diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/genenetwork.scm | 9 | ||||
| -rw-r--r-- | gn/packages/python24.scm | 59 | ||||
| -rw-r--r-- | gn/packages/web.scm | 13 |
3 files changed, 70 insertions, 11 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 214f040..36975bd 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -694,10 +694,9 @@ written in C") (base32 "1s735dj8kf98gf5w58p10zzyc5766gn27j4j5yh07ksadg7h1kdi")))) (build-system gnu-build-system) - (propagated-inputs + (native-inputs `(("ghostscript" ,ghostscript) ("graphviz" ,graphviz-2.26) - ("httpd" ,httpd22-mod-python-24) ("python24" ,python-2.4) ("python-piddle" ,python24-piddle) ("wget" ,wget))) @@ -708,8 +707,9 @@ written in C") (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"))) + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((piddle (assoc-ref inputs "python-piddle")) + (out (assoc-ref outputs "out"))) (substitute* "web/webqtl/networkGraph/networkGraphUtils.py" (("/usr/local/bin/neato") (which "neato")) (("/usr/local/bin/circo") (which "circo")) @@ -730,6 +730,7 @@ written in C") (("/usr/bin/python") (which "python")) (("/usr/bin/env python") (which "python"))) (substitute* "web/webqtl/base/webqtlConfigLocal.py" + (("/gnshare/gn") out) (("PythonPath.*") (string-append "PythonPath = '" (which "python") "'\n")) (("PIDDLE_FONT_PATH.*/lib") diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm index bae5304..916c33c 100644 --- a/gn/packages/python24.scm +++ b/gn/packages/python24.scm @@ -3,10 +3,12 @@ #:use-module (guix utils) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system python) #:use-module (gn packages python) #:use-module (past packages python) #:use-module (gnu packages compression) + #:use-module (gnu packages databases) #:use-module (gnu packages maths) #:use-module (gnu packages python-xyz) #:use-module (srfi srfi-1)) @@ -435,3 +437,60 @@ clusters (computers connected via network).") (synopsis "") (description "") (license license:bsd-3))) + +(define-public python24-mysqlclient + (package + (name "python24-mysqlclient") + (version "1.2.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PyMySQL/mysqlclient-python") + (commit "MySQLdb-1.2.5"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "193h09afkmz9nw2jlwfdikx1xj9sybswd2705k8jy48h1ks6fnbj")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2.4 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'dont-create-release-file + (lambda _ + (substitute* "setup_common.py" + (("MySQLdb/release.py") + (string-append (getcwd) "/release.py"))) + #t)) + (add-before 'check 'pre-check + (lambda _ + (call-with-output-file "/tmp/my.cnf" + (lambda (p) + (format p + "[mysqld]~@ + datadir=/tmp~@ + socket=/tmp/mysql.sock~%"))) + (system* "mysqld" "--defaults-file=/tmp/my.cnf" "--bootstrap") + ;(invoke "mysql" "-S" "/tmp/mysql.sock" + ; "-e" "'create database mysqldb_test charset utf8;'") + #t))) + #:tests? #f)) ; TODO: Run the test suite + (native-inputs + `(("mariadb" ,mariadb "dev") + ("mariadb:bin" ,mariadb) + ("python-nose" ,python24-nose) + ("python-setuptools" ,python24-setuptools))) + (inputs + `(("zlib" ,zlib))) + (home-page "http://mysql-python.sourceforge.net/") + (synopsis "Python interface to MySQL") + (description "MySQLdb is an interface to the popular MySQL database server +for Python. The design goals are: +@itemize +@item with Python database API version 2.0 +@item Thread-safety +@item Thread-friendliness (threads will not block each other) +@item Compatibility with MySQL-3.23 and later +@end itemize") + (license license:gpl2+))) diff --git a/gn/packages/web.scm b/gn/packages/web.scm index a6ce42f..a9ec973 100644 --- a/gn/packages/web.scm +++ b/gn/packages/web.scm @@ -370,10 +370,6 @@ connections and other data between hits and access to Apache internals.") (lambda _ ;; Make sure we're in the correct folder (chdir "../mod_python-3.3.1") - ;; We can't import cPickle because we don't wrap with Python. - (substitute* (find-files "." "\\.py$") - (("import cPickle") - "try:\n import cPickle\nexcept:\n import pickle as cPickle")) #t)) (add-after 'change-directory 'bootstrap-mod-python (lambda* (#:key inputs #:allow-other-keys) @@ -383,12 +379,15 @@ connections and other data between hits and access to Apache internals.") (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 + (string-append "PY_LIBS=\"" python + "/lib/libpython" py-version ".so " + " -lpthread -ldl -lutil -lm" ; LIB[SMC] + " -lpython" py-version " -lreadline -lssl -lcrypto" " -ltk" tcl-version " -ltcl" tcl-version " -lgdbm -ltirpc -lnsl -lz\"\n")) + (("PY_LDFLAGS=.*") + (string-append "PY_LDFLAGS=\"-Wl,-rpath=" python "/lib -Wl,-rpath=" python "/lib/python" py-version "/lib-dynload\"\n")) (("PY_INCLUDES=.*") (string-append "PY_INCLUDES=-I" python "/include/python" py-version "\n"))) (invoke "autoreconf" "-vfi")))) |