mvdbeek
58c82ad7f3
Fix vcf_bgzip mimetype, allow cors, tbi from metadata element
...
The mimetype would be text/plain otherwise, which is not compatible with
byte-range requests. `allow_cors` doesn't quite seem to work in my
tests, but we'll need this for jbrowse.
Also skips an additional conversion by using the tabix index, which
again is helpful when loading datasets from a shared history.
2020-04-24 13:39:20 +02:00
Daniel Blankenberg
d0acfaf0a1
fix for igv fasta having name=name=
2020-03-09 13:53:14 -04:00
Daniel Blankenberg
66856d25a1
missing igv genbank geda
2020-02-20 20:53:45 -05:00
Daniel Blankenberg
f012b3055b
IGV GEDAs only set genome if dbkey is set
2020-02-20 20:49:55 -05:00
Daniel Blankenberg
ef5e04d525
quote plus dbkeys in igv GEDAs
2020-02-20 20:23:55 -05:00
will
009611cf04
add .gitattributes file and normalize line endings to use LF instead of CLRF
2019-09-18 22:03:37 -04:00
Daniel Blankenberg
ad4734e0fc
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into geda-cors
2019-08-29 09:15:53 -04:00
Martin Cech
e5b0b8ae88
Merge branch 'release_19.05' into devmerge
2019-08-28 11:01:03 -04:00
Daniel Blankenberg
703c2e9ed1
Update intermine_simple.xml
2019-08-28 10:35:56 -04:00
Daniel Blankenberg
3b6e770caf
Update icn3d_simple.xml
2019-08-28 10:35:37 -04:00
Daniel Blankenberg
b391cf5606
inherit is declared in datatypes_conf.xml not within the display application itself.
2019-08-14 12:54:35 -04:00
Daniel Blankenberg
8dd9b2fe8c
Missing space
2019-07-17 09:58:17 -04:00
Daniel Blankenberg
dfb5a988e4
Add GEDA for iCn3D
2019-07-17 09:54:43 -04:00
Daniel Blankenberg
08547faddd
Intermine from Hack
2018-06-30 15:08:02 -07:00
Ann Loraine
ea22750604
Change BioViz URL to http://bioviz.org/galaxy.html from http://bioviz.org/igb/galaxy.html
2018-05-09 17:19:14 -04:00
Daniel Blankenberg
1fbdb35d6e
Have IGV bigWig display application make use of build_sites/ site_type config instead of direct filename.
2017-03-27 17:44:40 -04:00
Delphine-L
1d0f15d175
Edit of Authors
2016-12-16 13:50:38 -05:00
Delphine-L
27673f5e08
Addition of Genome fasta file loading in local IGV instance, and addition of fai format and fasta to fai converter
2016-12-16 13:39:51 -05:00
John Chilton
40fde4ecf6
Merge pull request #2348 from remimarenco/huba_datatype
...
Add the trackhub composite datatype
2016-07-22 11:07:43 -04:00
Devon Ryan
43a4a45cc8
Add the missing bigwig xml file for the IGV display application
2016-06-25 20:14:29 -04:00
remimarenco
611ade3552
Remove the strip_https attribute because we don't need it anymore
2016-06-03 19:59:26 -04:00
remiarenco
e0ffb2d8d0
Following advices: renamed the extension to 'trackhub', renamed the huba.xml to trackhub.xml, changed iteritems to items, removed hubAssembly.py to port it into tracks.py
2016-05-13 23:18:32 -04:00
remiarenco
0a9d038a5d
Add the composite datatype
2016-05-11 21:48:25 -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
915993bbd8
Add display_applications/iobio/vcf.xml.
2016-03-15 12:58:27 -04:00
Daniel Blankenberg
46728c5728
Add bam.iobio as a display application.
2016-03-15 12:56:54 -04:00
Eric Rasche
04120145c5
CDATA and linting
2015-06-16 22:34:09 -05:00
Daniel Blankenberg
97c450293b
IGV External displays cannot use a name with a comma in it, so replace commas with semicolons.
2015-05-14 15:59:44 -04:00
Daniel Blankenberg
3a998d0f2a
Tweak display application id to match interval to bed.
2015-05-14 14:57:04 -04:00
Daniel Blankenberg
f52bbbf50e
Add display for Interval files at IGV via bedstrict.
2015-05-14 14:51:43 -04:00
Daniel Blankenberg
74242d9f50
Add an External Display application for viewing gff/gtf files at IGV.
2015-04-02 10:57:05 -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
Dannon Baker
fd9bbf1fa3
Merged in lance_parsons/galaxy-central-pull-requests/igv-local-dbkey (pull request #488 )
...
Allow local IGV users to visualize custom genomes
2014-09-12 13:10:52 -04:00
Nate Coraor
ebf67f5fad
Fix references to config.ucsc_display_sites that I missed.
2014-09-10 14:37:33 -04:00
Lance Parsons
9e81adc5e6
Allow local IGV users to visualize custom genomes
2014-09-04 15:22:10 -04:00
Nate Coraor
9c0b88446b
Move ucsc_display_sites and gbrowse_display_sites into datatypes_conf.xml's new <build_sites> section, as per the suggestion by @nsoranzo.
2014-09-03 12:25:22 -04:00
Nate Coraor
337c0d5778
Remove the BuildSites class I recently created and merge its functionality back into util and the datatypes registry. As a result, the build_sites configuration moves to datatypes_conf.xml and display applications can now use configured build sites so that the path is not hardcoded into the individual committed display application files. from_file in the display applications is still supported.
2014-09-02 18:20:23 -04:00
Daniel Blankenberg
63eb557a6f
IGB can read over https just fine (but won't follow 307 Temporary Redirects). Remove strip_https flag from IGB external display applications.
2014-07-28 16:25:07 -04:00
dcnorris
3bc8bd3dca
converted tabs to spaces
2014-04-14 16:43:49 -04:00
dcnorris
e5201f8632
adding support for the visualization of gtf file format in IGB
2014-04-14 10:05:03 -04:00
dcnorris
326d023116
Reverted capitalization
2014-04-11 13:41:07 -04:00
dcnorris
1d5286610c
Added IGB display support for bed graph files
2014-04-10 09:48:59 -04:00
dcnorris
3049d6e5d0
removed dataset hash from the bookmark generated urls since they are not needed and make for ugly track names
2014-04-07 16:29:17 -04:00
hillrunner2008
9e4683e74e
Changed the link text to match other file formats
2014-04-03 15:05:36 +00:00
dcnorris
b875266e96
modified igb display xml files
2014-03-27 14:49:12 -04:00
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
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
Daniel Blankenberg
48d08a129f
Add name parameter to IGV external display applications.
2012-06-25 15:54:27 -04:00
Hiral Vora
6ebcf10e63
Adding IGB files.
2012-04-19 12:35:44 -04:00
Daniel Blankenberg
f6cbb7dab6
Fix for viewport generation in display_applications/ucsc/interval_as_bed.xml.
2012-03-20 13:10:21 -04:00
mvdbeek