From d856441a3eab2bc9b71391ca9daf666afc19ca51 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 3 Jun 2020 06:50:08 -0500 Subject: gn: Add python-2.4 version of mod-python --- gn/packages/web.scm | 78 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) (limited to 'gn') diff --git a/gn/packages/web.scm b/gn/packages/web.scm index 03fac11..4ea5625 100644 --- a/gn/packages/web.scm +++ b/gn/packages/web.scm @@ -1,8 +1,11 @@ (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 (gnu packages onc-rpc) + #:use-module (gn packages python24) #:use-module (gnu packages python) #:use-module (gnu packages web) #:use-module (guix packages) @@ -211,6 +214,81 @@ 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")) + (py-version (python:python-version python))) + (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 "\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) + ("libnsl" ,libnsl) + ("libtirpc" ,libtirpc) + ("python" ,python-2.4))))) + (define-public web-font-awesome (package (inherit font-awesome) -- cgit v1.2.3 From 21efb11c56e6b9cb49450467c5729433955abc42 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Jun 2020 16:13:20 -0500 Subject: Genenetwork1 --- gn/packages/genenetwork.scm | 19 +++++++++++-------- gn/packages/python24.scm | 3 +++ gn/packages/web.scm | 7 +++++++ 3 files changed, 21 insertions(+), 8 deletions(-) (limited to 'gn') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 1c2e8d2..08d070b 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)) @@ -686,6 +687,14 @@ 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 @@ -728,12 +737,6 @@ 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..ce666c6 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)) @@ -97,6 +98,8 @@ read read ssl ssl tcl tcl tk tk ,(version-major+minor (package-version tcl)) ,(v (list (search-path-specification (variable "PYTHONPATH") (files '("lib/python2.4/site-packages"))))) + (propagated-inputs + `(("readline" ,readline))) (inputs `(("libnsl" ,libnsl) ("libtirpc" ,libtirpc) diff --git a/gn/packages/web.scm b/gn/packages/web.scm index 4ea5625..8b44e23 100644 --- a/gn/packages/web.scm +++ b/gn/packages/web.scm @@ -7,6 +7,7 @@ #:use-module (gnu packages onc-rpc) #:use-module (gn packages python24) #:use-module (gnu packages python) + #:use-module (gnu packages readline) #:use-module (gnu packages web) #:use-module (guix packages) #:use-module (guix download) @@ -203,6 +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/") @@ -283,12 +285,17 @@ connections and other data between hits and access to Apache internals.") `(("autoconf" ,autoconf) ("automake" ,automake) ("flex" ,(@ (gnu packages flex) flex)))) + (propagated-inputs + `( + ("readline" ,readline) + )) (inputs `(("httpd" ,httpd) ("libnsl" ,libnsl) ("libtirpc" ,libtirpc) ("python" ,python-2.4))))) + (define-public web-font-awesome (package (inherit font-awesome) -- cgit v1.2.3 From 2d0841d7e10f987c21c95347477e32d2440abd9b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 4 Jun 2020 02:00:26 -0500 Subject: mod-python-24: Link to all python2.4 dependencies --- gn/packages/python24.scm | 2 -- gn/packages/web.scm | 21 ++++++++++----------- 2 files changed, 10 insertions(+), 13 deletions(-) (limited to 'gn') diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm index ce666c6..b24190d 100644 --- a/gn/packages/python24.scm +++ b/gn/packages/python24.scm @@ -98,8 +98,6 @@ read read ssl ssl tcl tcl tk tk ,(version-major+minor (package-version tcl)) ,(v (list (search-path-specification (variable "PYTHONPATH") (files '("lib/python2.4/site-packages"))))) - (propagated-inputs - `(("readline" ,readline))) (inputs `(("libnsl" ,libnsl) ("libtirpc" ,libtirpc) diff --git a/gn/packages/web.scm b/gn/packages/web.scm index 8b44e23..c683f5d 100644 --- a/gn/packages/web.scm +++ b/gn/packages/web.scm @@ -4,10 +4,10 @@ #:use-module (gnu packages autotools) #:use-module (gnu packages compression) #:use-module (gnu packages fonts) - #:use-module (gnu packages onc-rpc) #: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) @@ -264,12 +264,17 @@ connections and other data between hits and access to Apache internals.") (replace 'bootstrap (lambda* (#:key inputs #:allow-other-keys) (let* ((python (assoc-ref inputs "python")) - (py-version (python:python-version 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 "\n")) + (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")))) @@ -285,16 +290,10 @@ connections and other data between hits and access to Apache internals.") `(("autoconf" ,autoconf) ("automake" ,automake) ("flex" ,(@ (gnu packages flex) flex)))) - (propagated-inputs - `( - ("readline" ,readline) - )) (inputs `(("httpd" ,httpd) - ("libnsl" ,libnsl) - ("libtirpc" ,libtirpc) - ("python" ,python-2.4))))) - + ("python" ,python-2.4) + ,@(package-inputs python-2.4))))) (define-public web-font-awesome (package -- cgit v1.2.3 From ce0dd5075df243985259be06cca1bd302a3da275 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 4 Jun 2020 06:39:47 -0500 Subject: genenetwork service: use mod-python-24 --- gn/services/genenetwork.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gn') 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") "']\" -- cgit v1.2.3