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
f865e8359f
Deprecate size attribute of <param/> and remove it from tools
...
Also:
- dos2unix test/functional/tools/for_workflows/head.xml
- Single-quote text and data params in `<command/>`
- Remove deprecated `interpreter` attribute of `<command />`
2018-09-10 11:34:37 +01:00
Katrin Leinweber
f99f8667bc
Hyperlink DOIs against preferred resolver
2018-05-30 16:49:21 +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
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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
ed4132d9c0
Python3: Use open() instead of file()
2016-05-17 23:53:16 +01:00
Nicola Soranzo
39da6c3278
Fix the remaining 2180 flake8 errors in tools/ .
2016-02-10 18:46:03 +00:00
John Chilton
88239abf5c
Add more distribution tool citations.
...
xref #361 .
2015-10-05 15:16:50 +01:00
John Chilton
591519009b
Add citations to a few more tools.
2015-10-05 15:12:46 +01:00
peterjc
fce2184e5b
Make tool version explicit (Job runner would assume 1.0.0)
2015-03-09 15:21:48 +00:00
John Chilton
34e1273f9b
Rework pull request #489 memory handling to respect deployer set _JAVA_OPTIONS.
...
As discussed here https://bitbucket.org/galaxy/galaxy-central/pull-request/489/srma-tool-requires-at-least-2048m-memory/diff . Thanks to Bjoern for input.
2014-09-22 13:20:49 -04:00
Lance Parsons
0a3e5d274f
SRMA tool requires at least 2048m memory and LENIENT validation stringency
2014-09-04 16:12:51 -04:00
Dave Bouvier
448d9f55eb
Migrate 43 tools from the distribution to the tool shed.
2014-01-27 09:53:14 -05:00
Nicola Soranzo
62673b0134
Fix for failure preparing job: "NotFound: cannot find 'mfl'" with paired-end library.
...
Add mate FASTQ file to inputs.
'ls' param was not used.
Add missing '-mfl ' to MosaikBuild command.
Remove always empty $lm variable.
Add <version_command>.
2013-12-06 11:20:56 +01:00
Nicola Soranzo
926d6de51d
Specify mosaik v. 1.1.0021 (last compatible with the wrapper). Add requirement for samtools.
2013-12-06 11:17:25 +01:00
Nicola Soranzo
3e528ae02b
Enhance bowtie2 to utilize GALAXY_SLOTS configuration when available.
2013-11-16 00:53:52 +01:00
Nicola Soranzo
c4e9999a33
Enhance mosaik to utilize GALAXY_SLOTS configuration when available.
2013-11-16 00:53:35 +01:00
John Chilton
162e4de0e1
Enhance bfast to utilize GALAXY_SLOTS configuration when available.
2013-11-05 13:46:06 -06:00
John Chilton
60488bf064
Merged in nsoranzo/galaxy-central-tools2 (pull request #234 )
...
Bug fixes for 3 tools (rebased #222 )
2013-10-16 12:49:34 -05:00
Aysam Guerler
d9b284bf5e
Modify bowtie error handler
2013-10-16 11:03:51 -04:00
Ross Lazarus
c1af859f90
revert bowtie2 and tophat2 wrappers
2013-10-08 13:34:54 +11:00
Ross Lazarus
4caf74eaa6
backout -r 10806
2013-10-08 10:54:45 +11:00
Ross Lazarus
070ee188fa
backout -r 10800
2013-10-08 10:52:21 +11:00
Ross Lazarus
a17e071f38
hg backout -r 1092b0d
...
backout unintended commits to tophat and bowtie2 wrappers
2013-10-08 10:24:59 +11:00
Nicola Soranzo
f109dea17f
Fix for "syntax error near unexpected token `;;'".
...
<command> should not end with a semicolon, otherwise
BaseJobRunner.build_command_line() would create a bash command containing
';;' when appending metadata setting commands.
2013-10-04 18:15:22 +02:00
Ross Lazarus
7146ba9c38
tweaks. ready for branch merge
2013-08-12 13:04:57 +10:00
Ross Lazarus
a4622551de
branch merge with central
2013-08-08 15:38:10 +10:00
Aysam Guerler
59dea4d61f
Bowtie2: Added quotation marks to group selection and added basic tool test
2013-08-07 14:17:43 -04:00
Ross Lazarus
8604c3b542
fixing on_string again. Add job title to tophat2
2013-08-05 10:27:13 +10:00
Ross Lazarus
24dd794183
update bowtie2 wrapper
2013-08-04 17:44:45 +10:00
Aysam Guerler
fe048358fd
bowtie2 wrapper update
2013-07-19 14:56:39 -04:00
Aysam Guerler
3367d43d49
bowtie2 tool wrapper update
2013-07-19 14:30:38 -04:00
Jeremy Goecks
7538091308
Change order of Bowtie2 output datasets to put aligned reads at top of history.
2013-01-30 12:55:49 -05:00
Andrea Sbardellati
47630c9ed6
Add option for writing not aligned reads to file
...
Reviewed-by: Nicola Soranzo <soranzo@crs4.it >
2013-01-18 17:11:04 +01:00
Nicola Soranzo
b571178cc8
Add missing samtools requirement to bowtie2 wrapper
2013-01-10 18:50:51 +01:00
Jeremy Goecks
d254249fda
Fix bug in bowtie2 wrapper that prevented wrapper from working with old versions of samtools.
2013-01-08 09:25:16 -05:00
Jeremy Goecks
b9ed8bec42
Bowtie2 wrapper: move read group parameters out of full parameter settings and into own group.
2012-12-18 13:35:56 -05:00
Jeremy Goecks
1149f1fcf3
Add simple read group options for Bowtie2.
2012-12-18 12:08:47 -05:00
Dave Bouvier
917d5a72e8
Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.
2012-11-26 10:18:47 -05:00
Dave Bouvier
6a44e8f34a
Remove the bwa wrappers from the repository.
2012-10-01 09:24:33 -04:00
Jeremy Goecks
41682ee6c9
Output sorted BAM from Bowtie2.
2012-08-22 16:49:12 -04:00
Jeremy Goecks
6f2c3d6761
Have Bowtie2 wrapper produce BAM rather than SAM output.
2012-06-11 15:52:36 -04:00
Jeremy Goecks
0c12da85ba
Add min, max insert size parameters to bowtie2 wrapper.
2012-06-08 14:03:41 -04:00
Jeremy Goecks
a08c0c03ce
Fix bug in setting Bowtie2 parameters.
2012-06-08 13:48:37 -04:00
Jeremy Goecks
63fec8c332
Add preset alignment options to Bowtie2 wrapper and fix default in Tophat2 wrapper.
2012-06-06 15:27:59 -04:00
Jeremy Goecks
7c40df458e
Skeleton wrapper for Bowtie2.
2012-04-26 15:28:17 -04:00
Daniel Blankenberg
0372d1fe06
Fix for BWA -R option.
2012-04-10 09:24:25 -04:00
Daniel Blankenberg
8a6b0001c2
Minor fix for 04e8ed0cd930.
2011-11-29 17:35:14 -05:00
Nicola Soranzo