patch.patch")
+ ;; (search-patch "python2-htmlgen-Fix-test-for-random.patch")
+ ))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'modernize-imports
+ (lambda _
+ (substitute* "HTMLgen.py"
+ (("whrandom") "random"))
+ (substitute* "HTMLcalendar.py"
+ (("import regex") "import re as regex"))
+ (substitute* "HTMLutil.py"
+ (("import string, regex") "import re as regex\nimport string"))
+ (substitute* "HTMLtest.py"
+ (("import string, regex, regsub") "import re as regex\nimport string")
+ (("regsub.split") "re.split"))
+ #t))
+ (replace 'build
+ (lambda _
+ (invoke "python" "-m" "compileall" ".")))
+ (replace 'check
+ (lambda* (#:key (tests? '()) #:allow-other-keys)
+ (if tests?
+ (invoke "python" "HTMLtest.py")
+ #t)))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (lib (string-append out "/lib/python2.7/site-packages/htmlgen/")))
+ ;; Install libs and headers.
+ (for-each (lambda (file)
+ (install-file file lib))
+ (find-files "." "\\.py[c]?$"))
+ #t))))))
+ (home-page "https://packages.debian.org/unstable/python/python-htmlgen")
+ (synopsis "Genenetwork version of Python2 HTMLgen (defunkt project)")
+ (description #f)
+ (license #f)))
(define-public python2-htmlgen-2.2
(package
--
cgit v1.2.3
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')
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+))))
--
cgit v1.2.3
From 5a69fb0666a2bf53b13ab9490b3ed44e5dc944b4 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 16 Jan 2020 02:08:02 -0600
Subject: gn: Add GN1 service.
---
gn/services/genenetwork.scm | 58 +++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 58 insertions(+)
create mode 100644 gn/services/genenetwork.scm
(limited to 'gn')
diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm
new file mode 100644
index 0000000..0978cd2
--- /dev/null
+++ b/gn/services/genenetwork.scm
@@ -0,0 +1,58 @@
+(define-module (gn services genenetwork))
+
+(use-modules (gnu)
+ (gn packages genenetwork)
+ (gn packages python)
+ (gn packages web))
+(use-service-modules web)
+(use-package-modules python)
+
+(define %mod-python-path
+ (file-append mod-python "/lib/python2.7/site-packages"))
+
+(operating-system
+ (host-name "genenetwork")
+ (timezone "Etc/UTC")
+ (locale "en_US.utf8")
+
+ (bootloader (bootloader-configuration
+ (bootloader grub-bootloader)
+ (target "does-not-matter")))
+ (file-systems %base-file-systems)
+ ;; No firmware for VMs
+ (firmware '())
+
+ (packages (cons* python-2
+ mod-python
+ python2-qtlreaper
+ python2-htmlgen-gn
+ python2-json-GN1
+ python2-piddle
+ python2-pyx-GN1
+ python2-pyxlwriter
+ python2-svg-GN1
+ %base-packages))
+
+ (services (list (service httpd-service-type
+ (httpd-configuration
+ (config
+ (httpd-config-file
+ (server-name "www.genenetwork.org")
+ (document-root (file-append genenetwork "/web"))
+ (listen '("8811"))
+ (modules (cons*
+ (httpd-module
+ (name "python_module")
+ (file (file-append mod-python "/modules/mod_python.so")))
+ %default-httpd-modules))
+ (extra-config (list "\
+PythonPath \"sys.path+['" %mod-python-path "', '" (file-append genenetwork "/web/webqtl") "']\"
+
+ SetHandler python-program
+ PythonHandler mod_python.publisher
+ PythonAutoReload Off
+
+
+ SetHandler python-program
+ PythonHandler mod_python.testhandler
+")))))))))
--
cgit v1.2.3