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eb0bfbd98b46c4a85fc8a1004e4eccfcbbd0f6d9
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14 Commits
Author SHA1 Message Date
Dannon Baker 03351d2a9f Apply black to tools as well 2022-02-03 09:12:13 -05:00
Nicola Soranzo 452aba9ee3 Fix remaining issues reported by bugbear; add it to flake8 reqs 2021-01-16 05:58:15 +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 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
Daniel Blankenberg 87eebd3206 First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary. 
These changes should only affect output when an input block has a species appearing more than once, with the exception being the MAF to multiple FASTA blocks converters: the FASTA headers have been revised to included the sequence index for a species in a block as well as the block index.

A new tool "Split MAF Blocks by Species" has been added that will split MAF blocks into the complete combination of multiple blocks when a species appears more than once.
 2009-09-04 10:40:16 -04:00
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