diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/genenetwork.scm | 19 | ||||
| -rw-r--r-- | gn/packages/python24.scm | 1 | ||||
| -rw-r--r-- | gn/packages/web.scm | 84 | ||||
| -rw-r--r-- | gn/services/genenetwork.scm | 6 |
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") "']\" |