Nicola Soranzo
39c0000c1b
Bump minimum pip version to 20.3 . Ignore `--replace-pip and --no-replace-pip` startup options
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Pip 20.3 added support for PEP 600, i.e. manylinux wheels using platform
tags of the form "manylinux_${GLIBCMAJOR}_${GLIBCMINOR}_${ARCH}". Fix
installation of dependencies like pysam 0.20.0 wheels, which otherwise need
to be built from source and can fail as reported by @assuntad23 in
https://gist.github.com/assuntad23/3022db63a6878f044a209961dd40e592
Also:
- Install `wheel` to fix warning like `Using legacy setup.py install for
beaker, since package 'wheel' is not installed.`
- Drop unnecessary `defaults` channel from conda commands.
- Fix "SC2223: This default assignment may cause DoS due to globbing. Quote
it." errors reported by `shellcheck -x` .
2023-01-17 15:01:38 +00:00
Nicola Soranzo
157d9647ea
Update docs on adding Python dependencies
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to use Wheelforge instead of Starforge.
2022-09-09 17:26:30 +01:00
Nicola Soranzo
0df5c9a5fb
Updates for Poetry 1.2.0
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Also:
- Export only dev requirements to `lib/galaxy/dependencies/dev-requirements.txt` .
- Packages don't have a `requirements.txt` file.
2022-09-05 17:23:18 +01:00
Marius van den Beek and Nicola Soranzo
a11e29b6f7
More details on adding or updating framework dependencies
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-02-16 15:38:20 +01:00
mvdbeek
62362d541c
Clarify that we only need wheels if upstream doesn't provide
2022-02-16 12:02:08 +01:00
mvdbeek
2a84df94ad
Drop unpinned dependencies section
2022-02-16 11:58:56 +01:00
mvdbeek
9c7c5429ee
Touch up wheel building instructions
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This is far from complete, but better than sending people to the wrong
place.
2022-02-15 16:19:20 +01:00
mvdbeek
04f6cd7f84
Drop irrelvant uWSGI virtualenv tips in framework dependencies docs
2022-02-15 16:19:14 +01:00
Nicola Soranzo
437f51c2a6
Create Python3 virtualenv by default
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- Allow specifying Python to use to create virtualenv using GALAXY_PYTHON
environment variable.
- Integrate Python support docs from https://galaxyproject.org/admin/python/
- Update virtualenv installation to use v16.7.9
2020-02-09 02:54:24 +00:00
Nicola Soranzo
77d8dac19a
Various doc fixes
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- Merge invisible `doc/source/admin/reports.md` into
`doc/source/admin/reports.rst`
- Misc fixes and cleanups
2020-02-07 02:37:57 +00:00
pvanheus
ae3b0cfb55
Note cannot import name _remove_dead_weakref error and solution
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Having a different Python version on the Galaxy server vs the compute nodes can cause an error including the message `ImportError: cannot import name _remove_dead_weakref`. This adds text to describe the error and its resolution
2019-03-04 22:00:46 +02:00
Nicola Soranzo
c6f1183939
Update documentation about dependencies
2019-02-18 22:36:32 +00:00
John Chilton
c679b64272
Merge pull request #7065 from ic4f/dev
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Fix link to requirements.txt
2018-12-02 21:54:12 -05:00
Sergey Golitsynskiy
6703584714
Fix link to requirements.txt
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Dependency files rearranged (commit 1b0ccf6
2018-11-30 19:26:41 -05:00
Dannon Baker
35bc1b387a
Typos in admin docs.
2018-11-09 16:26:33 -05:00
mvdbeek
9f8c29520d
Use virtualenv when conda is on PATH
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This uses our proper pinned requirements and is sginificantly easier
to set up and maintain.
2018-11-07 14:20:05 +01:00
Nicola Soranzo
c83c5cb784
Change conda channel priority: conda-forge > bioconda
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xref. https://github.com/bioconda/bioconda-utils/issues/330
2018-10-08 11:02:23 +01:00
Nicola Soranzo
ad02c53154
Fix many links
2018-09-03 14:34:13 +01:00
Nate Coraor
8261a2398a
Make the startup scripts play just as nicely with Conda as they do with
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virtualenv.
2018-04-04 16:38:01 -04:00
Nate Coraor
6d8edce331
Admin doc corrections
2018-02-01 16:25:12 -05:00
Nate Coraor
6333e83a65
Doc corrections from @nsoranzo
2018-01-26 10:18:53 -05:00
Nate Coraor
fd96864bd6
Finish updates to framework dependencies doc
2018-01-25 12:36:11 -05:00
Nate Coraor
6bdd755aaf
WIP framework dependencies doc update
2018-01-25 12:36:11 -05:00
Martin Cech
bdcf4807ce
add basic Reports documentation
2017-03-27 15:39:54 -04:00
Dannon Baker
a7b1ce7670
Update doc
2016-03-09 09:09:52 -05:00
Nate Coraor
9c7c75b766
Typo
2016-02-05 09:45:30 -05:00
Nate Coraor
4b24d95f6f
Improve documentation about binary-compatibility.cfg. Resolves #1672 .
2016-02-04 11:07:31 -05:00
Nate Coraor
33ba1face9
Link from the 16.01 announcement to the Admin wheels documentation,
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document the process of adding new wheels.
2016-01-28 13:13:09 -05:00
Nate Coraor
168f453094
Suggest installing virtualenv from brew
2016-01-26 16:49:39 -05:00
Nate Coraor
9827f32775
conda-requirements.txt renamed to conda-environment.txt
2016-01-26 16:48:38 -05:00
Nate Coraor
dc801dc1f6
Add admin documentation for framework dependencies (wheels) for the
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16.01 release.
2016-01-26 16:17:49 -05:00
Nicola Soranzo