Changeset 1213:c347a203b94e

Show
Ignore:
Timestamp:
04/25/08 09:04:55 (9 months ago)
Author:
Greg Von Kuster <greg@bx.psu.edu>
branch:
default
convert_revision:
svn:9bcadc22-80f8-0310-8a53-c8f022958886/galaxy/trunk@2574
Message:

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.

Files:

Legend:

Unmodified
Added
Removed
Modified
Copied
Moved

  • tool_conf.xml.sample

    r1168 r1213  
    6969    <tool file="extract/extract_GFF_Features.xml" /> 
    7070  </section> 
     71  <!-- 
    7172  <section name="Pattern-Matching" id="patmat"> 
    7273    <tool file="patmat/findcluster_mysql.xml" /> 
    7374  </section> 
     75  --> 
    7476  <section name="Fetch Sequences" id="fetchSeq"> 
    7577    <tool file="extract/extract_genomic_dna.xml" /> 

  • tools/annotation_profiler/annotation_profiler_for_interval.py

    r1185 r1213  
    1 #!/usr/bin/env python2.4 
     1#!/usr/bin/env python 
    22#Dan Blankenberg 
    33#For a set of intervals, this tool returns the same set of intervals  
    …… 
    55#bases covered. The original intervals are repeated for each Table/Feature. 
    66 
    7 import struct, optparse, os, random 
     7import sys, struct, optparse, os, random 
    88from galaxy import eggs 
    99import pkg_resources; pkg_resources.require( "bx-python" ) 
    …… 
    1414except: 
    1515    pass 
     16 
     17assert sys.version_info[:2] >= ( 2, 4 ) 
    1618 
    1719class CachedRangesInFile: 

  • tools/encode/random_intervals_no_bits.py

    r1129 r1213  
    44import sys, random 
    55from copy import deepcopy 
    6  
     6from galaxy import eggs 
    77import pkg_resources 
    88pkg_resources.require( "bx-python" ) 

  • tools/filters/axt_to_lav.py

    r1012 r1213  
    1111""" 
    1212 
    13 import sys 
    14 import copy 
    15  
     13import sys, copy 
     14from galaxy import eggs 
    1615import pkg_resources 
    1716pkg_resources.require( "bx-python" ) 
    18  
    1917import bx.align.axt 
    2018import bx.align.lav 
    2119 
     20assert sys.version_info[:2] >= ( 2, 4 ) 
    2221 
    2322def usage(s=None): 

  • tools/filters/lav_to_bed.py

    r1012 r1213  
    11#!/usr/bin/env python 
    2  
    32#Reads a LAV file and writes two BED files. 
    43 
    5  
    64import sys 
     5from galaxy import eggs 
    76import pkg_resources 
    87pkg_resources.require( "bx-python" ) 
    98import bx.align.lav 
     9 
     10assert sys.version_info[:2] >= ( 2, 4 ) 
    1011 
    1112def main(): 

  • tools/filters/ucsc_gene_bed_to_exon_bed.py

    r1012 r1213  
    1 #!/usr/bin/env python2.3 
     1#!/usr/bin/env python 
    22 
    33""" 
    …… 
    1717 
    1818import optparse, string, sys 
     19 
     20assert sys.version_info[:2] >= ( 2, 4 ) 
    1921 
    2022def main(): 

  • tools/filters/ucsc_gene_bed_to_intron_bed.py

    r1012 r1213  
    1 #!/usr/bin/env python2.3 
     1#!/usr/bin/env python 
    22 
    33""" 
    …… 
    1717 
    1818import optparse, string, sys 
     19 
     20assert sys.version_info[:2] >= ( 2, 4 ) 
    1921 
    2022def main(): 

  • tools/filters/ucsc_gene_table_to_intervals.py

    r1012 r1213  
    1 #!/usr/bin/env python2.3 
     1#!/usr/bin/env python 
    22 
    33""" 
    …… 
    1717 
    1818import optparse, string, sys 
     19 
     20assert sys.version_info[:2] >= ( 2, 4 ) 
    1921 
    2022def main(): 

  • tools/maf/interval_maf_to_merged_fasta.xml

    r1129 r1213  
    4848  <tests> 
    4949    <test> 
    50       <param name="input1" value="1.bed" dbkey="hg17" format="bed"/> 
     50      <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> 
    5151      <param name="maf_source" value="cached"/> 
    5252      <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/> 
    …… 
    5555    </test> 
    5656    <test> 
    57       <param name="input1" value="1.bed" dbkey="hg17" format="bed"/> 
     57      <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> 
    5858      <param name="maf_source" value="user"/> 
    5959      <param name="maf_file" value="5.maf"/> 

  • tools/maf/maf_filter.py

    r1012 r1213  
    22#Filters a MAF file according to the provided code file, which is generated in maf_filter.xml <configfiles> 
    33import sys, os, shutil 
     4from galaxy import eggs 
    45import pkg_resources; pkg_resources.require( "bx-python" ) 
    56import bx.align.maf 

  • tools/maf/maf_limit_to_species.py

    r1172 r1213  
    1 #!/usr/bin/env python2.3 
     1#!/usr/bin/env python 
    22 
    33""" 
    …… 
    1313import bx.align.maf 
    1414import sys 
     15 
     16assert sys.version_info[:2] >= ( 2, 4 ) 
    1517 
    1618def main(): 

  • tools/maf/maf_to_bed.py

    r1172 r1213  
    1 #!/usr/bin/env python2.3 
     1#!/usr/bin/env python 
    22 
    33""" 
    …… 
    88import pkg_resources; pkg_resources.require( "bx-python" ) 
    99from bx.align import maf 
     10 
     11assert sys.version_info[:2] >= ( 2, 4 ) 
    1012 
    1113def __main__(): 

  • tools/maf/maf_to_fasta_concat.py

    r1172 r1213  
    1 #!/usr/bin/env python2.3 
     1#!/usr/bin/env python 
    22 
    33""" 
    …… 
    1212from bx.align import maf 
    1313from galaxy.tools.util import maf_utilities 
     14 
     15assert sys.version_info[:2] >= ( 2, 4 ) 
    1416 
    1517def __main__(): 

  • tools/maf/maf_to_fasta_multiple_sets.py

    r1172 r1213  
    1 #!/usr/bin/env python2.3 
     1#!/usr/bin/env python 
    22 
    33""" 
    …… 
    1010from bx.align import maf 
    1111from galaxy.tools.util import maf_utilities 
     12 
     13assert sys.version_info[:2] >= ( 2, 4 ) 
    1214 
    1315def __main__(): 

  • universe_wsgi.ini.sample

    r1101 r1213  
    143143 
    144144biomart = local:/// 
     145blat2wig = pbs:///blast 
     146blat_wrapper = pbs:///blast 
    145147encode_db1 = local:/// 
    146148encode_import_all_latest_datasets1 = local:/// 
    …… 
    150152encode_import_multi-species_sequence_analysis1 = local:/// 
    151153encode_import_transcription_regulation1 = local:/// 
     154generate_coverage_report = pbs:///blast 
    152155hbvar = local:/// 
     156hist_high_quality_score = pbs:///blast 
     157megablast_wrapper = pbs:///blast 
     158megablast_xml_parser = pbs:///blast 
    153159microbial_import1 = local:/// 
     160quality_score_distribution = pbs:///blast 
    154161ucsc_table_direct1 = local:/// 
    155162ucsc_table_direct_archaea1 = local:///