Mercurial > repos > mikel-egana-aranguren > oppl

changeset 20:46257c870179 draft

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New installation procedure added
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 08 Oct 2012 12:55:08 +0200
parents cc270db37d33
children ffde1fafa066
files README config_oppl_for_galaxy.sh install.sh sed_recipes stderr_wrapper.py wrapper.sh
diffstat 6 files changed, 86 insertions(+), 165 deletions(-) [+]
line wrap: on
line diff
--- a/README	Sat Oct 06 21:50:39 2012 +0200
+++ b/README	Mon Oct 08 12:55:08 2012 +0200
@@ -1,8 +1,55 @@
+INSTALLATION VIA MERCURIAL (RECOMMENDED)
+========================================
+
+1.- Stop Galaxy.
+
+2.- Move to galaxy-dist/tools/
+
+3.- Clone the OPPL-Galaxy repository with mercurial: 
+
+hg clone http://mikel-egana-aranguren@toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/oppl
+
+4.- Move to galaxy-dist/tools/oppl/ and run install.sh: 
+
+chmod +x install.sh
+./install.sh
+
+5.- Add the following lines to /galaxy-dist/tool_conf.xml:
+
+  <section name="Ontology Pre Processor Language" id="oppl">
+    <tool file="oppl/oppl.xml"/>
+    <tool file="oppl/inference.xml"/>
+    <tool file="oppl/query.xml"/>
+    <tool file="oppl/oppl_query.xml"/>
+    <tool file="oppl/merge.xml"/>
+  </section>
+
+6.- Start Galaxy.
+
+For updates: 
+
+1.- Stop Galaxy.
+
+2.- Move to galaxy-dist/tools/oppl/
+
+3.- Update local files: 
+
+hg update
+
+4.- Run install.sh: 
+
+./install.sh
+
+5.- Only edit /galaxy-dist/tool_conf.xml in case a tool (an XML file) has been added/removed.
+
+6.- Start Galaxy.
 
 
 
-MANUAL INSTALLATION
-============
+MANUAL INSTALLATION (DIRECT DOWNLOAD)
+=====================================
+
+Download and uncompress anywhere you like, and then:
 
 1.- Stop Galaxy.
 
@@ -22,27 +69,24 @@
 FaCT++-linux-v1.5.2/ 
 FaCT++-OSX-v1.5.2/
  
-3.- Create directory /galaxy-dist/tools/OPPL/
+3.- Create directory /galaxy-dist/tools/oppl/
 
 4.- Copy oppl.xml, inference.xml, query.xml, oppl_query.xml and 
-merge.xml to /galaxy-dist/tools/OPPL/
+merge.xml to /galaxy-dist/tools/oppl/
 
 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
 
   <section name="Ontology Pre Processor Language" id="oppl">
-    <tool file="OPPL/oppl.xml"/>
-    <tool file="OPPL/inference.xml"/>
-    <tool file="OPPL/query.xml"/>
-    <tool file="OPPL/oppl_query.xml"/>
-    <tool file="OPPL/merge.xml"/>
+    <tool file="oppl/oppl.xml"/>
+    <tool file="oppl/inference.xml"/>
+    <tool file="oppl/query.xml"/>
+    <tool file="oppl/oppl_query.xml"/>
+    <tool file="oppl/merge.xml"/>
   </section>
 
 6.- Start Galaxy.
 
 
-INSTALLATION VIA MERCURIAL AND SHELL SCRIPT
-
-
 
 FORESEEN FEATURES
 =================
--- a/config_oppl_for_galaxy.sh	Sat Oct 06 21:50:39 2012 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-#!/bin/sh
-
-# Remove Kate backup files
-rm *~
-
-# Wrapper does not work
-# cp stderr_wrapper.py /home/mikel/galaxy/galaxy-dist/tools/OPPL/
-
-# Local installation 
-
-cp oppl.xml /home/mikel/galaxy/galaxy-dist/tools/OPPL/
-cp inference.xml /home/mikel/galaxy/galaxy-dist/tools/OPPL/
-cp query.xml /home/mikel/galaxy/galaxy-dist/tools/OPPL/
-cp oppl_query.xml /home/mikel/galaxy/galaxy-dist/tools/OPPL/
-cp merge.xml /home/mikel/galaxy/galaxy-dist/tools/OPPL/
-
-cp oppl_galaxy.jar /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/
-cp inference.jar /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/
-cp query.jar /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/
-cp oppl_query.jar /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/
-cp merge.jar /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/
-
-cp -r FaCT++-linux-v1.5.2 /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/
-
-cp -r oppl_galaxy_lib /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/
-cp -r inference_lib /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/
-cp -r query_lib /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/
-cp -r oppl_query_lib /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/
-cp -r merge_lib /home/mikel/galaxy/galaxy-dist/tool-data/shared/jars/
-
-# Copy src from Eclipse for release 
-
-cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/fi/dia/oeg/oppl/galaxy/OPPLGalaxy.java ./src/
-cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/fi/dia/oeg/oppl/galaxy/GalaxyOWLAPI.java ./src/
-cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/fi/dia/oeg/oppl/galaxy/InferenceGalaxy.java ./src/
-cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/fi/dia/oeg/oppl/galaxy/OWLQueryGalaxy.java ./src/
-cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/fi/dia/oeg/oppl/galaxy/OWLQueryGalaxy.java ./src/
-cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/cbgp/opplquery/oppl/galaxy/OPPLQueryGalaxy.java ./src/
-cp /home/mikel/UPM/Eclipse_Workspace/OPPL_Galaxy/src/es/upm/cbgp/opplquery/oppl/galaxy/MergeImportedOntologies.java ./src/
-
-# Copy files for google code release ('Backup' release, not open to public)
-
-cp *.jar /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/
-cp *.xml /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/
-cp -r *_lib /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/
-cp -r FaCT++-* /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/
-cp -r src /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/
-cp -r test-data /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/
-cp README /home/mikel/UPM/Paper/SWAT4LS_2011/JBS_review/oppl-galaxy.src/
-
-# ##### NOTES
-
-# To kill Galaxy easily: ./run.sh --reload
-
-# Usual mercurial session: update, status, add, commit -m 'Changes', push
-
-
-
--- a/install.sh	Sat Oct 06 21:50:39 2012 +0200
+++ b/install.sh	Mon Oct 08 12:55:08 2012 +0200
@@ -1,3 +1,32 @@
 #!/bin/sh
 
-# Shell script for installing OPPL-Galaxy
\ No newline at end of file
+# Shell script for installing OPPL-Galaxy
+
+# This script assumes that it is living in galaxy-dist/tools/oppl/
+# if that is not the case, simply edit the var $jars bellow
+
+jars="../../tool-data/shared/jars/"
+
+cp oppl_galaxy.jar $jars
+cp inference.jar $jars
+cp query.jar $jars
+cp oppl_query.jar $jars
+cp merge.jar $jars
+
+cp -r FaCT++-linux-v1.5.2 $jars
+cp -r oppl_galaxy_lib $jars
+cp -r inference_lib $jars
+cp -r query_lib $jars
+cp -r oppl_query_lib $jars
+cp -r merge_lib $jars
+
+echo 'Now you should edit /galaxy-dist/tool_conf.xml:'
+echo '  <section name="Ontology Pre Processor Language" id="oppl">'
+echo '    <tool file="oppl/oppl.xml"/>'
+echo '    <tool file="oppl/inference.xml"/>'
+echo '    <tool file="oppl/query.xml"/>'
+echo '    <tool file="oppl/oppl_query.xml"/>'
+echo '    <tool file="oppl/merge.xml"/>'
+echo '  </section>'
+
+# Foreseen feature: directly edit /galaxy-dist/tool_conf.xml with sed or something
\ No newline at end of file
--- a/sed_recipes	Sat Oct 06 21:50:39 2012 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-less Elk_output.text | sed s/INFO/X/ > output
-less Elk_output.text | sed s/.*org.semanticweb.elk.reasoner.*// > output
-less Elk_output.text | sed /.*org.semanticweb.elk.reasoner.*/d > output
-
-| sed /.*org.semanticweb.elk.reasoner.*/d 
-less Elk_output.text | sed /^\s*\<.*\>/d 
-
-
--- a/stderr_wrapper.py	Sat Oct 06 21:50:39 2012 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Wrapper that execute a program and its arguments but reports standard error
-messages only if the program exit status was not 0
-Example: ./stderr_wrapper.py myprog arg1 -f arg2
-"""
-
-import sys, subprocess
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-def stop_err( msg ):
-    sys.stderr.write( "%s\n" % msg )
-    sys.exit()
-
-def __main__():
-    # Get command-line arguments
-    args = sys.argv
-    # Remove name of calling program, i.e. ./stderr_wrapper.py
-    args.pop(0)
-    # If there are no arguments left, we're done
-    if len(args) == 0:
-        return
-
-    # If one needs to silence stdout 
-    #args.append( ">" )
-    #args.append( "/dev/null" )
-
-    cmdline = " ".join(args)
-    try:
-        # Run program
-        proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
-        returncode = proc.wait()
-        # Capture stderr, allowing for case where it's very large
-        stderr = ''
-        buffsize = 1048576
-        try:
-            while True:
-                stderr += proc.stderr.read( buffsize )
-                if not stderr or len( stderr ) % buffsize != 0:
-                    break
-        except OverflowError:
-            pass
-        # Running Grinder failed: write error message to stderr
-        if returncode != 0:
-            raise Exception, stderr
-    except Exception, e:
-        # Running Grinder failed: write error message to stderr
-        stop_err( 'Error:\n' + str( e ) )
-
-
-if __name__ == "__main__": __main__()
\ No newline at end of file
--- a/wrapper.sh	Sat Oct 06 21:50:39 2012 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-#!/bin/sh
-
-# STDERR wrapper - discards STDERR if command execution was OK.
-
-#
-# This script executes a given command line,
-# while saving the STDERR in a temporary file.
-#
-# When the command is completed, it checks to see if the exit code was zero.
-# if so - the command is assumed to have succeeded - the STDERR file is discarded.
-# if not - the command is assumed to have failed, and the STDERR file is dumped to the real STDERR
-#
-#
-# Use this wrapper for tools which insist on writting stuff to STDERR
-# even if they succeeded -
-# which throws galaxy off balance.
-#
-#
-# Copyright 2009 (C) by Assaf Gordon
-# This file is distributed under the BSD license.
-
-TMPFILE=$(mktemp) || exit 1
-
-"$@" 2> $TMPFILE
-
-EXITCODE=$?
-# Exitcode != 0 ?
-if [ "$EXITCODE" -ne "0" ]; then
-       cat $TMPFILE >&2
-fi
-rm $TMPFILE
-
-exit $EXITCODE