Jeremy Goecks
b393ea6bbe
Trackster: bug fixes for read filtering.
2012-03-08 12:29:13 -05:00
Jeremy Goecks
047c1bff2f
Enable fasta_to_len conversion to use only first word in title; this is standards compliant and used by default for automatic conversion.
2012-03-08 11:09:14 -05:00
Greg Von Kuster
ea4db057f5
Fix for populating the tool panel and generating the integrated_tool_panel.xml file.
2012-03-07 13:35:34 -05:00
Dannon Baker
680a0ebbd5
Workflows: Multiple run workflows now copy input datasets to newly created histories when used.
2012-03-07 13:13:58 -05:00
Greg Von Kuster
7901ccf7f0
Fix for generating ToolSectionLabels in the integrated_tool_panel.xml file.
2012-03-06 17:15:38 -05:00
Daniel Blankenberg
8cd89ba26f
Fix for Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION) when downloading exported histories.
2012-03-06 15:43:32 -05:00
Daniel Blankenberg
9815e02e34
Fix for Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION) on downloads from a library.
2012-03-06 15:32:46 -05:00
Daniel Blankenberg
8cddff1ae5
Fix for 'Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION): Multiple Content-Disposition headers received.' error occuring when downloading certain datasets using Chrome browser.
2012-03-06 15:23:56 -05:00
Greg Von Kuster
fa3fd0dd65
Introduce a new integrated_tool_panle.xml file which is initially created by parsing all tool panel config files (e.g., tool_conf.xml, shed_tool_conf.xml, migrated_tools.xml, etc). After the file is created, the order of the items displayed in the tool panel is defined by integrated_tool_panel.xml. Galaxy admins can easily edit the file to change the order of items in the tool panel. After it is generated, all tool panel config files (e.g., tool_conf.xml, shed_tool_conf.xml, migrated_tools.xml, etc) will be used to load tools, workflows, etc, while integrated tool_panel.xml will define where they are displayed.
2012-03-06 14:50:55 -05:00
Jeremy Goecks
47df257ff9
Trackster: dynamic filtering of read tracks.
2012-03-05 15:10:31 -05:00
Daniel Blankenberg
bdb532db98
In library uploads, allow inheriting the existing datasets metadata when replacing. Allow setting library metadata when adding datasets from a history.
2012-03-05 13:25:14 -05:00
Dannon Baker
7ec78e35af
Add config option (sanitize_all_html, still enabled by default) to control strict dataset html output sanitization.
2012-03-05 12:00:53 -05:00
Greg Von Kuster
63fb46f9f1
Keep empty sections in the tool panel when deactivating / uninstalling a repository with tools.
2012-03-02 15:37:35 -05:00
Jeremy Goecks
b22c78b4ac
Merge
2012-03-02 14:35:57 -05:00
Greg Von Kuster
0423293a5b
Fixes for deactivating / uninstalling a repository containing tools.
2012-03-02 14:30:41 -05:00
Jeremy Goecks
2d16ed6bcf
Fix custom-build UI bugs.
2012-03-02 14:29:21 -05:00
Jeremy Goecks
4648507899
Decode visualization dataset ids before saving them.
2012-03-02 13:40:46 -05:00
Greg Von Kuster
abe913f81e
Fixes for managing installed repositories.
2012-03-02 13:33:58 -05:00
Greg Von Kuster
fc1cff34b5
Allow installed tools to have more than 1 entry in the tool panel, and several fixes for deactivating / activating / uninstalling / reinstalling repositories.
2012-03-01 15:04:51 -05:00
Dannon Baker
b1dd7eeaa0
Quick fix for ftp upload unicode normalization failure.
...
TODO: Refactor, shouldn't happen this way.
2012-03-01 09:31:18 -05:00
Dannon Baker
351ff6bec3
Cloud launch basics.
...
TODO: Tons of help text, shift instance dns wait to page level. pkey direct download.
2012-02-29 11:58:22 -05:00
Greg Von Kuster
fa550e100f
Fixes for installing tool shed repositories that contain tools when done by the InstallManager, and loading the tool panel with tools in an installed repository.
2012-02-29 11:34:10 -05:00
Jeremy Goecks
63856cbc9d
Fix incorrect sniffing for encodepeak datatype.
2012-02-29 10:42:40 -05:00
Daniel Blankenberg
69e5ac067c
Headers, which are important, are kept. Original ordering, which may be specifically needed by tools or external display applications is also maintained.
2012-02-29 09:36:03 -05:00
Jeremy Goecks
784ded84ae
Parameterize per-tool job runners so that parameter name/value pairs can be used to define multiple runners per tool. Documentation is in sample universe file. Add 'params' column to jobs table to store job parameters, and add source parameter for all jobs initiated in Trackster.
2012-02-28 17:50:26 -05:00
Greg Von Kuster
250171337c
Fix for installing a tool shed repository that includes tools.
2012-02-28 15:52:03 -05:00
Daniel Blankenberg
77b519c598
Fix for vcf_bgzip_to_tabix converter that was broken in changeset ac77414506d4
2012-02-28 14:51:22 -05:00
Greg Von Kuster
586df0eefb
Fix for generating metadata in a tool shed repository for a change set that contains data types but is not the repository tip.
2012-02-28 13:41:01 -05:00
Dannon Baker
631cb80f59
Merged in peterjc/galaxy-central/split_blast (pull request #37 )
2012-02-28 12:26:29 -05:00
Greg Von Kuster
e0942033ba
The InstallManager is now a stand-alone appication that attempts to load the tool panel as closely as possible to the way it was loaded before tools were migrated from the Galaxy distribution to the tool shed.
2012-02-28 11:38:08 -05:00
Dannon Baker
bea4f17704
Workflows: Additional rename options available to Rename Datasets action -- from Dave Walton.
...
Syntax:
#{inputs_file_variable | option 1 | option n}
where:
input_file_variable = is the name of a module input variable
| = the delimiter for added options. Optional if no options.
options = basename, upper, lower
basename = keep all of the file name except the extension
(everything before the final ".")
upper = force the file name to upper case
lower = force the file name to lower case
Example:
#{input1 | basename | upper}
2012-02-28 11:00:16 -05:00
Dannon Baker
2e6e3b2118
Preliminary autopacking for javascript.
...
Disabled by default (pack_scripts in universe_wsgi.ini) and the packed scripts are still in the distribution, to be removed at some point.
2012-02-24 17:47:47 -05:00
Nate Coraor
15e8dfe101
Include the job id in the error message when a job operation raises an exception in the PBS runner.
2012-02-24 15:49:54 -05:00
Dannon Baker
79c0ff99f1
FTP Upload - Normalize filesystem and input filename encodings prior to comparison.
...
Umlauts, etc will now behave properly in FTP upload dialog and will no longer default to "No data was entered in the upload form...".
2012-02-24 13:37:57 -05:00
Jeremy Goecks
e5e5cebe6b
Enable visualization of ENCODE peak tracks. Create 'encodepeak' datatype and add data providers for new datatype.
2012-02-23 12:23:36 -05:00
Jeremy Goecks
214fe94144
Bug fixes for ac77414506d4
2012-02-22 16:04:12 -05:00
Jeremy Goecks
f926c93b5b
Enable interval files to be converted to tabix.
2012-02-22 15:23:44 -05:00
Jeremy Goecks
f13eb27286
Enable interval files to be converted to interval_index and summary_tree datatypes.
2012-02-22 13:57:17 -05:00
Peter Cock
48d9b0499c
Basic BLAST XML merge implementation
2012-02-22 18:43:23 +00:00
Nate Coraor
410fcf87df
Make the job queue thread block on job recovery to avoid a race condition with jobs in the 'new' state. This should fix jobs showing up as 'ok' and then upon a later history reload showing up as 'error'.
2012-02-17 11:27:29 -05:00
Peter Cock
459ae7aff7
Explicit failure for merging XML files
2012-02-17 16:03:24 +00:00
Peter Cock
9b1a9f2328
Merged stdout/stderr was missing newline between tasks
2012-02-17 15:27:19 +00:00
Jeremy Goecks
0416175a87
Bug fixes for creating and saving visualizations.
2012-02-17 09:50:02 -05:00
Peter Cock
118ad8dda2
Size based FASTA splitting
2012-02-17 12:05:15 +00:00
Jeremy Goecks
d6c22052ec
Trackster bug fixes.
2012-02-16 23:02:14 -05:00
Peter Cock
9cf9a8423b
Simple FASTA splitting (no JSON metadata files)
2012-02-16 18:20:29 +00:00
Peter Cock
0b3c0aabed
Move FASTQ splitting from Sequence class to Fastq class
2012-02-16 12:15:48 +00:00
Jeremy Goecks
06da58a4bf
Trackster: save and restore tool state.
2012-02-14 15:34:18 -05:00
Greg Von Kuster
0a8e16c390
Encode application name and link name when sending as request params to display application.
2012-02-14 11:58:51 -05:00
Jeremy Goecks
9721927be4
Trackster: for flexibility, use dictionaries in all object constructors. Fixed bugs associated with saving/restoring visualizations.
2012-02-13 11:08:50 -05:00
Jeremy Goecks