commit/galaxy-central: dan: Fix for 2ee4a6b8419b where chromInfo from custom dbkeys when no custom dbkeys have been defined would cause an error.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/1638bc414549/
changeset: 1638bc414549
user: dan
date: 2011-11-30 23:22:30
summary: Fix for 2ee4a6b8419b where chromInfo from custom dbkeys when no custom dbkeys have been defined would cause an error.
affected #: 1 file
diff -r c6f70cccce287702f18c518175bec4a5e8ace23c -r 1638bc41454922e24dfa5e01d840fbf5ea505782 lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -192,7 +192,7 @@
incoming[ "chromInfo" ] = db_dataset.file_name
else:
# For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared.
- if trans.user and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ):
+ if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ):
# Custom build.
custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ]
build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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11 years, 1 month
commit/galaxy-central: dan: Add no_options validator to built-in reference genome selector in GATK tools.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/c6f70cccce28/
changeset: c6f70cccce28
user: dan
date: 2011-11-30 19:29:21
summary: Add no_options validator to built-in reference genome selector in GATK tools.
affected #: 13 files
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/count_covariates.xml
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -146,6 +146,7 @@
<options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/depth_of_coverage.xml
--- a/tools/gatk/depth_of_coverage.xml
+++ b/tools/gatk/depth_of_coverage.xml
@@ -194,6 +194,7 @@
<options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/indel_realigner.xml
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -124,6 +124,7 @@
<options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/realigner_target_creator.xml
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -112,6 +112,7 @@
<options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history">
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/table_recalibration.xml
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -129,6 +129,7 @@
<options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/unified_genotyper.xml
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -154,6 +154,7 @@
<options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_annotator.xml
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -157,6 +157,7 @@
<options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_apply_recalibration.xml
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -109,6 +109,7 @@
<options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_combine.xml
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -121,6 +121,7 @@
<options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> --></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_eval.xml
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -160,6 +160,7 @@
<options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_filtration.xml
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -110,6 +110,7 @@
<options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_recalibrator.xml
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -156,6 +156,7 @@
<options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variants_validate.xml
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -96,6 +96,7 @@
<options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options>
+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! -->
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Provide chromInfo correctly during conversions of datasets with custom build dbkeys.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/2ee4a6b8419b/
changeset: 2ee4a6b8419b
user: jgoecks
date: 2011-11-30 19:06:12
summary: Provide chromInfo correctly during conversions of datasets with custom build dbkeys.
affected #: 1 file
diff -r 665853dfd9e12e137f26777d1a2d2167df4b4275 -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -191,7 +191,16 @@
db_datasets[ "chromInfo" ] = db_dataset
incoming[ "chromInfo" ] = db_dataset.file_name
else:
- incoming[ "chromInfo" ] = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey )
+ # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared.
+ if trans.user and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ):
+ # Custom build.
+ custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ]
+ build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] )
+ chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name
+ else:
+ # Default to built-in build.
+ chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey )
+ incoming[ "chromInfo" ] = chrom_info
inp_data.update( db_datasets )
# Determine output dataset permission/roles list
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: richard_burhans: python version of "phyloP interspecies conservation scores" tool
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/665853dfd9e1/
changeset: 665853dfd9e1
user: richard_burhans
date: 2011-11-30 18:05:59
summary: python version of "phyloP interspecies conservation scores" tool
affected #: 3 files
diff -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 -r 665853dfd9e12e137f26777d1a2d2167df4b4275 tool-data/add_scores.loc.sample
--- a/tool-data/add_scores.loc.sample
+++ b/tool-data/add_scores.loc.sample
@@ -1,21 +1,20 @@
-#This is a sample file distributed with Galaxy that enables tools to use a
-#directory of gzipped genome files for use with add_scores. You will need to
-#supply these files and then create a add_scores.loc file similar to this one
-#(store it in this directory) that points to the directories in which those
-#files are stored. The add_scores.loc file has this format (white space
-#characters are TAB characters):
+#This is a sample file distributed with Galaxy that lists the BigWig files
+#available for use with the add_scores (phyloP interspecies conservation
+#scores) tool. You will need to supply these BigWig files and then create
+#an add_scores.loc file similar to this one (store it in this directory)
+#that lists their locations. The add_scores.loc file has the following
+#format (white space characters are TAB characters):
#
-#<build><file_path>
+#<build><BigWig_file_path>
#
#So, for example, if your add_scores.loc began like this:
#
-#hg18 /galaxy/data/hg18/misc/phyloP
+#hg18 /galaxy/data/hg18/misc/phyloP44way.primate.bw
#
-#then your /galaxy/data/hg18/misc/phyloP directory would need to contain
-#the following gzipped files, among others:
+#then your /galaxy/data/hg18/misc/ directory would need to contain a
+#BigWig file named phyloP44way.primate.bw, among others:
#
-#-rw-r--r-- 1 g2data g2data 161981190 2010-03-19 12:48 chr10.phyloP44way.primate.wigFix.gz
-#-rw-r--r-- 1 g2data g2data 54091 2010-03-19 12:56 chr10_random.phyloP44way.primate.wigFix.gz
-#-rw-r--r-- 1 g2data g2data 158621990 2010-03-19 12:46 chr11.phyloP44way.primate.wigFix.gz
+#-rw-r--r-- 1 g2data g2data 6057387572 Nov 23 10:11 phyloP44way.primate.bw
#
-#hg18 /galaxy/data/hg18/misc/phyloP
+#hg18 /galaxy/data/hg18/misc/phyloP44way.primate.bw
+#hg19 /galaxy/data/hg19/misc/phyloP46way.primate.bw
diff -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 -r 665853dfd9e12e137f26777d1a2d2167df4b4275 tools/evolution/add_scores.py
--- /dev/null
+++ b/tools/evolution/add_scores.py
@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+
+import sys
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "bx-python" )
+pkg_resources.require( "numpy" )
+from bx.bbi.bigwig_file import BigWigFile
+import os
+
+################################################################################
+
+def die( message ):
+ print >> sys.stderr, message
+ sys.exit(1)
+
+def open_or_die( filename, mode='r', message=None ):
+ if message is None:
+ message = 'Error opening {0}'.format( filename )
+ try:
+ fh = open( filename, mode )
+ except IOError, err:
+ die( '{0}: {1}'.format( message, err.strerror ) )
+ return fh
+
+################################################################################
+
+class LocationFile( object ):
+ def __init__( self, filename, comment_chars=None, delimiter='\t', key_column=0 ):
+ self.filename = filename
+ if comment_chars is None:
+ self.comment_chars = ( '#' )
+ else:
+ self.comment_chars = tuple( comment_chars )
+ self.delimiter = delimiter
+ self.key_column = key_column
+ self._map = {}
+ self._populate_map()
+
+ def _populate_map( self ):
+ try:
+ with open( self.filename ) as fh:
+ line_number = 0
+ for line in fh:
+ line_number += 1
+ line = line.rstrip( '\r\n' )
+ if not line.startswith( self.comment_chars ):
+ elems = line.split( self.delimiter )
+ if len( elems ) <= self.key_column:
+ die( 'Location file {0} line {1}: less than {2} columns'.format( self.filename, line_number, self.key_column + 1 ) )
+ else:
+ key = elems.pop( self.key_column )
+ if key in self._map:
+ if self._map[key] != elems:
+ die( 'Location file {0} line {1}: duplicate key "{2}"'.format( self.filename, line_number, key ) )
+ else:
+ self._map[key] = elems
+ except IOError, err:
+ die( 'Error opening location file {0}: {1}'.format( self.filename, err.strerror ) )
+
+ def get_values( self, key ):
+ if key in self._map:
+ rval = self._map[key]
+ if len( rval ) == 1:
+ return rval[0]
+ else:
+ return rval
+ else:
+ die( 'key "{0}" not found in location file {1}'.format( key, self.filename ) )
+
+################################################################################
+
+def main():
+ input_filename, output_filename, loc_filename, loc_key, chrom_col, start_col = sys.argv[1:]
+
+ # open input, output, and bigwig files
+ location_file = LocationFile( loc_filename )
+ bigwig_filename = location_file.get_values( loc_key )
+ bwfh = open_or_die( bigwig_filename, message='Error opening BigWig file {0}'.format( bigwig_filename ) )
+ bw = BigWigFile( file=bwfh )
+ ifh = open_or_die( input_filename, message='Error opening input file {0}'.format( input_filename ) )
+ ofh = open_or_die( output_filename, mode='w', message='Error opening output file {0}'.format( output_filename ) )
+
+ # make column numbers 0-based
+ chrom_col = int( chrom_col ) - 1
+ start_col = int( start_col ) - 1
+ min_cols = max( chrom_col, start_col )
+
+ # add score column to imput file
+ line_number = 0
+ for line in ifh:
+ line_number += 1
+ line = line.rstrip( '\r\n' )
+ elems = line.split( '\t' )
+ if len( elems ) > min_cols:
+ chrom = elems[chrom_col].strip()
+ # base-0 position in chrom
+ start = int( elems[start_col] )
+ score_list = bw.get( chrom, start, start + 1 )
+ score_list_len = len( score_list )
+ if score_list_len == 1:
+ beg, end, score = score_list[0]
+ score_val = '{0:1.3f}'.format( score )
+ elif score_list_len == 0:
+ score_val = 'NA'
+ else:
+ die( '{0} line {1}: chrom={2}, start={3}, score_list_len = {4}'.format( input_filename, line_number, chrom, start, score_list_len ) )
+ print >> ofh, '\t'.join( [line, score_val] )
+ else:
+ print >> ofh, line
+
+ bwfh.close()
+ ifh.close()
+ ofh.close()
+
+################################################################################
+
+if __name__ == "__main__":
+ main()
+
diff -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 -r 665853dfd9e12e137f26777d1a2d2167df4b4275 tools/evolution/add_scores.xml
--- a/tools/evolution/add_scores.xml
+++ b/tools/evolution/add_scores.xml
@@ -1,8 +1,8 @@
<tool id="hgv_add_scores" name="phyloP" version="1.0.0"><description>interspecies conservation scores</description>
- <command>
- add_scores $input1 ${input1.metadata.dbkey} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${GALAXY_DATA_INDEX_DIR}/add_scores.loc $out_file1
+ <command interpreter="python">
+ add_scores.py "$input1" "$out_file1" "${GALAXY_DATA_INDEX_DIR}/add_scores.loc" "${input1.metadata.dbkey}" "${input1.metadata.chromCol}" "${input1.metadata.startCol}"
</command><inputs>
@@ -34,7 +34,7 @@
<help>
.. class:: warningmark
-This currently works only for build hg18.
+This currently works only for builds hg18 and hg19.
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11 years, 1 month
commit/galaxy-central: dan: Fix for frames inside of frames issue introduced in 5db0da0007fc. Seen when require_login=True.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/36998f5a7ddb/
changeset: 36998f5a7ddb
user: dan
date: 2011-11-30 16:20:15
summary: Fix for frames inside of frames issue introduced in 5db0da0007fc. Seen when require_login=True.
affected #: 1 file
diff -r 834de698004e1306b4424d0a8dbd3e7c1938ee9c -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -407,6 +407,7 @@
def _ensure_logged_in_user( self, environ, session_cookie ):
# The value of session_cookie can be one of
# 'galaxysession' or 'galaxycommunitysession'
+ # Currently this method does nothing unless session_cookie is 'galaxysession'
if session_cookie == 'galaxysession':
# TODO: re-engineer to eliminate the use of allowed_paths
# as maintenance overhead is far too high.
@@ -436,8 +437,8 @@
host = None
if host in UCSC_SERVERS:
return
- if self.request.path not in allowed_paths:
- self.response.send_redirect( url_for( controller='root', action='index' ) )
+ if self.request.path not in allowed_paths:
+ self.response.send_redirect( url_for( controller='root', action='index' ) )
def __create_new_session( self, prev_galaxy_session=None, user_for_new_session=None ):
"""
Create a new GalaxySession for this request, possibly with a connection
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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11 years, 1 month
commit/galaxy-central: greg: Revert 2 changes made in 5db0da0007fc in an attempt to correct the broken behavior of rendering Galaxy correctly when using apache proxying, possibly in adition to requiring users to login.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/834de698004e/
changeset: 834de698004e
user: greg
date: 2011-11-30 15:16:37
summary: Revert 2 changes made in 5db0da0007fc in an attempt to correct the broken behavior of rendering Galaxy correctly when using apache proxying, possibly in adition to requiring users to login.
affected #: 2 files
diff -r de03f821784bcbe04a7514ad3d8e43fb1b635e4b -r 834de698004e1306b4424d0a8dbd3e7c1938ee9c lib/galaxy/web/controllers/user.py
--- a/lib/galaxy/web/controllers/user.py
+++ b/lib/galaxy/web/controllers/user.py
@@ -358,7 +358,7 @@
else:
refresh_frames = [ 'masthead', 'history' ]
message, status, user, success = self.__validate_login( trans, webapp, **kwd )
- if success and referer and not referer.startswith( url_for( trans.request.base + url_for( controller='user', action='logout' ) ) ):
+ if success and referer and not referer.startswith( trans.request.base + url_for( controller='user', action='logout' ) ):
redirect_url = referer
elif success:
redirect_url = url_for( '/' )
diff -r de03f821784bcbe04a7514ad3d8e43fb1b635e4b -r 834de698004e1306b4424d0a8dbd3e7c1938ee9c templates/webapps/galaxy/base_panels.mako
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -142,7 +142,11 @@
menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] )
if app.config.get_bool( 'enable_tracks', False ):
menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] )
- menu_options.append( [ 'Logout', h.url_for( controller='/user', action='logout', webapp='galaxy' ), "_top" ] )
+ if app.config.require_login:
+ logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout', webapp='galaxy' )
+ else:
+ logout_url = h.url_for( controller='/user', action='logout', webapp='galaxy' )
+ menu_options.append( [ 'Logout', logout_url, "_top" ] )
menu_options.append( None )
menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] )
menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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11 years, 1 month
commit/galaxy-central: dan: Minor fix for 04e8ed0cd930.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/b751663f3f64/
changeset: b751663f3f64
user: dan
date: 2011-11-29 23:35:14
summary: Minor fix for 04e8ed0cd930.
affected #: 1 file
diff -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 -r b751663f3f64ea794951f57b2ff4686debd1b455 tools/sr_mapping/PerM.xml
--- a/tools/sr_mapping/PerM.xml
+++ b/tools/sr_mapping/PerM.xml
@@ -13,7 +13,7 @@
#if $s.space == "color"
"${s.sourceOfRef.index.fields.path}"
#elif $s.space == "base"
- "${s.sourceOfRef.index.fields.path"
+ "${s.sourceOfRef.index.fields.path}"
#end if
#end if
#if $s.mate.singleOrPairs == "single":
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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11 years, 2 months
commit/galaxy-central: dan: Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/04e8ed0cd930/
changeset: 04e8ed0cd930
user: dan
date: 2011-11-29 23:30:14
summary: Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools.
affected #: 13 files
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/metag_tools/megablast_wrapper.xml
--- a/tools/metag_tools/megablast_wrapper.xml
+++ b/tools/metag_tools/megablast_wrapper.xml
@@ -2,7 +2,7 @@
<description> compare short reads against htgs, nt, and wgs databases</description><command interpreter="python">
megablast_wrapper.py
- --db_build="${ filter( lambda x: str( x[0] ) == str( $source_select ), $__app__.tool_data_tables[ 'blastdb' ].get_fields() )[0][-1] }"
+ --db_build="${source_select.fields.path}"
--input=$input_query
--word_size=$word_size
--identity_cutoff=$iden_cutoff
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_rna/tophat_color_wrapper.xml
--- a/tools/ngs_rna/tophat_color_wrapper.xml
+++ b/tools/ngs_rna/tophat_color_wrapper.xml
@@ -19,7 +19,7 @@
#if $refGenomeSource.genomeSource == "history":
--own-file=$refGenomeSource.ownFile
#else:
- --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes_color' ].get_fields() )[0][-1] }"
+ --indexes-path="${refGenomeSource.index.fields.path}"
#end if
## Are reads single-end or paired?
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_rna/tophat_wrapper.xml
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -17,7 +17,7 @@
#if $refGenomeSource.genomeSource == "history":
--own-file=$refGenomeSource.ownFile
#else:
- --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }"
+ --indexes-path="${refGenomeSource.index.fields.path}"
#end if
## Are reads single-end or paired?
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_simulation/ngs_simulation.xml
--- a/tools/ngs_simulation/ngs_simulation.xml
+++ b/tools/ngs_simulation/ngs_simulation.xml
@@ -4,7 +4,7 @@
<command interpreter="python">
ngs_simulation.py
#if $in_type.input_type == "built-in"
- --input="${ filter( lambda x: str( x[0] ) == str( $in_type.genome ), $__app__.tool_data_tables[ 'ngs_sim_fasta' ].get_fields() )[0][-1] }"
+ --input="${in_type.genome.fields.path}"
--genome=$in_type.genome
#else
--input=$in_type.input1
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/picard/rgPicardASMetrics.xml
--- a/tools/picard/rgPicardASMetrics.xml
+++ b/tools/picard/rgPicardASMetrics.xml
@@ -6,7 +6,7 @@
#if $genomeSource.refGenomeSource == "history":
--ref-file "$genomeSource.ownFile"
#else
- --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
+ --ref "${genomeSource.index.fields.path}"
#end if
</command><requirements><requirement type="package">picard</requirement></requirements>
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/PerM.xml
--- a/tools/sr_mapping/PerM.xml
+++ b/tools/sr_mapping/PerM.xml
@@ -11,9 +11,9 @@
$s.sourceOfRef.ref
#else
#if $s.space == "color"
- "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_color_indexes' ].get_fields() )[0][-1] }"
+ "${s.sourceOfRef.index.fields.path}"
#elif $s.space == "base"
- "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_base_indexes' ].get_fields() )[0][-1] }"
+ "${s.sourceOfRef.index.fields.path"
#end if
#end if
#if $s.mate.singleOrPairs == "single":
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bowtie_color_wrapper.xml
--- a/tools/sr_mapping/bowtie_color_wrapper.xml
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml
@@ -58,7 +58,7 @@
#end if
#else
##use pre-built index
- --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes_color' ].get_fields() )[0][-1] }"
+ --ref="${refGenomeSource.index.fields.path}"
#end if
--paired=$singlePaired.sPaired
#if $singlePaired.sPaired == "single":
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bowtie_wrapper.xml
--- a/tools/sr_mapping/bowtie_wrapper.xml
+++ b/tools/sr_mapping/bowtie_wrapper.xml
@@ -61,8 +61,7 @@
#end if
#else
##use pre-built index
- ##--ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }"
- --ref="${ refGenomeSource.index.fields.path }"
+ --ref="${refGenomeSource.index.fields.path}"
#end if
--paired=$singlePaired.sPaired
#if $singlePaired.sPaired == "single":
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bwa_color_wrapper.xml
--- a/tools/sr_mapping/bwa_color_wrapper.xml
+++ b/tools/sr_mapping/bwa_color_wrapper.xml
@@ -14,7 +14,7 @@
--dbkey=$dbkey
#else:
##use precomputed indexes
- --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes_color' ].get_fields() )[0][-1] }"
+ --ref="${genomeSource.indices.fields.path}"
--do_not_build_index
#end if
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bwa_wrapper.xml
--- a/tools/sr_mapping/bwa_wrapper.xml
+++ b/tools/sr_mapping/bwa_wrapper.xml
@@ -17,7 +17,7 @@
--dbkey=$dbkey
#else:
##use precomputed indexes
- --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }"
+ --ref="${genomeSource.indices.fields.path}"
--do_not_build_index
#end if
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/lastz_paired_reads_wrapper.xml
--- a/tools/sr_mapping/lastz_paired_reads_wrapper.xml
+++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml
@@ -12,7 +12,7 @@
--input1=$source.input1
--ref_sequences=$input1.metadata.sequences
#else:
- --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }"
+ --input1="${source.input1_2bit.fields.path}"
#end if
--output=$output1
--lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR}
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/lastz_wrapper.xml
--- a/tools/sr_mapping/lastz_wrapper.xml
+++ b/tools/sr_mapping/lastz_wrapper.xml
@@ -12,7 +12,7 @@
--input1=$source.input1
--ref_sequences=$input1.metadata.sequences
#else:
- --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }"
+ --input1="${source.input1_2bit.fields.path}"
--ref_sequences="None"
#end if
#if $params.source_select=="pre_set":
diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/mosaik.xml
--- a/tools/sr_mapping/mosaik.xml
+++ b/tools/sr_mapping/mosaik.xml
@@ -13,7 +13,7 @@
#end if
MosaikBuild -fr
#if $genomeSource.refGenomeSource == 'indexed':
- ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] }
+ ${genomeSource.indexReference.fields.path}
#else:
$genomeSource.historyReference
#end if
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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11 years, 2 months
commit/galaxy-central: dan: Fix tab to 4 spaces in tool_conf.xml.sample.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0532712a2708/
changeset: 0532712a2708
user: dan
date: 2011-11-29 23:07:06
summary: Fix tab to 4 spaces in tool_conf.xml.sample.
affected #: 1 file
diff -r 9ee4e2e41fd60c75c2b87d55648c538438809430 -r 0532712a2708855e77d1a6a9a1099121983458a4 tool_conf.xml.sample
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -469,7 +469,7 @@
<tool file="human_genome_variation/lps.xml" /><tool file="human_genome_variation/hilbertvis.xml" /><tool file="human_genome_variation/freebayes.xml" />
- <tool file="human_genome_variation/master2pg.xml" />
+ <tool file="human_genome_variation/master2pg.xml" /></section><section name="Genome Diversity" id="gd"><tool file="genome_diversity/extract_primers.xml" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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