2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c4145b92bc2a/
Changeset: c4145b92bc2a
Branch: trevorw/specify-thirdparty-cookies-must-not-be-b-1392909850239
User: trevorw
Date: 2014-02-20 16:27:57
Summary: specify third-party cookies must not be blocked - repository.py
third-party cookies are normally (and hopefully) disabled for privacy
Affected #: 1 file
diff -r eae95d5fa975e1eef4de219564cb976720f18440 -r c4145b92bc2a9e63778950aef4d53723bcd353ee lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -870,7 +870,7 @@
'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) )
else:
- message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url
+ message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable third-party cookies in your browser. ' % galaxy_url
return trans.show_error_message( message )
if changeset_revision == repository.tip( trans.app ):
# If changeset_revision is the repository tip, there are no additional updates.
@@ -2047,7 +2047,7 @@
return trans.response.send_redirect( url )
else:
message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url
- message += 'You may need to enable cookies in your browser. '
+ message += 'You may need to enable third-party cookies in your browser. '
status = 'error'
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_valid_categories',
https://bitbucket.org/galaxy/galaxy-central/commits/952558f0dc0b/
Changeset: 952558f0dc0b
User: greg
Date: 2014-02-20 17:14:38
Summary: Merged in trevorw/galaxy-central-2/trevorw/specify-thirdparty-cookies-must-not-be-b-1392909850239 (pull request #326)
specify third-party cookies must not be blocked - repository.py
Affected #: 1 file
diff -r 3158b15d961f6bef5db25b26d4bc0593f1b58d57 -r 952558f0dc0ba52355e87ef2d0ccef37f7f51bec lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -870,7 +870,7 @@
'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) )
else:
- message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url
+ message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable third-party cookies in your browser. ' % galaxy_url
return trans.show_error_message( message )
if changeset_revision == repository.tip( trans.app ):
# If changeset_revision is the repository tip, there are no additional updates.
@@ -2047,7 +2047,7 @@
return trans.response.send_redirect( url )
else:
message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url
- message += 'You may need to enable cookies in your browser. '
+ message += 'You may need to enable third-party cookies in your browser. '
status = 'error'
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_valid_categories',
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/3158b15d961f/
Changeset: 3158b15d961f
User: dan
Date: 2014-02-20 17:07:16
Summary: Fix for ToolEvaluator with optional Dataset Input selected.
Affected #: 1 file
diff -r 3789ce7ddf1ac171a10956989818b4425486c44d -r 3158b15d961f6bef5db25b26d4bc0593f1b58d57 lib/galaxy/tools/evaluation.py
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -181,9 +181,11 @@
tool=self,
name=input.name
)
- real_path = dataset.file_name
- if real_path in input_dataset_paths:
- wrapper_kwds[ "dataset_path" ] = input_dataset_paths[ real_path ]
+ if dataset:
+ #A None dataset does not have a filename
+ real_path = dataset.file_name
+ if real_path in input_dataset_paths:
+ wrapper_kwds[ "dataset_path" ] = input_dataset_paths[ real_path ]
input_values[ input.name ] = \
DatasetFilenameWrapper( dataset, **wrapper_kwds )
elif isinstance( input, SelectToolParameter ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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4 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c82a791e23a6/
Changeset: c82a791e23a6
User: natefoo
Date: 2014-02-20 16:51:42
Summary: Remove obsolete DRMAA_python egg from eggs.ini.
Affected #: 1 file
diff -r 9c673e0ea8919fea6941f24fdf6936686840bb71 -r c82a791e23a62b0821ad0b0f1bccc49541eb3583 eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -9,12 +9,11 @@
[general]
repository = http://eggs.galaxyproject.org
; these eggs must be scrambled for your local environment
-no_auto = pbs_python DRMAA_python
+no_auto = pbs_python
[eggs:platform]
bx_python = 0.7.1
Cheetah = 2.2.2
-DRMAA_python = 0.2
MarkupSafe = 0.12
mercurial = 2.2.3
MySQL_python = 1.2.3c1
https://bitbucket.org/galaxy/galaxy-central/commits/59e325832026/
Changeset: 59e325832026
User: natefoo
Date: 2014-02-20 16:52:19
Summary: Minor updates to comments/documentation in universe_wsgi.ini.sample
Affected #: 1 file
diff -r c82a791e23a62b0821ad0b0f1bccc49541eb3583 -r 59e325832026a2f3cbdb031eef02c8ef690c3f03 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -3,7 +3,7 @@
# environment. To tune the application for a multi-user production
# environment, see the documentation at:
#
-# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server
+# http://usegalaxy.org/production
#
# Throughout this sample configuration file, except where stated otherwise,
@@ -11,7 +11,7 @@
# values are set to the default value.
# Examples of many of these options are explained in more detail in the wiki:
#
-# http://wiki.g2.bx.psu.edu/Admin/Config
+# https://wiki.galaxyproject.org/Admin/Config
#
# Config hackers are encouraged to check there before asking for help.
@@ -140,9 +140,12 @@
# Other tool config files must include the tool_path as an attribute in the <toolbox> tag.
#tool_path = tools
-# Path to the directory in which managed tool dependencies are placed. To use
-# the dependency system, see the documentation at:
-# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
+# Path to the directory in which tool dependencies are placed. This is used by
+# the tool shed to install dependencies and can also be used by administrators
+# to manually install or link to dependencies. For details, see:
+# https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
+# If this option is not set to a valid path, installing tools with dependencies
+# from the Tool Shed will fail.
#tool_dependency_dir = None
# Enable automatic polling of relative tool sheds to see if any updates
@@ -169,7 +172,7 @@
# Directory where data used by tools is located, see the samples in that
# directory and the wiki for help:
-# http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
+# https://wiki.galaxyproject.org/Admin/DataIntegration
#tool_data_path = tool-data
# Directory where chrom len files are kept, currently mainly used by trackster
@@ -196,6 +199,10 @@
# directory.
#cluster_files_directory = database/pbs
+# Mako templates are compiled as needed and cached for reuse, this directory is
+# used for the cache
+#template_cache_path = database/compiled_templates
+
# External service types config file, defines what types of external_services configurations
# are available in Galaxy.
#external_service_type_config_file = external_service_types_conf.xml
@@ -532,7 +539,7 @@
# -- Data Libraries
# These library upload options are described in much more detail in the wiki:
-# http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
+# https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
# Add an option to the library upload form which allows administrators to
# upload a directory of files.
@@ -590,7 +597,7 @@
# User authentication can be delegated to an upstream proxy server (usually
# Apache). The upstream proxy should set a REMOTE_USER header in the request.
# Enabling remote user disables regular logins. For more information, see:
-# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
+# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
#use_remote_user = False
# If use_remote_user is enabled and your external authentication
@@ -618,7 +625,7 @@
# users (email addresses). These users will have access to the Admin section
# of the server, and will have access to create users, groups, roles,
# libraries, and more. For more information, see:
-# http://wiki.g2.bx.psu.edu/Admin/Interface
+# https://wiki.galaxyproject.org/Admin/Interface
#admin_users = None
# Force everyone to log in (disable anonymous access).
@@ -723,8 +730,8 @@
# separate Galaxy into multiple processes. There are more than one way to do
# this, and they are explained in detail in the documentation:
#
-# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal…
-#
+# https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
+
# By default, Galaxy manages and executes jobs from within a single process and
# notifies itself of new jobs via in-memory queues. Jobs are run locally on
# the system on which Galaxy is started. Advanced job running capabilities can
https://bitbucket.org/galaxy/galaxy-central/commits/3789ce7ddf1a/
Changeset: 3789ce7ddf1a
User: natefoo
Date: 2014-02-20 16:52:31
Summary: Remove empty/renamed sections in tool_conf.xml.main
Affected #: 1 file
diff -r 59e325832026a2f3cbdb031eef02c8ef690c3f03 -r 3789ce7ddf1ac171a10956989818b4425486c44d tool_conf.xml.main
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -154,9 +154,6 @@
<tool file="multivariate_stats/kpca.xml" /><tool file="multivariate_stats/kcca.xml" /></section>
- <section id="clustal" name="Multiple Alignments">
- <tool file="rgenetics/rgClustalw.xml" />
- </section><section id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" />
@@ -227,8 +224,4 @@
<tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section>
- <section id="ngs-rna-tools" name="NGS: RNA Analysis">
- <label id="rna_seq" text="RNA-seq" />
- <label id="filtering" text="Filtering" />
- </section></toolbox>
https://bitbucket.org/galaxy/galaxy-central/commits/15e8a74a9521/
Changeset: 15e8a74a9521
Branch: stable
User: natefoo
Date: 2014-02-20 16:52:31
Summary: Remove empty/renamed sections in tool_conf.xml.main
Affected #: 1 file
diff -r a89bbdfd4a71671d575d9a0a3a9f8abeba3f7b21 -r 15e8a74a95215bf2cc775e9848ca4a5ecc7e945f tool_conf.xml.main
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -154,9 +154,6 @@
<tool file="multivariate_stats/kpca.xml" /><tool file="multivariate_stats/kcca.xml" /></section>
- <section id="clustal" name="Multiple Alignments">
- <tool file="rgenetics/rgClustalw.xml" />
- </section><section id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" />
@@ -227,8 +224,4 @@
<tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section>
- <section id="ngs-rna-tools" name="NGS: RNA Analysis">
- <label id="rna_seq" text="RNA-seq" />
- <label id="filtering" text="Filtering" />
- </section></toolbox>
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/eae95d5fa975/
Changeset: eae95d5fa975
User: dannon
Date: 2014-02-20 01:33:27
Summary: Update boto to 2.25.0 in anticipation of supporting VPC
Affected #: 1 file
diff -r 85c38536c31583ef06db42c1f54d6248b79f96a5 -r eae95d5fa975e1eef4de219564cb976720f18440 eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -35,7 +35,7 @@
amqp = 1.4.3
anyjson = 0.3.3
Beaker = 1.4
-boto = 2.5.2
+boto = 2.25.0
decorator = 3.1.2
docutils = 0.7
drmaa = 0.6
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/ee315625cf4e/
Changeset: ee315625cf4e
User: dan
Date: 2014-02-19 22:15:48
Summary: Fix for DatasetListWrapper with optional inputs.
Affected #: 1 file
diff -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b -r ee315625cf4e394bca8a05f25c82e78c978ed50c lib/galaxy/tools/wrappers.py
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -206,10 +206,12 @@
datasets = [datasets]
def to_wrapper( dataset ):
- real_path = dataset.file_name
wrapper_kwds = kwargs.copy()
- if real_path in dataset_paths:
- wrapper_kwds[ "dataset_path" ] = dataset_paths[ real_path ]
+ if dataset:
+ #A None dataset does not have a filename
+ real_path = dataset.file_name
+ if real_path in dataset_paths:
+ wrapper_kwds[ "dataset_path" ] = dataset_paths[ real_path ]
return DatasetFilenameWrapper( dataset, **wrapper_kwds )
list.__init__( self, map( to_wrapper, datasets ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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