Nicola Soranzo
178a1efb30
Remove outdated fimo wrapper and galaxy-sequence-utils dependency
...
The fimo tool was removed from `tool_conf.xml.sample` in 2014
(commit fa11d10c8bhttps://github.com/galaxyproject/tools-iuc/pull/499 ).
This bundled version doesn't probably work any more and is not
available on the UseGalaxy.* servers.
This allows us to remove `galaxy-sequence-utils` from the project
dependencies, since the other 2 tools
(`lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml`
and `tools/maf/vcf_to_maf_customtrack.xml`) correctly specify it as a
requirement.
2024-10-04 12:33:26 +01:00
Dannon Baker
03351d2a9f
Apply black to tools as well
2022-02-03 09:12:13 -05:00
John Chilton
54e8d22fa7
Check types of modules without type annotations in the their signatures on new modules.
...
https://mypy.readthedocs.io/en/stable/command_line.html#cmdoption-mypy-check-untyped-defs
> it type checks the body of every function, regardless of whether it has type annotations. (By default the bodies of functions without annotations are not type checked.)
2021-10-11 16:08:26 -04:00
Nicola Soranzo
f5cd88465e
Make str.join()s more efficient
...
by using generator expressions and tuples instead of lists.
2020-01-23 11:06:32 +00:00
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
39da6c3278
Fix the remaining 2180 flake8 errors in tools/ .
2016-02-10 18:46:03 +00:00
John Chilton
d6ec2f021c
Specify meme requirement for fimo tool.
2012-02-02 21:29:30 -06:00
Daniel Blankenberg
cf4dbf7f6a
Have fimo.xml use fields.path approach instead of directly filtering on data table.
2011-11-22 12:21:05 -05:00
Daniel Blankenberg
378c5eeacd
Tool help updates.
2011-09-21 04:11:07 -04:00
Daniel Blankenberg
8768351b99
Add FIMO tool from MEME suite.
2011-08-22 14:52:11 -04:00
Ross Lazarus
d53c3e984f
Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository
...
This is a backout of commit 5765
2011-07-06 09:44:56 +10:00
Ross Lazarus
86b55bb0c0
branch merge
2011-07-05 12:40:43 +10:00
Kanwei Li
43db543f1f
Update test-data files for meme 4.6.0
2011-02-25 14:58:35 -05:00
Daniel Blankenberg
d892a301e3
Add MEME tool configuration file.
2011-02-01 11:17:44 -05:00
Nicola Soranzo