1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fd24924488a5/
Changeset: fd24924488a5
User: davebgx
Date: 2014-04-02 15:13:33
Summary: Fix issue in migrations where the same complex repository would be installed once for each repository that depends on it.
Affected #: 1 file
diff -r 6b9ebef104e83067a614e0f98b466d7f99050743 -r fd24924488a575516696595a8e61e276d795f2b5 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -57,8 +57,9 @@
print error_message
else:
root = tree.getroot()
- self.tool_shed_url = suc.get_url_from_tool_shed( self.app, root.get( 'name' ) )
- self.tool_shed = suc.clean_tool_shed_url( self.tool_shed_url )
+ defined_tool_shed_url = root.get( 'name' )
+ self.tool_shed_url = suc.get_url_from_tool_shed( self.app, defined_tool_shed_url )
+ self.tool_shed = suc.clean_tool_shed_url( defined_tool_shed_url )
self.repository_owner = common_util.REPOSITORY_OWNER
index, self.shed_config_dict = suc.get_shed_tool_conf_dict( app, self.migrated_tools_config )
# Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/383bd3e846b9/
Changeset: 383bd3e846b9
User: greg
Date: 2014-04-02 13:22:01
Summary: Don't require categories and status attributes to be associated with a repository being imported from a capsule, although they should always exist.
Affected #: 1 file
diff -r 69e3ed08c38219005aba4952716cc7f4afa184f0 -r 383bd3e846b97f5dc72422ff47dfdd98e3f132f5 lib/tool_shed/util/repository_maintenance_util.py
--- a/lib/tool_shed/util/repository_maintenance_util.py
+++ b/lib/tool_shed/util/repository_maintenance_util.py
@@ -135,7 +135,8 @@
( str( name ), str( username ))
import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) )
else:
- if repository_archive_dict[ 'status' ] is None:
+ status = repository_archive_dict.get( 'status', None )
+ if status is None:
# The repository does not yet exist in this Tool Shed and the current user is authorized to import
# the current archive file.
type = repository_archive_dict.get( 'type', 'unrestricted' )
@@ -154,7 +155,7 @@
# exist in the current Tool Shed, the category will not be created, so it will not be associated with
# the repository.
category_ids = []
- category_names = repository_archive_dict[ 'category_names' ]
+ category_names = repository_archive_dict.get( 'category_names', [] )
for category_name in category_names:
category = suc.get_category_by_name( trans, category_name )
if category is None:
@@ -182,8 +183,7 @@
else:
# The repository either already exists in this Tool Shed or the current user is not authorized to create it.
ok = True
- results_message += 'Import not necessary: repository status for this Tool Shed is: %s.' % \
- str( repository_archive_dict[ 'status' ] )
+ results_message += 'Import not necessary: repository status for this Tool Shed is: %s.' % str( status )
import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) )
return import_results_tups
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6ecb31395618/
Changeset: 6ecb31395618
User: Jeremy Goecks
Date: 2014-04-01 20:45:34
Summary: Fix for 615d504: do not use downsampling when all reads can be returned.
Affected #: 1 file
diff -r 6f4c44ef44a3d2df0778c0d4b6b27efc8014c1db -r 6ecb313956184d2d78f503ee918618d218ed9791 lib/galaxy/visualization/data_providers/genome.py
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -971,7 +971,10 @@
threshold = float( max_vals )/ num_reads
iterator = itertools.chain( iter( [ first_read ] ), iterator )
- if iterator_type == 'sequential':
+ # Use specified iterator type, save for when threshold is >= 1.
+ # A threshold of >= 1 indicates all reads are to be returned, so no
+ # sampling needed and seqential iterator will be used.
+ if iterator_type == 'sequential' or threshold >= 1:
read_iterator = iterator
elif iterator_type == 'random':
read_iterator = _random_read_iterator( iterator, threshold )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/803730aa8abf/
Changeset: 803730aa8abf
User: davebgx
Date: 2014-04-01 19:08:02
Summary: Pass shell=True to subprocess.Popen, which eliminates the need to escape double quotes and prepend /bin/sh -c to a tool dependency shell command.
Affected #: 1 file
diff -r 7755367b06981f35fbc6911935513439c7e5445f -r 803730aa8abfa842bfceb8d4563b906d3bdf42d1 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
@@ -300,13 +300,13 @@
retain control over the process. This method is named "complex" because it uses queues and
threads to execute a command while capturing and displaying the output.
"""
- wrapped_command = shlex.split( '/bin/sh -c "%s"' % str( command ) )
# Launch the command as subprocess. A bufsize of 1 means line buffered.
- process_handle = subprocess.Popen( wrapped_command,
+ process_handle = subprocess.Popen( str( command ),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
bufsize=1,
close_fds=False,
+ shell=True,
cwd=state.env[ 'lcwd' ] )
pid = process_handle.pid
# Launch the asynchronous readers of the process' stdout and stderr.
@@ -616,10 +616,10 @@
with lcd( current_dir ):
with settings( warn_only=True ):
for tarball_name in tarball_names:
- # Use raw strings so that python won't automatically unescape the \", needed because handle_command wraps
- # the provided command in /bin/sh -c "<command>".
+ # Use raw strings so that python won't automatically unescape the quotes before passing the command
+ # to subprocess.Popen.
cmd = r'''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS;
- Rscript -e \"install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)\"''' % \
+ Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % \
( str( tarball_name ) )
cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
@@ -675,10 +675,10 @@
# gem file from rubygems.org with or without version number
if gem_version:
# Specific ruby gem version was requested.
- # Use raw strings so that python won't automatically unescape the \", needed because handle_command wraps
- # the provided command in /bin/sh -c "<command>".
+ # Use raw strings so that python won't automatically unescape the quotes before passing the command
+ # to subprocess.Popen.
cmd = r'''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
- gem install %s --version \"=%s\"''' % ( gem, gem_version)
+ gem install %s --version "=%s"''' % ( gem, gem_version)
else:
# no version number given
cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
@@ -835,8 +835,8 @@
return_code = handle_command( app, tool_dependency, install_dir, full_setup_command )
if return_code:
return tool_dependency
- # Use raw strings so that python won't automatically unescape the \", needed because handle_command wraps
- # the provided command in /bin/sh -c "<command>".
+ # Use raw strings so that python won't automatically unescape the quotes before passing the command
+ # to subprocess.Popen.
site_packages_command = r"%s -c 'import os, sys; print os.path.join(sys.prefix, \"lib\", \"python\" + sys.version[:3], \"site-packages\")'" % os.path.join( venv_directory, "bin", "python" )
output = handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True )
if output.return_code:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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