thobalose
6c580b8c9d
Updated volume kwds.
2018-10-09 13:22:55 +02:00
Dannon Baker
ae546cef79
Merge remote-tracking branch 'upstream/release_18.01' into release_18.05
2018-05-25 10:21:54 -04:00
Nate Coraor
221d92f681
Don't use the notebook URL itself for keepalive checks
2018-05-24 15:03:04 -04:00
Nate Coraor
deda753de9
Do not append '/' to 'js' in GIE static path, this breaks uWSGI static
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routing.
2018-04-05 14:17:36 -04:00
Björn Grüning
83ab849f38
change hicexplorer image name
2017-12-09 17:29:42 +01:00
Enis Afgan
566f6ba123
Update Jupyter IE default image ( #5095 )
2017-11-30 18:16:04 +01:00
Dannon Baker
f34e6a1e2e
Merge pull request #4737 from xgaia/askomics-ie
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AskOmics Interactive Environment
2017-11-15 10:01:45 -05:00
Dannon Baker
7d674e1de0
Left off semicolon.
2017-11-15 09:40:52 -05:00
Dannon Baker
1d5f0d2b61
Fixes to askomics javascript
2017-11-15 09:39:54 -05:00
Dannon Baker
21bdc78c5e
Update hicexplorer use of galaxy.interactive_environments
2017-11-02 17:48:07 -04:00
Dannon Baker
a279300012
Minor cleanup.
2017-11-02 17:46:41 -04:00
Dannon Baker
e8abd20da9
Update neo use of galaxy.interactive_environments
2017-11-02 17:42:50 -04:00
Dannon Baker
2c1ffcfe36
Consolidate require scope for phinch.
2017-11-02 17:40:40 -04:00
Dannon Baker
9dfe82f7ca
Update phinch use of galaxy.interactive_environments
2017-11-02 17:39:28 -04:00
Dannon Baker
b533fc7b50
Update ethercalc use of galaxy.interactive_environments
2017-11-02 17:35:29 -04:00
Dannon Baker
bd34c750ae
Update bam_iobio use of galaxy.interactive_environments
2017-11-02 17:30:42 -04:00
Dannon Baker
5fc47e3bcd
Update rstudio use of galaxy.interactive_environments
2017-11-02 17:27:37 -04:00
Dannon Baker
f7ccdd7c74
Fix jupyter javascript; this all needs a ton of disentanglement and standardization.
2017-11-02 16:08:38 -04:00
Dannon Baker
2004f31ad5
Fix really wonky IE requires to work with AMD modules correctly.
2017-11-02 15:29:56 -04:00
Nate Coraor
1f6df5580b
Fix the spinner for the GIE container readiness check.
2017-10-19 13:56:21 -04:00
xgaia
04370ebff9
use build-in password generator for api key
2017-10-05 10:44:11 +02:00
xgaia
e55121f655
remove license file
2017-10-03 15:24:04 +02:00
xgaia
4d5facb985
remove files
2017-10-03 15:20:03 +02:00
xgaia
c994005fcc
add askomics interactive environment
2017-10-03 15:15:35 +02:00
Dannon Baker
f709ddcfe6
Add requirejs config to cachebust IE require'd files.
2017-09-27 14:53:24 -04:00
Dannon Baker
c235382cee
No need for this keep_alive invocation after all; removes the commented out code.
2017-09-27 08:15:06 -04:00
Dannon Baker
40900d76a9
Re-enable keepalive, build client.
2017-09-27 07:54:27 -04:00
Nate Coraor
180bfe7184
Treat timeouts and errors the same, except that timeouts step the
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ajax timeout of the next request. Also fixes for toastr messages.
2017-09-26 16:41:50 -04:00
Nate Coraor
7edeedd7fe
Additional GIE spinning fixes for when the error condition is not a
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timeout.
2017-09-26 16:41:50 -04:00
Nate Coraor
04b03b2853
Make the URL spinner actually work.
2017-09-22 16:45:21 -04:00
Nate Coraor
4f9d5df34f
WIP a bunch of GIE javascript that probabaly won't work
2017-09-22 13:23:55 -04:00
Eric Rasche
508fdb9d2b
Merge pull request #3330 from bgruening/hicbrowser
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HiCBrowser as Galaxy IE
2017-09-08 14:18:18 +02:00
Max Schaefer
43ddd47320
Add missing var declarations.
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In all these cases, a variable was not declared to be a local using `var` (and hence was implicitly interpreted as a global variable), but all uses of that variable were preceded by a definition within the same function, suggesting that the variable was, in fact, meant to be local, not global.
2017-08-16 15:22:42 +01:00
pvanheus
00928743bf
Correct name of neo4j datatype class
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Its neo4j.Neo4jDB: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/neo4j.py#L89
2017-06-23 23:25:09 +02:00
Thoba Lose
009f44c25f
using sanbi-sa image.
2017-06-22 15:00:03 +02:00
Thoba Lose
842d14a0e6
Upgrade IE to Neo4j:3.1
2017-06-13 14:48:42 +02:00
Nate Coraor
4b3a361a88
Update Jupyter image to 17.05
2017-05-02 12:07:10 -04:00
John Chilton
6201c61d72
Add a note about use_volumes to Jupyter and RStudio GIEs.
2017-05-01 12:38:05 -04:00
John Chilton
9bc24aeef0
Update rstudio to match additional hid handling of Jupyter.
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Ping @erasche - does this work? I'm not sure how rstudio handles the existing DATASET_HID.
2017-04-28 12:14:45 -04:00
John Chilton
5a6e53f728
Rework Jupyter IE for additional_ids handling.
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- Add a new option ``use_volumes`` to the Docker config.
- If using volumes, do nothing differently.
- If not using volumes, set ADDITIONAL_IDS in the environment for the IE itself to fetch (requires https://github.com/bgruening/docker-jupyter-notebook/pull/17 ).
2017-04-28 12:11:10 -04:00
Eric Rasche
60a05c1811
more touch-ups and easier vimdiffing with jupyter configs
2017-04-25 21:59:30 +00:00
Eric Rasche
b1c6d3363d
remove old versions
2017-04-25 21:13:33 +00:00
Eric Rasche
80324d08a5
17.01 version of rstudio
2017-04-25 21:05:51 +00:00
Nate Coraor
a2b8b43179
Generate proper url for readiness endpoint
2017-04-17 16:50:52 -04:00
Nate Coraor
abe6434916
Update ethercalc GIE for readiness checking
2017-04-17 16:49:21 -04:00
Daniel Blankenberg
21e5731355
Fix for EtherCalc IE image specification.
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Will allow EtherCalc to work in 17.05.
2017-03-27 11:58:59 -04:00
Eric Rasche
18a26c5f37
Merge pull request #3699 from shiltemann/ethercalc
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Ethercalc Interactive Environment
2017-03-24 06:14:52 +00:00
Nate Coraor
08f66a924b
GIE container waiting and swarm management.
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1. Create a new API endpoint and client spin to wait for GIE containers to
become ready. IEs are not required to use it, but usage does require
a slight change to their `load_notebook()` functions.
2. Add a Docker swarm manager daemon that runs automatically
to add nodes when services are waiting, clean up exited services, and
remove idle nodes. Shuts down automatically when there's nothing to
do.
The format of the GIE proxy session database has changed, if GIEs are
running when you restart Galaxy, they will be interrupted. If you run
the GIE proxy separate from Galaxy, you should restart it after
upgrading.
2017-03-13 21:31:55 -04:00
Nate Coraor
293726c579
Support Docker Engine swarm mode
2017-03-03 10:27:18 -05:00
Saskia Hiltemann
d47f582d15
remove commented section
2017-03-02 21:04:37 +01:00
thobalose