Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.

tool_conf.xml.sample

@@ -68,9 +68,11 @@
     <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
     <tool file="extract/extract_GFF_Features.xml" />
   </section>
+  <!--
   <section name="Pattern-Matching" id="patmat">
     <tool file="patmat/findcluster_mysql.xml" />
   </section>
+  -->
   <section name="Fetch Sequences" id="fetchSeq">
     <tool file="extract/extract_genomic_dna.xml" />
   </section>

tools/annotation_profiler/annotation_profiler_for_interval.py

@@ -1,10 +1,10 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/env python
 #Dan Blankenberg
 #For a set of intervals, this tool returns the same set of intervals 
 #with 2 additional fields: the name of a Table/Feature and the number of
 #bases covered. The original intervals are repeated for each Table/Feature.
 
-import struct, optparse, os, random
+import sys, struct, optparse, os, random
 from galaxy import eggs
 import pkg_resources; pkg_resources.require( "bx-python" )
 import bx.intervals.io
@@ -14,6 +14,8 @@ try:
 except:
     pass
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 class CachedRangesInFile:
     fmt = 'I'
     fmt_size = struct.calcsize( fmt )

tools/encode/random_intervals_no_bits.py

@@ -3,7 +3,7 @@
 #%prog bounding_region_file mask_intervals_file intervals_to_mimic_file out_file mask_chr mask_start mask_end interval_chr interval_start interval_end interval_strand use_mask allow_strand_overlaps
 import sys, random
 from copy import deepcopy
-
+from galaxy import eggs
 import pkg_resources
 pkg_resources.require( "bx-python" )
 import bx.intervals.io

tools/filters/axt_to_lav.py

@@ -10,15 +10,14 @@ The application reads an AXT file from standard input and writes a LAV file to
 standard out;  some statistics are written to standard error.
 """
 
-import sys
-import copy
-
+import sys, copy
+from galaxy import eggs
 import pkg_resources
 pkg_resources.require( "bx-python" )
-
 import bx.align.axt
 import bx.align.lav
 
+assert sys.version_info[:2] >= ( 2, 4 )
 
 def usage(s=None):
     message = """

tools/filters/lav_to_bed.py

@@ -1,13 +1,14 @@
 #!/usr/bin/env python
-
 #Reads a LAV file and writes two BED files.
 
-
 import sys
+from galaxy import eggs
 import pkg_resources
 pkg_resources.require( "bx-python" )
 import bx.align.lav
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def main():
 
     try:

tools/filters/ucsc_gene_bed_to_exon_bed.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.3
+#!/usr/bin/env python
 
 """
 Read a table dump in the UCSC gene table format and print a tab separated
@@ -17,6 +17,8 @@ options:
 
 import optparse, string, sys
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def main():
 
     # Parse command line    

tools/filters/ucsc_gene_bed_to_intron_bed.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.3
+#!/usr/bin/env python
 
 """
 Read a table dump in the UCSC gene table format and print a tab separated
@@ -17,6 +17,8 @@ options:
 
 import optparse, string, sys
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def main():
 
     # Parse command line    

tools/filters/ucsc_gene_table_to_intervals.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.3
+#!/usr/bin/env python
 
 """
 Read a table dump in the UCSC gene table format and print a tab separated
@@ -17,6 +17,8 @@ options:
 
 import optparse, string, sys
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def main():
 
     # Parse command line    

tools/maf/interval_maf_to_merged_fasta.xml

@@ -47,14 +47,14 @@
   </outputs>
   <tests>
     <test>
-      <param name="input1" value="1.bed" dbkey="hg17" format="bed"/>
+      <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/>
       <param name="maf_source" value="cached"/>
       <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/>
       <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>
       <output name="out_file1" file="interval_maf_to_merged_fasta_out.dat" />
     </test>
     <test>
-      <param name="input1" value="1.bed" dbkey="hg17" format="bed"/>
+      <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/>
       <param name="maf_source" value="user"/>
       <param name="maf_file" value="5.maf"/>
       <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>

tools/maf/maf_filter.py

@@ -1,6 +1,7 @@
 #Dan Blankenberg
 #Filters a MAF file according to the provided code file, which is generated in maf_filter.xml <configfiles>
 import sys, os, shutil
+from galaxy import eggs
 import pkg_resources; pkg_resources.require( "bx-python" )
 import bx.align.maf
 

tools/maf/maf_limit_to_species.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.3
+#!/usr/bin/env python
 
 """
 Read a maf file and write out a new maf with only blocks having the 
@@ -13,6 +13,8 @@ import pkg_resources; pkg_resources.require( "bx-python" )
 import bx.align.maf
 import sys
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def main():
 
     species = sys.argv[1].split( ',' )

tools/maf/maf_to_bed.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.3
+#!/usr/bin/env python
 
 """
 Read a maf and output intervals for specified list of species.
@@ -8,6 +8,8 @@ from galaxy import eggs
 import pkg_resources; pkg_resources.require( "bx-python" )
 from bx.align import maf
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def __main__():
         
     input_filename = sys.argv[1]

tools/maf/maf_to_fasta_concat.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.3
+#!/usr/bin/env python
 
 """
 Read a maf and print the text as a fasta file, concatenating blocks
@@ -12,6 +12,8 @@ import pkg_resources; pkg_resources.require( "bx-python" )
 from bx.align import maf
 from galaxy.tools.util import maf_utilities
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def __main__():
     print "Restricted to species:", sys.argv[1]
     

tools/maf/maf_to_fasta_multiple_sets.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.3
+#!/usr/bin/env python
 
 """
 Read a maf and print the text as a fasta file.
@@ -10,6 +10,8 @@ import pkg_resources; pkg_resources.require( "bx-python" )
 from bx.align import maf
 from galaxy.tools.util import maf_utilities
 
+assert sys.version_info[:2] >= ( 2, 4 )
+
 def __main__():
     print "Restricted to species:", sys.argv[3]
     

universe_wsgi.ini.sample

@@ -142,6 +142,8 @@ static_style_dir = %(here)s/static/june_2007_style/blue
 [galaxy:tool_runners]
 
 biomart = local:///
+blat2wig = pbs:///blast
+blat_wrapper = pbs:///blast
 encode_db1 = local:///
 encode_import_all_latest_datasets1 = local:///
 encode_import_chromatin_and_chromosomes1 = local:///
@@ -149,8 +151,13 @@ encode_import_gencode1 = local:///
 encode_import_genes_and_transcripts1 = local:///
 encode_import_multi-species_sequence_analysis1 = local:///
 encode_import_transcription_regulation1 = local:///
+generate_coverage_report = pbs:///blast
 hbvar = local:///
+hist_high_quality_score = pbs:///blast
+megablast_wrapper = pbs:///blast
+megablast_xml_parser = pbs:///blast
 microbial_import1 = local:///
+quality_score_distribution = pbs:///blast
 ucsc_table_direct1 = local:///
 ucsc_table_direct_archaea1 = local:///
 ucsc_table_direct_test1 = local:///