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13 Commits
Author SHA1 Message Date
Nicola Soranzo 452aba9ee3 Fix remaining issues reported by bugbear; add it to flake8 reqs 2021-01-16 05:58:15 +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 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 1d17a29c79 Fixes for pycodestyle 2.2.0 2016-11-15 16:56:50 +00:00
Nicola Soranzo 11b4f3a60c Fix import order and Python3 compatibility for tools/ 
xref #1715
 2016-09-29 19:26:22 +01:00
Nicola Soranzo 69cda48690 Remove remaining references to galaxy.eggs . flake8 some files in tools/ . 2015-10-26 19:29:13 +00:00
Nicola Soranzo 22d4a1d8c3 dos2unix of tools/ directory. Some whitespace and PEP-8 fixes. 2015-05-15 12:40:52 +01:00
Daniel Blankenberg 377c2427a7 Allow workflows that contain tools that had parameters added to them after the workflow was created to be edited. Workflows containing tools with added parameters can still not be run until after they are edited and saved. Default values are provided in the workflow building mode. 
Allow most MAF tools to allow limiting of output species. MAF tools which do not allow species limiting include Extract Pairwise MAF blocks, MAF Coverage stats, and Filter MAF blocks by Size.

The functionality of Filter MAF blocks by Species and Filter MAF blocks by Size is now available in Filter MAF by specified attributes. Unfortunately tests are still not able to be written for the Filter MAF by specified attributes tool.
 2009-02-04 14:55:45 -05:00
Nate Coraor 7560751dc8 Separate framework and tool environments. 
Whether running locally or via PBS, $PATH should now be handled in your
user's environment.

This also fixes problems like PYTHONPATH on the new blast nodes being
wrong (because they are x86_64 and the frontends are i686).

Note that you can actually start Galaxy without having an eggs dir now.
 2008-04-11 20:11:21 +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
Greg Von Kuster 4dd1f044e1 Removed tool version directiories for some of the tools...the rest soon. 2008-03-03 16:14:06 +00:00
Greg Von Kuster a2f475b55a Added tool version directories for maf tool directory. 2008-02-22 18:35:01 +00:00
Daniel Blankenberg 5b1552ffa8 Fix memory issues when dealing with MAF tools. 
Add new bx-python eggs.

Reorganize all MAF tools into a unified directory, and update tool_conf.

Remember to update tool_conf.xml from one of the samples (tool_conf.xml.sample or tool_conf.xml.main).
 2008-01-16 18:01:09 +00:00