mvdbeek
9d45e2b0db
Remove unused legacy controller things
2021-06-19 16:28:56 +02:00
Nicola Soranzo
d26b3d9848
Fix all E203, E741 and W504 flake8 errors
2021-01-18 10:35:41 +00:00
Nicola Soranzo
9d74bba7fb
Drop support for retired Python 3.5
...
Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
2020-10-07 11:52:13 +01:00
Nicola Soranzo
0c931235af
Change all remaining old-style classes to new style
2018-09-17 12:26:07 +01:00
Nicola Soranzo
18221ae931
paster.pid/log to galaxy.pid/log reference update
...
Fix errors in `first_startup` jobs:
https://travis-ci.org/galaxyproject/galaxy/jobs/316342622#L1029
Introduced in https://github.com/galaxyproject/galaxy/pull/4475
2017-12-15 15:34:47 +00:00
Nicola Soranzo
6f722861cf
Python3: fix moved imports
...
Add `.ci/check_py3_compatibility.sh` script to find library modules
that have been moved in Python3. Fix errors found by the script.
2017-12-15 01:03:28 +00:00
Nicola Soranzo
d1bc98dfcb
Python3: fix remaining print statements
...
Remove some debugging prints.
Fix import order.
Consolidate exception logging in ToolShed database migrations.
2017-10-12 18:34:29 +01:00
Nicola Soranzo
a353b2e88f
Fix E127 errors introduced by previous commit
...
using:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 .
```
2017-08-17 11:35:39 +01:00
Nicola Soranzo
21b44bf348
Fix all E201 and E202 style errors
...
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
2017-08-17 11:35:39 +01:00
E Rasche
2f992d90ae
Rebase
2017-06-01 16:43:21 +00:00
Nate Coraor
86a7880e48
Update Nagios check
2017-02-07 11:25:59 +11:00
Nicola Soranzo
1d17a29c79
Fixes for pycodestyle 2.2.0
2016-11-15 16:56:50 +00:00
Nicola Soranzo
cc336f61c0
Make some files compatible with Python3
...
Also enlarge the set of files tested with flake8 under Python3
2016-06-03 19:24:46 +01:00
Nicola Soranzo
6ba6f798ec
Fix more E203 flake8 errors
2016-05-17 23:53:16 +01:00
Nicola Soranzo
8a43b2b492
Python 3: use "as" instead of comma in except clause
2016-05-17 23:53:16 +01:00
John Chilton
f0272e02f7
Merge pull request #2109 from mvdbeek/fix_debian_init_script
...
Update debian init script
2016-04-08 13:18:03 -04:00
Marius van den Beek
d6a7acab99
Update debian init script
...
to include instructions for starting galaxy >= 16.01.
2016-04-08 16:55:45 +02:00
Marius van den Beek
0de8832715
Change program name to galaxy_web
2016-04-06 14:46:12 +02:00
Marius van den Beek
974a9adc1b
Add sample supervisor config
...
for galaxy served by uwsgi, with seperate handlers.
2016-04-06 12:02:38 +02:00
Mikael Loaec
1aaf65e8b6
missing ;; in case stop
2016-03-11 20:43:24 +01:00
Mikael Loaec
d9c00771d0
adding blank line to separate function
2016-03-11 18:24:43 +01:00
Mikael Loaec
6d6b637299
removing lock files creation and deletion because of rigths problems in case of using galaxy user
2016-03-11 18:20:17 +01:00
Mikael Loaec
0697364f9d
adding contrib init for reports and modifying status check to have output by process in case multiprocess
2016-03-11 17:21:22 +01:00
Nicola Soranzo
af2f93b236
flake8 contrib/ .
2015-09-09 19:34:42 +01:00
Nicola Soranzo
cc9b0bed85
Fix all E712 errors. Standardize sqlalchemy imports.
2015-07-14 20:49:34 +01:00
Nate Coraor
8fadc6392b
Rename universe_wsgi.ini -> galaxy.ini everywhere.
2014-09-15 16:43:51 -04:00
Nate Coraor
1b6f2bf27a
Fix check_galaxy for recent framework changes.
2012-11-27 15:57:05 -05:00
Nate Coraor
624fa70cbc
Remove contrib/multiprocess.sh since run.sh can run all of the processes itself now.
2012-08-08 11:12:42 -04:00
Nate Coraor
f866c529a8
Provide a modified check_galaxy.py that is suitable for use with nagios.
2012-05-26 15:00:36 -04:00
Greg Von Kuster
e00f7d04fc
Add script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample contributed by Anne Pajon.
2012-03-28 10:58:19 -04:00
Nate Coraor
9b5e9992f0
Fedora(/RHEL/SL/CentOS) init script, thanks Brad Chapman!
2011-12-05 14:55:00 -05:00
Nate Coraor
e8ab977d8b
Add the "Galaxy ls" script to contrib/. Thanks, Simon McGowan.
2011-09-06 11:51:01 -04:00
Greg Von Kuster
3eacfa47ea
Add Assaf Gordon's collect_job_timings.sh script.
...
This shell script produces the report, combining information from SGE's QACCT with the galaxy job/dataset information.
The output contains:
job, user, tool name, dbkey, total input size in bytes, waiting time in SGE queue, actual SGE executiong running time, and some other tidbits.
This allows finding how much running time each user had on the cluster,
how much time each tool/user spend idly waiting,
and some possible correlations between tools, dbkeys, input size and running time.
The script is tightly coupled with SGE and PostgreSQL, but can probably be adapted to PBS/MySQL.
2011-07-21 13:55:24 -04:00
Florent Angly
a26e479b86
MacOS X daemon launcher:
...
* fixed bad XML
* better default parameters
* improved documentation
2010-12-13 13:54:22 +10:00
Nate Coraor
d8281a6e77
add multiprocess.sh example script for running multiple galaxy processes. instructions coming later.
2010-05-20 17:00:12 -04:00
Nate Coraor
a51ce47c40
Add contributed Debian init script and OS X LaunchDaemon plist from James Casbon, and my Solaris SMF manifest.
2009-10-30 12:41:17 -04:00
mvdbeek