mvdbeek
67b9851d3e
Resolve lazy toolbox stack onto current store-infra
2026-07-28 17:27:29 +02:00
mvdbeek
2e8ff72353
Toolbox filters: typed ToolFilterContext + parity for lazy /api/tools
...
``LazyToolBox.to_dict(in_panel=False)`` was serving entries straight from
the index, bypassing ``FilterFactory`` — so admin and user toolbox
filters silently didn't apply on the lazy path.
Introduce a typed ``ToolFilterContext`` protocol that documents the
attribute surface filters can read; both ``Tool`` and ``ToolIndexEntry``
satisfy it. ``ToolIndexEntry`` grows ``require_login``, ``tool_type``,
and ``tags`` so the stock filters (``_not_hidden``,
``_handle_authorization``) work against the entry without materialising
a Tool. ``_handle_authorization`` does the ``DataManagerTool`` admin
check inline (reads ``tool_type`` and ``context.trans.app.config``),
which avoids needing an ``allow_user_access`` method on the entry.
``LazyToolBox.to_dict`` now runs ``_build_filter_method`` against every
entry — the same code path the eager toolbox uses.
2026-07-28 17:27:13 +02:00
mvdbeek
4784f88e59
Drop http://genome-test.gi.ucsc.edu/cgi-bin/das/dsn from sample build sites
2025-08-01 10:52:07 +02:00
Daniel Blankenberg
9091acc690
Update q2view_display.loc.sample
2022-07-05 09:43:29 -07:00
Daniel Blankenberg
797d63a01f
Add q2view display application.
2022-07-05 09:43:29 -07:00
Nolan Woods
b7e1238c6b
Remove redundant default build
2020-11-09 14:35:21 -08:00
Daniel Blankenberg
dfb5a988e4
Add GEDA for iCn3D
2019-07-17 09:54:43 -04:00
Daniel Blankenberg
428c6632f0
Remove errant space in intermine_simple_display.loc.sample
2019-02-04 14:32:02 -05:00
Nicola Soranzo
926f0abde2
Update UCSC builds
2018-08-22 15:24:25 +01:00
Daniel Blankenberg
58c68d408f
add missing intermine_simple_display.loc.sample
2018-07-06 09:16:58 -04:00
Björn Grüning
cac9c980df
remove obsolete line
2017-04-07 17:13:56 +02:00
Bjoern Gruening
ab1f7eae4d
synchronise against latest UCSC versions
2017-04-05 15:17:57 +02:00
peterjc
2956f94aa0
BLAST database *.loc.sample files
2016-11-04 17:00:13 +00:00
Daniel Blankenberg
04b7d11f05
Add hg38 to main for ucsc_build_sites.txt.sample
2016-07-27 12:16:21 -04:00
Daniel Blankenberg
55074c8f33
Add Phinch as an external display application. Currently linking to a personal copy of Phinch, since it requires https://github.com/PitchInteractiveInc/Phinch/pull/54
2016-04-01 15:38:53 -04:00
Daniel Blankenberg
e6bb45b29a
typo
2016-03-15 14:09:51 -04:00
Daniel Blankenberg
0c57453c96
Add vcf.iobio as a display application.
2016-03-15 12:57:47 -04:00
Daniel Blankenberg
46728c5728
Add bam.iobio as a display application.
2016-03-15 12:56:54 -04:00
Dannon Baker
7f3ee5b167
Merge pull request #612 from lparsons/manual_builds
...
Move manual_builds.txt to manual_builds.txt.sample
2015-09-24 17:10:49 -04:00
Lance Parsons
5810a853b0
Move manual_builds.txt to manual_builds.txt.sample to allow for customization
2015-08-18 14:00:30 -04:00
Lance Parsons
aceb822470
Remove fastx_clipper_sequences.txt, moved to toolshed
2015-08-18 13:47:25 -04:00
Dannon Baker
ee4f077c52
Per @yhoogstrate's suggestion https://github.com/galaxyproject/galaxy/commit/c0c286a9c69dcb23a50a0b9b249cd6e5b09a3aad#commitcomment-12594774 , retab .loc.samples
2015-08-10 20:04:51 -04:00
Daniel Blankenberg
8d2f9f77eb
Update modencode dbkeys in gbrowse_build_sites.txt
2015-05-20 12:47:01 -04:00
Daniel Blankenberg
c17a9ca15d
Re-enable IGV local external display application by default. Add hg38 as available genome. We should probably update this view to either allow any genome or to function like the current web_link_main.
2015-03-26 10:47:58 -04:00
Daniel Blankenberg
1260d07a28
Have IGV external display application load a set of links for available genomes via a tool data table that reads a URL ( http://igv.broadinstitute.org/genomes/genomes.txt ). The manually specified builds links should now be used to add additional builds, or for alias mapping (e.g. hg_g1k_v37-->b37).
2015-02-27 15:50:28 -05:00
Daniel Blankenberg
0ea41e7419
Comment out igv local external display application link by default, since it is confusing users (most do not have a local igv running).
2015-02-11 20:39:38 +00:00
Lance Parsons
f77324d3a3
Removed blastdb_p.loc.sample, moved to tool-shed repo
2014-12-10 12:43:33 -05:00
Nate Coraor
4227d0eabb
Remove additional pieces from old genome index system.
2014-07-27 02:48:40 -04:00
Dave Bouvier
a3018feb02
Migrate 22 tools from the distribution to the tool shed.
2014-05-19 13:01:46 -04:00
Dave Bouvier
83af05b1f2
Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
2014-04-01 11:04:32 -04:00
Nate Coraor
794484e8c3
Rename ucsc_build_sites.txt to .sample.
2014-02-27 16:37:48 -05:00
Nate Coraor
9c64fc123e
Remove broken and/or obsolete tools.
2014-01-27 13:58:31 -05:00
Dave Bouvier
448d9f55eb
Migrate 43 tools from the distribution to the tool shed.
2014-01-27 09:53:14 -05:00
Ross Lazarus
93c3148b4c
backout -r 10811
2013-10-08 10:56:03 +11:00
Ross Lazarus
66b690d599
backout -r 10802
2013-10-08 10:53:45 +11:00
Ross Lazarus
59bd638b82
updated ucsc builds
2013-10-07 10:41:50 +11:00
Ross Lazarus
87b1203b4a
branch merge
2013-10-05 09:56:05 +10:00
Dave Bouvier
962be8d8ec
Remove sam_fa_indices.loc.sample from tool-data. Update migration xml to the correct revisions of cufflinks repositories.
2013-10-01 15:49:08 -04:00
Dannon Baker
9544149163
Include hg19 in ucsc_build_sites.txt
2013-09-19 09:59:49 -04:00
Ross Lazarus
652fec3488
monkeypatches to output.py
2013-08-07 09:45:35 +10:00
Nate Coraor
812aebdd62
Backout af20b15f7eda, these changes will be reapplied after tools using the sam_fa_indices data table have been migrated to the Tool Shed in their original state and updated to use the new table format.
2013-07-30 12:44:05 -04:00
Nicola Soranzo
70996cfb3d
Add new loc file for SAMtools indexes to support genome variants
2013-04-18 19:25:55 +02:00
Jeremy Goecks
6b1165be53
Improved documentation in bowtie2 loc file.
2013-02-13 11:04:54 -05:00
James Taylor
a4318d4817
genetrack: Purge all genetrack support (since it no longer exists), other than leaving filetype for backward compatibility
2013-02-03 23:21:17 -05:00
Dave Bouvier
917d5a72e8
Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.
2012-11-26 10:18:47 -05:00
Dave Bouvier
c2eeee7b9f
Migrate BWA to the tool shed.
2012-09-28 15:35:44 -04:00
Daniel Blankenberg
bb15315fed
Refactor GBrowse external display application. Update WormBase with latest builds and to be able to use reference sites.
2012-08-22 12:35:23 -04:00
Dave Bouvier
36dbacf8f1
Cleaned up code, added searchable list of NCBI builds.
2012-07-05 09:56:54 -04:00
Dave Bouvier
33a50cd7ee
Also added missing publicbuilds.txt
2012-06-26 15:18:19 -04:00
Dave Bouvier
8096e294a6
Added missing builds.txt for Ensembl, fixed erroneous first line in output.
2012-06-26 15:10:25 -04:00
mvdbeek