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changeset 1:f77ce4f92b46 draft

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Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
author crs4
date Fri, 31 Jan 2014 05:44:03 -0500
parents 7af33315bc5e
children bad8a51514dd
files COPYING edge_pro.py edge_pro.xml get_edge_data.py readme.rst tool_dependencies.xml
diffstat 6 files changed, 64 insertions(+), 59 deletions(-) [+]
line wrap: on
line diff
--- a/COPYING	Mon Sep 09 06:11:47 2013 -0400
+++ b/COPYING	Fri Jan 31 05:44:03 2014 -0500
@@ -1,4 +1,4 @@
-Copyright © 2012-2013 CRS4 Srl. http://www.crs4.it/
+Copyright © 2012-2014 CRS4 Srl. http://www.crs4.it/
 Created by:
 Paolo Uva <paolo.uva@crs4.it>
 Nicola Soranzo <nicola.soranzo@crs4.it>
--- a/edge_pro.py	Mon Sep 09 06:11:47 2013 -0400
+++ b/edge_pro.py	Fri Jan 31 05:44:03 2014 -0500
@@ -37,55 +37,25 @@
     (options, args) = parser.parse_args()
     if len(args) > 0:
         parser.error('Wrong number of arguments')
-    
+
     # Build command
-    if options.input2:
-        input2_flag = '-v %s' % (options.input2)
-    else:
-        input2_flag = ''
-    if options.num_threads is not None:
-        num_threads_flag = '-t %d' % options.num_threads
-    else:
-        num_threads_flag = ''
-    if options.minInsertSize is not None:
-        minInsertSize_flag = '-m %d' % options.minInsertSize
-    else:
-        minInsertSize_flag = ''
-    if options.maxInsertSize is not None:
-        maxInsertSize_flag = '-M %d' % options.maxInsertSize
-    else:
-        maxInsertSize_flag = ''
-    if options.window is not None:
-        window_flag = '-w %d' % options.window
-    else:
-        window_flag = ''
-    if options.utrSize is not None:
-        utrSize_flag = '-i %d' % options.utrSize
-    else:
-        utrSize_flag = ''
-    if options.similarity is not None:
-        similarity_flag = '-x %s' % options.similarity
-    else:
-        similarity_flag = ''
-    if options.readLength is not None:
-        readLength_flag = '-l %d' % (options.readLength)
-    else:
-        readLength_flag = ''
-    if options.minCoverage is not None:
-        minCoverage_flag = '-c %d' % options.minCoverage
-    else:
-        minCoverage_flag = ''
-    
+    input2_flag = '-v %s' % (options.input2) if options.input2 else ''
+    num_threads_flag = '-t %d' % options.num_threads if options.num_threads is not None else ''
+    minInsertSize_flag = '-m %d' % options.minInsertSize if options.minInsertSize is not None else ''
+    maxInsertSize_flag = '-M %d' % options.maxInsertSize if options.maxInsertSize is not None else ''
+    window_flag = '-w %d' % options.window if options.window is not None else ''
+    utrSize_flag = '-i %d' % options.utrSize if options.utrSize is not None else ''
+    similarity_flag = '-x %s' % options.similarity if options.similarity is not None else ''
+    readLength_flag = '-l %d' % (options.readLength) if options.readLength is not None else ''
+    minCoverage_flag = '-c %d' % options.minCoverage if options.minCoverage is not None else ''
+
     wd = tempfile.mkdtemp()
     try:
         prefix = os.path.join(wd, 'out')
         cl = 'edge.pl -g %s -p %s -r %s -u %s -o %s %s %s %s %s %s %s %s %s %s' % (options.genome, options.ptt, options.rnt, options.input1, prefix, input2_flag, num_threads_flag, minInsertSize_flag, maxInsertSize_flag, window_flag, utrSize_flag, similarity_flag, readLength_flag, minCoverage_flag)
-        print cl
-        
-        if options.out_log:
-            sout = open(options.out_log, 'w')
-        else:
-            sout = sys.stdout
+        print "EDGE-pro command to be executed:\n %s" % (cl)
+
+        sout = open(options.out_log, 'w') if options.out_log else sys.stdout
         try:
             subprocess.check_call(cl, stdout=sout, stderr=subprocess.STDOUT, shell=True) # need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there
         finally:
--- a/edge_pro.xml	Mon Sep 09 06:11:47 2013 -0400
+++ b/edge_pro.xml	Fri Jan 31 05:44:03 2014 -0500
@@ -1,11 +1,12 @@
 <tool id="edge_pro" name="EDGE-pro" version="1.0.0">
   <description>Gene expression in Prokaryotes</description>
   <requirements>
+    <requirement type="package" version="2.1.0">bowtie2</requirement>
     <requirement type="package" version="1.3.1">edge-pro</requirement>
   </requirements>
   <command interpreter="python">
     edge_pro.py
-    \${EDGE_PRO_SITE_OPTIONS:---num-threads=4}
+    --num-threads=\${GALAXY_SLOTS:-4}
     
     ## Mandatory input parameters
     --genome $genome
--- a/get_edge_data.py	Mon Sep 09 06:11:47 2013 -0400
+++ b/get_edge_data.py	Fri Jan 31 05:44:03 2014 -0500
@@ -4,7 +4,7 @@
 import optparse
 import sys
 
-class GetData:
+class GetData(object):
 
     def __init__(self, gbkid, fnafile, pttfile, rntfile, gfffile):
         self.gbkid = gbkid
@@ -14,9 +14,6 @@
         self.gfffile = gfffile
         self.ftpurl = 'ftp.ncbi.nlm.nih.gov'
         self.folder = '/genomes/Bacteria/'
-
-    def getData(self):
-        """ """
         strainName = self._getStrainName()
         print strainName
         if not strainName:
@@ -25,7 +22,7 @@
         ftp.login()
         newDir = self.folder + strainName
         ftp.cwd(newDir)
-        
+
         directoryFiles = []
         ftp.retrlines('NLST',  directoryFiles.append)
         for fileName in directoryFiles:
@@ -58,7 +55,7 @@
         ftp = FTP(self.ftpurl)
         ftp.login()
         ftp.cwd(self.folder)
-        
+
         straindirectories = []
         ftp.retrlines("NLST " , straindirectories.append)
         #print "scanning directories..."
@@ -77,7 +74,6 @@
 
 
 def __main__():
-    """ main function """
     parser = optparse.OptionParser()
     parser.add_option('-i', dest='gbkid', help='RefSeq Genomic Accession ID')
     parser.add_option('--fna', dest='fnafile', help='Output FASTA file name')
@@ -87,9 +83,8 @@
     (options, args) = parser.parse_args()
     if len(args) > 0:
         parser.error('Wrong number of arguments')
-    
-    S = GetData(options.gbkid, options.fnafile, options.pttfile, options.rntfile, options.gfffile)
-    S.getData()
+
+    GetData(options.gbkid, options.fnafile, options.pttfile, options.rntfile, options.gfffile)
 
 
 if __name__ == "__main__":
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Fri Jan 31 05:44:03 2014 -0500
@@ -0,0 +1,35 @@
+EDGE-pro wrapper
+================
+
+Dependencies of EDGE-pro which need to be installed separetely
+--------------------------------------------------------------
+
+- Switch_ Perl module.
+
+.. _Switch: http://search.cpan.org/~rgarcia/Switch/Switch.pm
+
+Configuration
+-------------
+
+EDGE-pro tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see http://wiki.galaxyproject.org/Admin/Config/Jobs and http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
+
+If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool.
+
+If instead you are using an older Galaxy release, you should also add a line
+
+  GALAXY_SLOTS=N; export GALAXY_SLOTS
+
+(where N is the number of CPU cores allocated by the job runner for this tool) to the file
+
+  <tool_dependencies_dir>/edge-pro/1.3.1/crs4/edge_pro/<hash_string>/env.sh
+
+Version history
+---------------
+
+- Release 1: Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
+- Release 0: Initial release in the Tool Shed.
+
+Development
+-----------
+
+Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!
--- a/tool_dependencies.xml	Mon Sep 09 06:11:47 2013 -0400
+++ b/tool_dependencies.xml	Fri Jan 31 05:44:03 2014 -0500
@@ -1,5 +1,8 @@
 <?xml version="1.0"?>
 <tool_dependency>
+  <package name="bowtie2" version="2.1.0">
+    <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
   <package name="edge-pro" version="1.3.1">
     <install version="1.0">
       <actions>
@@ -14,14 +17,15 @@
           <destination>$INSTALL_DIR/bin</destination>
         </action>
         <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
         </action>
       </actions>
     </install>
     <readme>
 Dependencies of EDGE-pro which needs to be installed separately:
-- bowtie2 ( http://bowtie-bio.sourceforge.net/bowtie2/ ), in particular bowtie2, bowtie2-align and bowtie2-build need to be in the $PATH . These are usually already installed for Galaxy;
-- Switch Perl core module ( http://search.cpan.org/~rgarcia/Switch/Switch.pm ).
+- Switch Perl module ( http://search.cpan.org/~rgarcia/Switch/Switch.pm ).
+
+Configuration: Previously (until Release 0), the EDGE_PRO_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use (--num-threads). This is not used anymore and may be removed.
     </readme>
   </package>
 </tool_dependency>