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Author SHA1 Message Date
Anton Nekrutenko 076398c821 Changed grouping output to tabular 2009-01-22 12:46:37 -05:00
Nate Coraor 19e1000818 Update welcome page with Anton's copy from security 2009-01-22 12:29:44 -05:00
Greg Von Kuster 7e11ac9d9f Fixes in the upload tool for removing temporary files. 2009-01-22 11:22:39 -05:00
Greg Von Kuster 705994a0fc Fixes for formatting end of line chars in html when displaying dataset.info. Also change the biomart tool version. 2009-01-22 08:50:52 -05:00
Greg Von Kuster 7e21fb74a3 Fixes for Biomart and UCSC to better ensure the data type is correctly set. A data type of "tabular" is now the default, and data will be sniffed if this is the data type. 2009-01-21 17:03:39 -05:00
Wen-Yu Chung 498fbac868 remove the usage of hast tables in the fasta-tools 2009-01-19 15:47:02 -05:00
Nate Coraor 4bb40fba54 Flush newly created users directly in __get_or_create_remote_user, solves 
the new user creation when using remote_user bug found by Ross Lazarus.
Also, external users get a random password now (makes the secret key
safer if a bad guy gets the database).
 2009-01-19 11:47:29 -05:00
Guruprasad Anada 50b46e60e3 Removed an option from grouping tool, which is now part of the LCA tool under Taxonomy. 2009-01-16 13:30:01 -05:00
Greg Von Kuster fa6155cc3f Eliminate the use of the "order=" for the sniffers in datatypes.conf - since we've moved from using an ini file to an xml file, ordering is implicit. 2009-01-15 14:23:53 -05:00
Guruprasad Anada ee8779987e More changes to mutability tool. 2009-01-15 13:10:04 -05:00
Greg Von Kuster b7aaa17bc3 Change History.copy() back to use datasets rather than active_datasets. Add checks in set_peek() to properly set peek on purged datasets. Fixes sharing a history that contains purged datasets. 2009-01-15 10:49:01 -05:00
Guruprasad Anada d46171ea21 Fixed a bug in microsatellite mutability tool. 2009-01-15 10:42:22 -05:00
Greg Von Kuster 87a77c62f2 Add a SelectToolParameterWrapper object and a wrap method to Tool.execute() that allows for things like the following in tool configs: 
<outputs>
  <data format="input" name="output" label="Blat on {<input_param>.value_label}" />
</outputs>

Also replace EOL chars with <br> in a tool's output data.info so that they are displayed in HTML.
 2009-01-14 17:20:22 -05:00
Greg Von Kuster 6976c383ad When copying a history, only copy active_datasets - fixes sharing a history containing purged datasets. 2009-01-14 16:15:51 -05:00
Nate Coraor 8e376dea50 Improvements to job recovery and clarification of the false path's job id 2009-01-14 10:49:14 -05:00
Nate Coraor 19e13df63a Move setting of the working directory to the wrapper's init method instead. 2009-01-14 08:50:31 -05:00
Nate Coraor f37e747d49 Set the working directory in the wrapper when recovering jobs at startup. 2009-01-14 08:43:00 -05:00
Guruprasad Anada e25946e9b9 Tool to find the least common ancestor added under Taxonomy section. 2009-01-13 12:18:08 -05:00
Greg Von Kuster 8001f0110d Eliminate boilerplate code to track memory_usage, keeping the class and config settings for possible future use. 2009-01-13 11:33:17 -05:00
Greg Von Kuster 051a78bc39 Add new tool config for flymine production server. 2009-01-13 10:55:08 -05:00
Greg Von Kuster a0ba39f0f8 Fix for data source tools that were broken due to the new "outputs_to_working_directory" config setting. Request parameters are now temporarily written to the output dataset if this config setting is either True or False. 2009-01-13 10:34:39 -05:00
Nate Coraor 9dbad8f623 galaxy.config.resolve_path is not absolute... 2009-01-09 17:18:18 -05:00
Nate Coraor 2f0f2dfb9a Make the PBS script/stdout/stderr directory configurable. 2009-01-09 17:08:49 -05:00
Nate Coraor 1423af2fd5 Add an option to override the output dataset(s) path, so they may be written to 
the working directory.  This allows administrators to mount datasets read-only
on cluster nodes.
 2009-01-09 15:59:29 -05:00
Nate Coraor 68d4d00997 Allow upstream proxy to set wsgi.url_scheme, so link generation is 
correct if the proxy uses a different transport with clients than it
does with Galaxy.  This doesn't work automatically.  In Apache, you'd
need to set the header yourself:

  RequestHeader set X-URL-SCHEME https

For a discussion on how this affects links to the UCSC Genome Browser,
see:

http://mail.bx.psu.edu/pipermail/galaxy-user/2009-January/000430.html
 2009-01-09 14:07:16 -05:00
Nate Coraor 76a02fcf76 Fix from James Casbon for a problem he has experienced when using remote_user (a new user creation seems to be attempted before a session exists). 2009-01-08 11:04:19 -05:00
Greg Von Kuster ad33e0bc5a Fix for my last commit. 2009-01-07 15:33:35 -05:00
Greg Von Kuster 86c7a80c31 Add support for NCBI Blast XML data format. 2009-01-07 12:20:35 -05:00
Greg Von Kuster fd25567658 log exceptions when removing temporary files when upload fails. 2009-01-06 13:29:03 -05:00
Greg Von Kuster 3ed821a39d Better exception handling, messaging for upload utility. 2009-01-06 11:35:49 -05:00
Guruprasad Anada cc80d63745 Added a new option to the grouping tool to facilitate picking of random entries from columns not chosen for either grouping or aggregate operations. 2009-01-06 11:11:24 -05:00
Nate Coraor d337613eeb megablast fix from Anton 2009-01-05 15:26:17 -05:00
Nate Coraor 80f42e4199 Since tempfiles seem to occasionally be left behind, allow logging of 
open tempfiles, including a traceback (to determine callers) if
LOG_TEMPFILES is set in the environment when Galaxy starts.  This
should be considered temporary and will be removed when it's determined
where/how this happens.
 2008-12-23 13:28:27 -05:00
Guruprasad Anada 54dc919413 Script to enumerate GOPS JOIN jobs that could have returned an incorrect result before the issue with minimum overlap was fixed last week. 2008-12-22 13:35:01 -05:00
Guruprasad Anada 8c7c765480 Modified sort options in grouping tool to work correctly on older and newer versions of unix sort. Also included functional tests. 2008-12-22 12:15:02 -05:00
Wen-Yu Chung b31191d4bd fix for short read score distribution tool. restore test data. 2008-12-19 14:25:43 -05:00
Wen-Yu Chung 170f9d2d77 fixed for short read build distribution tool. remove unused arrays. also update test data output. 2008-12-19 12:25:52 -05:00
Greg Von Kuster 4dc6d12546 Yet another fix for the deleted histories report. 2008-12-19 11:05:54 -05:00
Greg Von Kuster 98135a27bb Fix for deleted histories report in the system controller. 2008-12-19 10:55:42 -05:00
Greg Von Kuster 373519b650 Add security to reports app, fixes reports. 2008-12-19 09:53:32 -05:00
Greg Von Kuster 42ca95a373 Enhance the tool panel, now supports following tags: 
<toolbox>
    <tool file="data_source/upload.xml"/>            # tools outside sections
    <label text="Basic Tools" id="basic_tools" />    # labels outside sections
    <workflow id="529fd61ab1c6cc36" />               # workflows outside sections
    <section name="Get Data" id="getext">            # sections
        <tool file="data_source/biomart.xml" />      # tools inside sections
        <label text="In Section" id="in_section" />  # labels inside sections
        <workflow id="adb5f5c93f827949" />           # workflows inside sections
    </section>
</toolbox>
 2008-12-18 16:35:26 -05:00
Greg Von Kuster 5a1637dc28 Pass in a session cookie name when building the app - this enables the Galaxy session to use a different cookie from the Galaxy reports session. Also add exception handling to decoding the session key so server errors won't result from attempting to retrieve an invalid session key from the db. 2008-12-18 09:32:43 -05:00
Guruprasad Anada 14e8c4fcad speed enhancement for incorrect_gops_jobs script. 2008-12-17 12:13:38 -05:00
Guruprasad Anada 42263dd8b2 Fix for a minor bug in my previous commit. 2008-12-17 11:25:35 -05:00
Guruprasad Anada b84c1cb2ab Enhancing incorrect_Gops_job script to output only those jobs whose output has changed since the BitSetSafeReaderWrapper was fixed. 2008-12-17 11:01:57 -05:00
James Taylor d2dfd2db26 Allow workflows to recognize "data_meta" filters in dynamic options as 
forcing runtime validation.
 2008-12-16 17:30:19 -05:00
Nate Coraor cbaf4609d9 Update bx-python to r459 2008-12-16 14:31:00 -05:00
Greg Von Kuster ae84867027 Server errors thrown when switching between Galaxy and reports in the same browser was due to the id_secret being different in the Galaxy config and the reports config, so add comments to ensure this is not repeated. 2008-12-16 10:04:30 -05:00
Greg Von Kuster c730aad62c Some code cleanup in framework/__init__.py 2008-12-15 17:04:06 -05:00
Greg Von Kuster c90a09e782 Fix for the users reports. 2008-12-15 11:25:47 -05:00