1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/1f6c7be22ba9/
changeset: 1f6c7be22ba9
user: richard_burhans
date: 2012-03-22 18:03:01
summary: Updates to Human Genome Variation tools
Rename Human Genome Variation to Phenotype Association
affected #: 76 files
Diff too large to display.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/4d48285fcaa6/
changeset: 4d48285fcaa6
user: jgoecks
date: 2012-03-22 14:58:42
summary: Convert dbkeys from string to dict before checking for dbkey when including chrom info in jobs. Thanks Andrew Warren.
affected #: 1 file
diff -r ee4a47ed53712fe87c5372f667c9058147415c04 -r 4d48285fcaa65c7895768069ea197acf9d66b1ed lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -195,7 +195,7 @@
else:
# For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared.
chrom_info = None
- if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ):
+ if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ):
# Custom build.
custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ]
if 'fasta' in custom_build_dict:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/ee4a47ed5371/
changeset: ee4a47ed5371
user: greg
date: 2012-03-21 22:50:25
summary: Fix for checker for certain tools eliminated from the distribution.
affected #: 1 file
diff -r e439813f0748dd615b2a7ad18b5de9cbd68b4f9d -r ee4a47ed53712fe87c5372f667c9058147415c04 lib/galaxy/tool_shed/migrate/common.py
--- a/lib/galaxy/tool_shed/migrate/common.py
+++ b/lib/galaxy/tool_shed/migrate/common.py
@@ -9,7 +9,7 @@
from galaxy.tool_shed import install_manager
from galaxy.tool_shed.migrate.common import *
-def check_for_missing_tools( tool_panel_config, latest_tool_migration_script_number ):
+def check_for_missing_tools( tool_panel_configs, latest_tool_migration_script_number ):
# Get the 000x_tools.xml file associated with the current migrate_tools version number.
tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) )
# Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config.
@@ -20,17 +20,18 @@
if elem.tag == 'repository':
for tool_elem in elem.findall( 'tool' ):
migrated_tool_configs.append( tool_elem.get( 'file' ) )
- # Parse the proprietary tool_panel_config (the default is tool_conf.xml) and generate the list of missing tool config file names.
+ # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names.
missing_tool_configs = []
- tree = util.parse_xml( tool_panel_config )
- root = tree.getroot()
- for elem in root:
- if elem.tag == 'tool':
- missing_tool_configs = check_tool_tag_set( elem, migrated_tool_configs, missing_tool_configs )
- elif elem.tag == 'section':
- for section_elem in elem:
- if section_elem.tag == 'tool':
- missing_tool_configs = check_tool_tag_set( section_elem, migrated_tool_configs, missing_tool_configs )
+ for tool_panel_config in tool_panel_configs:
+ tree = util.parse_xml( tool_panel_config )
+ root = tree.getroot()
+ for elem in root:
+ if elem.tag == 'tool':
+ missing_tool_configs = check_tool_tag_set( elem, migrated_tool_configs, missing_tool_configs )
+ elif elem.tag == 'section':
+ for section_elem in elem:
+ if section_elem.tag == 'tool':
+ missing_tool_configs = check_tool_tag_set( section_elem, migrated_tool_configs, missing_tool_configs )
return missing_tool_configs
def check_tool_tag_set( elem, migrated_tool_configs, missing_tool_configs ):
file_path = elem.get( 'file', None )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/79236000c5bd/
changeset: 79236000c5bd
user: greg
date: 2012-03-21 21:53:26
summary: Enable the installation of the emboss_5 repository from the tool shed under the condition that any of its contained tools are defined in a local tool_conf.xml file.
affected #: 2 files
diff -r b1d33edc5dffc055867abefa7a666d0957eb0d00 -r 79236000c5bdceaf98546d66f002d5a40b006f74 lib/galaxy/tool_shed/migrate/versions/0002_tools.py
--- /dev/null
+++ b/lib/galaxy/tool_shed/migrate/versions/0002_tools.py
@@ -0,0 +1,17 @@
+"""
+The Emboss 5.0.0 tools have been eliminated from the distribution and the Emboss datatypes have been removed from
+datatypes_conf.xml.sample. You should remove the Emboss datatypes from your version of datatypes_conf.xml. The
+repositories named emboss_5 and emboss_datatypes from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu
+will be installed into your local Galaxy instance at the location discussed above by running the following command.
+
+vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
+sh ./scripts/migrate_tools/0002_tools.sh
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+"""
+
+import sys
+
+def upgrade():
+ print __doc__
+def downgrade():
+ pass
diff -r b1d33edc5dffc055867abefa7a666d0957eb0d00 -r 79236000c5bdceaf98546d66f002d5a40b006f74 scripts/migrate_tools/0002_tools.xml
--- a/scripts/migrate_tools/0002_tools.xml
+++ b/scripts/migrate_tools/0002_tools.xml
@@ -1,7 +1,7 @@
<?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" />
- <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="b94ca591877b">
+ <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="7334f6d0ac17"><tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /><tool id="EMBOSS: backtranseq2" version="5.0.0" file="emboss_backtranseq.xml" /><tool id="EMBOSS: banana3" version="5.0.0" file="emboss_banana.xml" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/b1d33edc5dff/
changeset: b1d33edc5dff
user: natefoo
date: 2012-03-21 21:52:12
summary: Add a link to the documentation about managing datasets to the disk usage display on the user prefs page.
affected #: 1 file
diff -r 17ca70b3cc5fdafa895488d3d24a2c89204acd47 -r b1d33edc5dffc055867abefa7a666d0957eb0d00 templates/user/index.mako
--- a/templates/user/index.mako
+++ b/templates/user/index.mako
@@ -37,6 +37,7 @@
%if trans.app.config.enable_quotas:
Your disk quota is: <strong>${trans.app.quota_agent.get_quota( trans.user, nice_size=True )}</strong>.
%endif
+ Is your usage more than expected? See the <a href="http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets" target="_blank">documentation</a> for tips on how to find all of the data in your account.
</p>
%endif
%else:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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