vjalili
5a784890de
Update a comment in the default config of OIDC backends.
2018-09-17 10:56:38 -07:00
vjalili
56fb283d9b
Add a comment on why user does not see a consent screen with Google.
2018-09-17 10:43:49 -07:00
vjalili
04a75bd33b
Change default prompt option for Google OIDC IdP.
2018-09-17 09:41:29 -07:00
Nicola Soranzo
64bb339a31
Merge pull request #6641 from martenson/rename-and-document-config-value
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document config for sniffing compressed files, enable by default
2018-09-08 00:32:08 +01:00
Helena Rasche
89405fae94
Merge pull request #6648 from mblue9/add_seurat_datatype
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Add Seurat datatype: rdata.seurat
2018-09-06 16:03:33 +02:00
John Chilton
b9d07aed22
Merge pull request #6662 from nsoranzo/doc_fixes2
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Various link and documentation fixes
2018-09-03 17:26:05 -04:00
sb635
56d55399eb
removing top and gro sniffers, at least for now
2018-09-03 19:03:13 +02:00
simonbray
ea34aa84be
adding 4 new GROMACS datatypes: cpt, xtc, top, and gro
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shrinking test files
2018-09-03 19:03:13 +02:00
Nicola Soranzo
59c1ed2266
Various doc fixes
2018-09-03 14:34:13 +01:00
Nicola Soranzo
ad02c53154
Fix many links
2018-09-03 14:34:13 +01:00
Maria Doyle
9f14fcb100
Add Seurat datatype: rdata.seurat
2018-08-29 08:32:28 +10:00
Martin Cech
b34414adc8
switch the default to sniff compressed datatypes
2018-08-28 13:38:44 -04:00
Martin Cech
e0d1208834
document the sniff_compressed_dynamic_datatypes_default config and include in sample
2018-08-28 10:09:27 -04:00
Marius van den Beek
a3fc0b9f32
Merge pull request #6312 from jmchilton/tuple_operations
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Lists-as-tuples collection operations
2018-08-26 09:19:49 +02:00
Chris Barnett
33794fa318
add vel datatype,register and example
2018-08-20 15:42:51 +02:00
Chris Barnett
c63e4fde41
register dcd datatype
2018-08-17 09:30:51 +02:00
Bjoern Gruening
e42829f036
register datatype
2018-08-13 23:20:05 +02:00
John Chilton
84597a1235
Lists-as-tuples collection operations.
2018-08-08 10:28:56 -04:00
Dannon Baker
c9d17545d8
Config rebuild, and a few typos.
2018-08-06 10:01:20 -04:00
Dannon
2f9520e6a2
Merge pull request #6505 from VJalili/remove_deprecated_openid_backends
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Remove the deprecated AOL openid backend.
2018-07-17 09:55:31 -04:00
John Chilton
347e3124f4
Merge pull request #6467 from mvdbeek/fix_upload_tool_py3
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Make upload tool python3 compatible
2018-07-17 09:26:01 -04:00
vjalili
43c9c9624a
Remove deprecated AOL openid backend.
2018-07-16 15:22:03 -07:00
mvdbeek
c5fa023c26
Use webob.compat's FieldStorage in the remaining codebase
2018-07-16 20:15:12 +01:00
John Chilton
8a85270629
Fix and docs for advanced container options in job_conf.xml.
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These options were added in #2790 but you know how @jmchilton is about documentation. The bug fix is to fix selecting the first valid option if multiple ones are present instead of just the first option which may be invalid given the other configured destination parameters.
2018-07-16 09:52:13 -04:00
Dannon
8df7cafe3a
Merge pull request #6444 from blankenberg/intermine
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Intermine Enhancements
2018-07-06 06:54:29 -07:00
Björn Grüning
14ef3b8643
Merge branch 'dev' into topic/daa
2018-07-05 00:07:19 +02:00
Daniel Blankenberg
5b0088ae43
Update InterMine
2018-07-01 16:21:41 -07:00
Daniel Blankenberg
433d464870
Update InterMine
2018-07-01 16:20:13 -07:00
Daniel Blankenberg
08547faddd
Intermine from Hack
2018-06-30 15:08:02 -07:00
Nicola Soranzo
31e78461bd
Merge branch 'release_18.05' into dev
2018-06-23 00:05:40 +01:00
Nicola Soranzo
e0c269291a
Merge branch 'release_18.01' into release_18.05
2018-06-23 00:04:32 +01:00
mvdbeek
5f24794efd
Add basic .bai datatype
2018-06-22 19:50:43 +02:00
Dannon Baker
fa2b6baef7
Revert "Remove bam to bai converter"
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This reverts commit 7e2727bc0a
2018-06-22 13:22:51 -04:00
Nicola Soranzo
76dee1970a
Add gafa.sqlite datatype
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Generated by the GAFA tool:
https://toolshed.g2.bx.psu.edu/view/earlhaminst/gafa/
Can be visualised with the Aequatus.js plugin (PR forthcoming).
Work in collaboration with @anilthanki as part of the GeneSeqToFamily
project:
https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily
2018-06-21 15:45:50 +01:00
Dannon Baker
f9ba72f0ae
Merge remote-tracking branch 'upstream/release_18.05' into dev
2018-06-20 10:15:29 -04:00
M Bernt
46788b99b2
added sniffer entry in data_types.conf.sample
2018-06-20 10:57:08 +02:00
M Bernt
1a2cd725bb
added daa (diamond alignment) datatype
2018-06-20 10:54:43 +02:00
guerler
b0212ff45c
Add phylip for msa viewer
2018-06-19 17:23:52 -04:00
guerler
f6888a32d6
Add fasta datatype to msa viewer
2018-06-19 14:14:44 -04:00
Björn Grüning
e9efb47b59
Merge pull request #6302 from davebx/cuffdiff_datatype
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Add specific datatype for CuffDiff SQLite database.
2018-06-18 20:58:22 +02:00
Marius van den Beek
02974b79c7
Merge pull request #5640 from Mataivic/patch-1
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Add a FilterEmptyDatasetsTool and allow filtering tools to apply to arbitrary collection structures
2018-06-17 12:25:03 +02:00
mvdbeek
8a4d18fba1
Add filter empty collection tool
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I think having a separate tool for this task makes sense and makes the
distinction between empty and fialed datasets clearer.
2018-06-13 11:35:21 +02:00
Nicola Soranzo
d66a63012a
Replace unmaintained pycrypto dependency with pycryptodome
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Minimum secret key length for Blowfish was increased from 4 to 5 bytes.
First argument to Blowfish.new() must be a bytestring, and the `mode`
argument is no more optional.
Remove unused `encode_id` function from `scripts/api/common.py` .
Documentation updated, then rebuilt with `make config-rebuild` .
2018-06-13 03:07:04 +01:00
Sebastian Kapust
3c36bec290
Fix tool search overlay link
2018-06-08 13:24:50 -04:00
Dave B
b9233b282b
Add specific datatype for CuffDiff SQLite database.
2018-06-07 12:40:33 -04:00
Dave B
9c58c51ea6
Merge pull request #6206 from gregvonkuster/newick
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Add the newick extension for the Newick datatype,
2018-06-06 10:26:54 -04:00
greg
8cecfe3042
Add the newick ext to the phylocanvas plugin
2018-06-06 08:42:31 -04:00
Sebastian Kapust
3ec5787f59
Fix tool search overlay link
2018-06-05 17:47:29 +02:00
Björn Grüning
1954c9dc63
Merge pull request #6201 from cmonjeau/add_sbml_datatype
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New datatype: SBML
2018-06-01 22:39:12 +02:00
Dannon
5ba71f580f
Merge pull request #6215 from natefoo/dynamic-rule-dynamic-reload
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Enable automatic reload of dynamic job rules on change
2018-06-01 11:38:24 -04:00
vjalili