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%20Scali... -# +# 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/ -- This is a commit notification from bitbucket.org. 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