opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-21 13:50:20 +08:00
Code Issues Packages Projects Releases Wiki Activity

Splitting out UCS2 and UCS4 eggs for linux. Run scripts check

Browse Source 
waht python is available and use the right directory. Factored
path stuff out of shell scripts into a shared 'setup_paths.sh'.
This commit is contained in:
James Taylor
2007-12-06 01:27:33 +00:00
parent 0160211343
commit a50b8007ef
5 changed files with 13 additions and 111 deletions
Download Patch File Download Diff File Expand all files Collapse all files
cleanup_datasets.sh
+1 -32
View File
@@ -1,36 +1,5 @@
#!/bin/sh
## Set MACHTYPE to something,
MACHTYPE=`uname -m`
[ "$MACHTYPE" = "Power Macintosh" ] && MACHTYPE="powerpc"
LC_ALL=POSIX
export MACHTYPE LC_ALL
KERNEL=`uname -s | tr "A-Z" "a-z"`
ARCH="$KERNEL-$MACHTYPE"
echo "Architecture appears to be $ARCH"
UNIVERSE_HOME=`pwd`
PYTHONPATH=$UNIVERSE_HOME/lib:$UNIVERSE_HOME/eggs
export UNIVERSE_HOME PYTHONPATH
## For PBS - if you need to force node paths (i.e. the arch the frontend
## runs on is not the same arch as the compute nodes or Galaxy is
## installed in a different path on the node).
#NODEMACH="i686"
#NODEARCH="linux-i686"
#NODEPATH=$PATH
## Certain tools (EMBOSS, PAML...) are not distributed with Galaxy.
## If you have them installed, add their bin directories to the PATH.
PATH=$PATH:/depot/apps/$MACHTYPE/bin:/home/universe/$ARCH/EMBOSS/bin:/home/universe/$ARCH/ImageMagick/bin:/home/universe/$ARCH/PAML/paml3.15/bin
## NODEPATH defaults to $PATH
: ${NODEPATH:=$PATH}
export PATH NODEPATH
echo "python path: $PYTHONPATH"
source setup_paths.sh
python2.4 ./scripts/cleanup_datasets.py universe_wsgi.ini $@
nosetests.sh
+2 -15
View File
@@ -1,20 +1,7 @@
#!/bin/sh
## Set MACHTYPE to something,
MACHTYPE=`uname -m`
if [[ $MACHTYPE = "Power Macintosh" ]]; then MACHTYPE="powerpc"; fi
export MACHTYPE
export LC_ALL=POSIX
source setup_paths.sh
KERNEL=`uname -s | tr "A-Z" "a-z"`
ARCH="$KERNEL-$MACHTYPE"
echo "Architecture appears to be $ARCH"
export UNIVERSE_HOME=`pwd`
export PATH=$PATH:$UNIVERSE_HOME/arch/$ARCH/bin:/depot/apps/$MACHTYPE/bin:/home/universe/$ARCH/EMBOSS/EMBOSS-3.0.0/bin:/home/universe/$ARCH/EMBOSS/bin:/home/universe/$ARCH/ImageMagick/bin
export PYTHONPATH=$UNIVERSE_HOME/lib:$UNIVERSE_HOME/modules:$UNIVERSE_HOME/eggs:$UNIVERSE_HOME/arch/$ARCH/lib/python:eggs/NoseHTML-0.2-py2.4.egg
echo "python path: $PYTHONPATH"
export PYTHONPATH=$PYTHONPATH:eggs/NoseHTML-0.2-py2.4.egg
python2.4 ./scripts/nosetests.py $@
run.sh
+1 -32
View File
@@ -1,35 +1,6 @@
#!/bin/sh
## Set MACHTYPE to something,
MACHTYPE=`uname -m`
[ "$MACHTYPE" = "Power Macintosh" ] && MACHTYPE="powerpc"
LC_ALL=POSIX
export MACHTYPE LC_ALL
KERNEL=`uname -s | tr "A-Z" "a-z"`
ARCH="$KERNEL-$MACHTYPE"
echo "Architecture appears to be $ARCH"
UNIVERSE_HOME=`pwd`
PYTHONPATH=$UNIVERSE_HOME/lib:$UNIVERSE_HOME/eggs
export UNIVERSE_HOME PYTHONPATH
## For PBS - if you need to force node paths (i.e. the arch the frontend
## runs on is not the same arch as the compute nodes or Galaxy is
## installed in a different path on the node).
#NODEMACH="i686"
#NODEARCH="linux-i686"
#NODEPATH=$PATH
## Certain tools (EMBOSS, PAML...) are not distributed with Galaxy.
## If you have them installed, add their bin directories to the PATH.
PATH=$PATH:/depot/apps/$MACHTYPE/bin:/home/universe/$ARCH/EMBOSS/bin:/home/universe/$ARCH/ImageMagick/bin:/home/universe/$ARCH/PAML/paml3.15/bin
## NODEPATH defaults to $PATH
: ${NODEPATH:=$PATH}
export PATH NODEPATH
source setup_paths.sh
# Create directories
CREATE_DIRS="
@@ -43,6 +14,4 @@ for CREATE_DIR in $CREATE_DIRS; do
fi
done
echo "python path: $PYTHONPATH"
python2.4 ./scripts/paster.py serve universe_wsgi.ini $@
scripts/check_python_ucs.py
Executable
+8
View File
@@ -0,0 +1,8 @@
#!/usr/bin/env python2.4
import sys
if sys.maxunicode > 65535:
print "UCS4"
else:
print "UCS2"
update_metadata.sh
+1 -32
View File
@@ -1,36 +1,5 @@
#!/bin/sh
## Set MACHTYPE to something,
MACHTYPE=`uname -m`
[ "$MACHTYPE" = "Power Macintosh" ] && MACHTYPE="powerpc"
LC_ALL=POSIX
export MACHTYPE LC_ALL
KERNEL=`uname -s | tr "A-Z" "a-z"`
ARCH="$KERNEL-$MACHTYPE"
echo "Architecture appears to be $ARCH"
UNIVERSE_HOME=`pwd`
PYTHONPATH=$UNIVERSE_HOME/lib:$UNIVERSE_HOME/eggs
export UNIVERSE_HOME PYTHONPATH
## For PBS - if you need to force node paths (i.e. the arch the frontend
## runs on is not the same arch as the compute nodes or Galaxy is
## installed in a different path on the node).
#NODEMACH="i686"
#NODEARCH="linux-i686"
#NODEPATH=$PATH
## Certain tools (EMBOSS, PAML...) are not distributed with Galaxy.
## If you have them installed, add their bin directories to the PATH.
PATH=$PATH:/depot/apps/$MACHTYPE/bin:/home/universe/$ARCH/EMBOSS/bin:/home/universe/$ARCH/ImageMagick/bin:/home/universe/$ARCH/PAML/paml3.15/bin
## NODEPATH defaults to $PATH
: ${NODEPATH:=$PATH}
export PATH NODEPATH
echo "python path: $PYTHONPATH"
source setup_paths.sh
python2.4 ./scripts/update_metadata.py universe_wsgi.ini $@