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56 Commits
Author SHA1 Message Date
mvdbeek f2fbfe49d6 Update error message when building ucsc_build_sites.txt fails 
Fixes https://github.com/galaxyproject/galaxy/issues/14478
 2022-08-18 16:33:47 +02:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00
Martin Cech 3e43fac8c4 remove bash script for cron 
it calls already removed python script
 2021-10-08 14:10:50 +02:00
Nicola Soranzo 3028d7ccc5 Activate virtualenv in updateucsc.sh.sample 
Otherwise Python 2 is used or `requests` may be missing.
 2021-04-07 17:50:11 +01:00
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 d5a406cef7 Fix errors reported by new flake8 3.7.3 2019-01-31 13:47:21 +00:00
Nicola Soranzo c852de734d Fix cron/build_chrom_db.py 
Fix the following errors:

```
$ python cron/build_chrom_db.py tool-data/shared/ucsc/chrom/ tool-data/shared/ucsc/builds.txt
Retrieving hg38
Failed to retrieve hg38: Problem parsing line ''
Retrieving hg19
Failed to retrieve hg19: Problem parsing line ''
...
```

Broken in commit 9b8e76f9d9 .
 2018-08-22 15:24:25 +01:00
Dannon Baker 2839475967 Update ucsc genome-test server URL. 2018-08-10 11:19:13 -04:00
Nicola Soranzo 48aca7dce8 Update to flake8-import-order 0.16 2017-12-01 11:09:57 +00:00
Nicola Soranzo 9b4de72ca6 Fix all E722 errors and ignore E741 
Introduced in flake8 3.5.0
Fix import order.
 2017-10-24 11:29:09 +01:00
Nicola Soranzo 9b1832abb1 Fix import order for cron/, scripts/ and test/ 2017-09-25 23:44:39 +01:00
E Rasche 290971ca7a more review comments 2017-09-25 11:39:15 +02:00
E Rasche 75df58ae86 fix 2017-09-25 11:39:14 +02:00
E Rasche b326130984 import ordering 2017-09-25 11:39:14 +02:00
E Rasche db04002986 remove unused imports 2017-09-25 11:39:13 +02:00
E Rasche 9b8e76f9d9 Convert urllib to requests 
Which has built-in protection against urls like "file:///tmp/a"
 2017-09-25 11:39:13 +02:00
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
Nicola Soranzo 404b855dd2 Make updateucsc.sh.sample usable without any change 2017-06-14 17:45:54 +01:00
Nicola Soranzo ebfdb598f6 Lint updateucsc.sh.sample 2017-06-14 17:45:54 +01:00
Nate Coraor 08f66a924b GIE container waiting and swarm management. 
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
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 ee721c5d36 Check len files during download from UCSC. 
Do not create file in case of errors, so the cron script will not
overwrite a good file with a bad one.
 2015-11-12 11:01:51 +00:00
Nicola Soranzo cd456e186d Print to stderr when calling sys.exit(1) 2015-09-11 19:05:37 +01:00
Nicola Soranzo 2c61543d72 Lint cron/ . 2015-07-13 00:13:21 +01:00
Nicola Soranzo 717b2064f4 Fix missing substitution from f98d4b27a0 . 2015-06-24 12:26:30 +01:00
Nicola Soranzo 9130734512 Simplify code. 2015-06-24 12:15:54 +01:00
Nicola Soranzo 56f9303fce PEP-8 fixes. 2015-06-24 12:12:27 +01:00
David Trudgian f98d4b27a0 Use passed in URL for getbuilds 2015-06-22 11:52:25 -05:00
Nate Coraor e4e5df04de Make the UCSC Browser to pull new builds from (in the cron script) a 
command line argument. Default is UCSC Main, but for Galaxy Test and
Main we use UCSC Test.
 2015-03-02 14:56:01 -05:00
Dannon Baker dba89dff83 Convert everything from elementtree to stdlib xml module. 2015-01-29 16:10:56 -05:00
Dannon Baker 00f80427fe Delete *ancient* cron/cleanup_datsets.py content, but leave a nice deprecation warning and pointer for those who might actually be using it in cron jobs. 2014-12-17 11:00:29 -05:00
Björn Grüning be132e8ff1 Hide the GALAXY env variable. This enables us to set it externally and just call the script. Very useful in docker containers. 2014-10-22 13:10:32 +00:00
Nate Coraor 8623ef71fd Create builds.txt from UCSC's Main browser, not Test. 2014-08-01 13:12:58 -04:00
Nate Coraor 4227d0eabb Remove additional pieces from old genome index system. 2014-07-27 02:48:40 -04:00
Dave Bouvier 334983c4df Added script to update NCBI builds list, replaced Broad data source with direct URL, cleaned up help text. 2012-08-23 16:36:58 -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
Dave Bouvier f44aa3553d Added Ensembl build parser. Improved genome downloader interface. Added post-download indexing feature. 2012-06-25 09:39:41 -04:00
Kelly Vincent d3d26a7149 Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds 2011-03-29 13:59:07 -04:00
Kelly Vincent b5ee9ee8c7 Modified script that adds manual builds to add build even if chrom length details not present; added a few new manual builds 2011-03-10 13:28:33 -05:00
Nate Coraor 4186a549de POSIXize/Bournize updateucsc.sh.sample 2009-09-10 17:31:05 -04:00
Daniel Blankenberg 481f69fb6f Have update_ucsc.sh.sample add 'chrom' dir to tool-data/shared/ucsc as needed. This empty directory was lost from the repository in the svn to hg conversion. 2009-08-10 14:00:47 -04:00
Kanwei Li e6777af8eb Typos in cron/README.txt 2009-08-03 13:25:47 -04:00
Nate Coraor c998a43692 Apparently I only committed these fixes to security. Recommit of changeset 2015:7a447128f2cd from security, Make UCSC build update scripts find elementtree properly 2009-01-24 12:13:47 -05:00
Daniel Blankenberg 86f0862aa4 Move ucsc and gbrowse data from static to tool-data/shared. 
Cron scripts on test and main will need to be updated when the server is.

GOPS complement tool and annotation profiler will now correctly use chromosome lengths files if available.
 2008-06-03 18:53:26 +00:00
Nate Coraor 0113b008a1 Forgot to getopt -n... 2008-05-06 13:14:49 +00:00
Nate Coraor e617b271e7 Add -n option to check_galaxy.py cron wrapper. 2008-05-05 16:07:16 +00:00
Greg Von Kuster af3b0669aa Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4. 2008-03-28 15:24:50 +00:00