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authorBonfaceKilz2020-06-04 15:48:13 +0300
committerBonfaceKilz2020-06-04 15:48:13 +0300
commit697fdd4b85f4b6d2e709667ea2fc47b39b16969b (patch)
tree20dcbda52a8f051f1ce4ffa832db8b076444762c /gn
parent89f8fa2776fcd01ed30baf2f1edf1deec1d2da62 (diff)
parentce0dd5075df243985259be06cca1bd302a3da275 (diff)
downloadguix-bioinformatics-697fdd4b85f4b6d2e709667ea2fc47b39b16969b.tar.gz
Merge branch 'master' of http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/genenetwork.scm19
-rw-r--r--gn/packages/python24.scm1
-rw-r--r--gn/packages/web.scm84
-rw-r--r--gn/services/genenetwork.scm6
4 files changed, 99 insertions, 11 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index c174ce2..9f36779 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -29,8 +29,8 @@
#:use-module (gnu packages version-control)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
- #:use-module (gnu packages xml)
#:use-module (gnu packages wget)
+ #:use-module (gnu packages xml)
#:use-module (gn packages bioinformatics)
#:use-module (gn packages crates-io)
#:use-module (gn packages elixir)
@@ -40,7 +40,8 @@
#:use-module (gn packages phewas)
#:use-module (gn packages python)
#:use-module (gn packages python24)
- #:use-module (gn packages statistics))
+ #:use-module (gn packages statistics)
+ #:use-module (gn packages web))
@@ -687,6 +688,14 @@ written in C")
(base32
"1s735dj8kf98gf5w58p10zzyc5766gn27j4j5yh07ksadg7h1kdi"))))
(build-system gnu-build-system)
+ (propagated-inputs
+ `(("ghostscript" ,ghostscript)
+ ("graphviz" ,graphviz-2.26)
+ ("httpd" ,httpd)
+ ("python24" ,python-2.4)
+ ("mod-python-24" ,mod-python-24)
+ ("python-piddle" ,python24-piddle)
+ ("wget" ,wget)))
(arguments
`(#:tests? #f ; no tests
#:phases
@@ -729,12 +738,6 @@ written in C")
(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")
diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm
index d9b5694..b24190d 100644
--- a/gn/packages/python24.scm
+++ b/gn/packages/python24.scm
@@ -14,6 +14,7 @@
#:use-module (gnu packages onc-rpc)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages readline)
#:use-module (gnu packages tcl)
#:use-module (gnu packages tls)
#:use-module (srfi srfi-1))
diff --git a/gn/packages/web.scm b/gn/packages/web.scm
index 03fac11..c683f5d 100644
--- a/gn/packages/web.scm
+++ b/gn/packages/web.scm
@@ -1,9 +1,13 @@
(define-module (gn packages web)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
+ #:use-module (gnu packages autotools)
#:use-module (gnu packages compression)
#:use-module (gnu packages fonts)
+ #:use-module (gn packages python24)
#:use-module (gnu packages python)
+ #:use-module (gnu packages readline)
+ #:use-module (gnu packages tcl)
#:use-module (gnu packages web)
#:use-module (guix packages)
#:use-module (guix download)
@@ -200,6 +204,7 @@ extensive prebuilt components, and powerful plugins built on jQuery.")
#t)))))
(inputs
`(("httpd" ,httpd)
+ ("readline" ,readline)
("python" ,python-2))) ; does not seem to build with python3.7+
(native-inputs `(("flex" ,(@ (gnu packages flex) flex))))
(home-page "http://modpython.org/")
@@ -211,6 +216,85 @@ will have access to advanced features such as ability to retain database
connections and other data between hits and access to Apache internals.")
(license license:asl2.0))))
+(define-public mod-python-24
+ (package
+ (inherit mod-python)
+ (name "mod-python-24")
+ (version "3.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://archive.apache.org/dist/httpd/"
+ "modpython/mod_python-" version ".tgz"))
+ (sha256
+ (base32
+ "0sss2xi6l1a2z8y6ji0cp8vgyvnhq8zrg0ilkvpj1mygbzyk28xd"))
+ (patches
+ (list
+ (origin
+ (method url-fetch)
+ (uri "https://sources.debian.org/data/main/liba/libapache2-mod-python/3.3.1-11/debian/patches/04_autoconf_python_multiarch.patch")
+ (file-name "mod-python-24-python-discovery.patch")
+ (sha256
+ (base32
+ "0n3zp8j6q0mp0scry7d2hi0baqkim42bqq2c81p4l6mizsy8ry4h")))
+ (origin
+ (method url-fetch)
+ (uri "https://sources.debian.org/data/main/liba/libapache2-mod-python/3.3.1-11/debian/patches/10_bts521965.patch")
+ (file-name "mod-python-24-apr13-compat.patch")
+ (sha256
+ (base32
+ "1k2cd2r13938fbm473sn0ivicaylkcqigyqn2wjir9ppch98kybg")))
+ (origin
+ (method url-fetch)
+ (uri "https://sources.debian.org/data/main/liba/libapache2-mod-python/3.3.1-11/debian/patches/20_apache24.patch")
+ (file-name "mod-python-24-apache24-compat.patch")
+ (sha256
+ (base32
+ "1bmcx7ki7y486x6490yppssr7dh3a0qyki6gjf2lj83gyh68c0r0")))))))
+ (arguments
+ `(#:tests? #f
+ #:imported-modules ((guix build python-build-system)
+ ,@%gnu-build-system-modules)
+ #:modules ((guix build gnu-build-system)
+ (guix build utils)
+ ((guix build python-build-system) #:prefix python:))
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'bootstrap
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((python (assoc-ref inputs "python"))
+ (tcl (assoc-ref inputs "tcl"))
+ (py-version (python:python-version python))
+ (tcl-version ,(version-major+minor (package-version tcl))))
+ (substitute* "configure.in"
+ (("PY_LIBS=.*")
+ (string-append "PY_LIBS=-L" python "/lib/python" py-version "\n"))
+ (("PY_LDFLAGS=.*")
+ (string-append "PY_LDFLAGS=\"-lpython" py-version
+ " -lreadline -lssl -lcrypto"
+ " -ltk" tcl-version " -ltcl" tcl-version
+ " -lgdbm -ltirpc -lnsl -lz\"\n"))
+ (("PY_INCLUDES=.*")
+ (string-append "PY_INCLUDES=-I" python "/include/python" py-version "\n")))
+ (invoke "autoreconf" "-vfi"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (install-file "src/mod_python.so" (string-append out "/modules"))
+ (with-directory-excursion "dist"
+ (invoke "python" "setup.py" "install" "--root=/"
+ (string-append "--prefix=" out)))
+ #t))))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("flex" ,(@ (gnu packages flex) flex))))
+ (inputs
+ `(("httpd" ,httpd)
+ ("python" ,python-2.4)
+ ,@(package-inputs python-2.4)))))
+
(define-public web-font-awesome
(package
(inherit font-awesome)
diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm
index 4693152..28e51e9 100644
--- a/gn/services/genenetwork.scm
+++ b/gn/services/genenetwork.scm
@@ -8,7 +8,7 @@
(use-package-modules python)
(define %mod-python-path
- (file-append mod-python "/lib/python2.4/site-packages"))
+ (file-append mod-python-24 "/lib/python2.4/site-packages"))
(operating-system
(host-name "genenetwork")
@@ -23,7 +23,7 @@
(firmware '())
(packages (cons* python-2.4
- mod-python
+ mod-python-24
python24-qtlreaper
;python24-htmlgen-gn
python24-json-GN1
@@ -43,7 +43,7 @@
(modules (cons*
(httpd-module
(name "python_module")
- (file (file-append mod-python "/modules/mod_python.so")))
+ (file (file-append mod-python-24 "/modules/mod_python.so")))
%default-httpd-modules))
(extra-config (list "\
PythonPath \"sys.path+['" %mod-python-path "', '" (file-append genenetwork1 "/web/webqtl") "']\"