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2707 Commits
Author SHA1 Message Date
Nicola Soranzo 775a771702 Merge branch 'release_20.01' into dev 2020-02-26 11:10:31 +01:00
mvdbeek d649338297 Fix TwoBitFile handle not opened in binary mode 
Fixes https://sentry.galaxyproject.org/sentry/main/issues/501741/:
```
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd7 in position 77: invalid continuation byte
  File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__
    iterable = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/middleware/statsd.py", line 34, in __call__
    req = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 143, in __call__
    return self.handle_request(environ, start_response)
  File "galaxy/web/framework/base.py", line 222, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/web/framework/decorators.py", line 57, in call_and_format
    rval = func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/api/genomes.py", line 41, in show
    region = self.app.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high)
  File "galaxy/visualization/genomes.py", line 395, in reference
    twobit = TwoBitFile(open(twobit_file_name))
  File "bx/seq/twobit.py", line 56, in __init__
    strng = file.read(TWOBIT_MAGIC_SIZE)
  File "python3.6/codecs.py", line 321, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
```
 2020-02-25 12:13:17 +01:00
Nicola Soranzo 739ab59eaa Merge branch 'release_20.01' into dev 2020-02-20 00:23:19 +00:00
Marius van den Beek b43c090d35 Merge pull request #9389 from mvdbeek/fix_tar_to_directory_dependency 
[20.01] Fix dependency for CONVERTER_tar_to_directory
 2020-02-19 20:26:22 +01:00
Marius van den Beek 8665316cac Merge pull request #9393 from mvdbeek/fix_maf_tools 
[20.01] Fix maf tools
 2020-02-19 20:25:58 +01:00
John Chilton 594fbb86b8 XML fix for joiner.xml. 2020-02-19 13:13:08 -05:00
Nicola Soranzo d4662fd952 Merge branch 'release_20.01' into dev 2020-02-19 12:43:07 +00:00
mvdbeek a1fef39956 Adjust bx-python imports for https://github.com/bxlab/bx-python/commit/fd08da3b49e89e0accd2c372d4a99427628ce432 2020-02-19 10:53:24 +01:00
mvdbeek 8e7c7915ba Adjust bx-python imports for https://github.com/bxlab/bx-python/commit/fd08da3b49e89e0accd2c372d4a99427628ce432 2020-02-19 10:53:01 +01:00
mvdbeek fb71055bfe Fix typo, other places that use wrong galaxy-util version 2020-02-19 09:56:02 +01:00
John Chilton 3ca67db5a7 Merge pull request #9336 from mvdbeek/legacy_tool_fixes 
[20.01] Add requirements, fix legacy tools and move them out of GALAXY_LIB_TOOLS_UNVERSIONED
 2020-02-18 08:52:04 -05:00
John Chilton 26327235cb Merge pull request #9345 from mvdbeek/converter_requirements 
[20.01] Add requirements to (almost) all converters, profile and minor fixes
 2020-02-14 14:24:29 -05:00
Nicola Soranzo 7d67b348c0 Merge branch 'release_20.01' into dev 2020-02-14 11:51:11 +00:00
Nicola Soranzo cbb071fc49 Remove GenomeSpace tools, OpenID, UI and requirements 2020-02-13 09:50:29 +00:00
mvdbeek 05e8117995 Move aggregate_scores_in_intervals2 out of GALAXY_LIB_TOOLS_UNVERSIONED 2020-02-12 09:47:36 +01:00
mvdbeek c05a9af4c8 Move wiggle_to_interval out of GALAXY_LIB_TOOLS_UNVERSIONED 2020-02-12 09:47:36 +01:00
mvdbeek 2549715563 Make join1 use proper requirements, move to GALAXY_LIB_TOOLS_VERSIONED 2020-02-12 09:47:36 +01:00
mvdbeek 1b7a36b2e4 Move secure_hash_message_digest to GALAXY_LIB_TOOLS_VERSIONED 
And give it its own dependency.
 2020-02-12 09:47:36 +01:00
mvdbeek 7d166eb24d Bump version and add profile 2020-02-12 09:47:36 +01:00
mvdbeek af4fdf7e1f Drop __next__ 2020-02-12 09:47:36 +01:00
mvdbeek eac0ff9d7f Fix vcf_to_maf_customtrack 2020-02-12 09:47:36 +01:00
Nicola Soranzo 7c1cacebbd Consistent "import" of maketrans 
Trying first with the most recent version is considered more Pythonic,
I think.
 2020-02-11 03:46:25 +00:00
mvdbeek 69642bffad Use context manager in CONVERTER_gff_to_bed_0 2020-02-09 16:44:20 +01:00
mvdbeek d355b778c5 Add python requirement to CONVERTER_bed_to_gff_0 2020-02-09 16:44:20 +01:00
Nicola Soranzo 81d20839f5 Merge branch 'release_20.01' into dev 2020-02-07 03:02:30 +00:00
Marius van den BeekandSergey Golitsynskiy 61bdd76f35 Update tools/plotting/bar_chart.py 
Co-Authored-By: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
 2020-02-06 16:28:52 +01:00
mvdbeek 2fe556959d Fix string module use 2020-02-06 16:18:28 +01:00
Nicola Soranzo 0a26ed38b2 Merge branch 'release_20.01' into dev 2020-02-05 15:26:27 +00:00
Nicola Soranzo 1dc1e5f219 Python3: unicodify the output of `subprocess.check_output()` 
By default it's a bytestring.

Also:
- don't use `shell=True`
- add a `splitlines()` forgotten in commit 670897ec5c
- raise exception instead of returning `error_info` in `docker_to_singularity()`
- use a random temp dir in `singularity_container_test()`
 2020-02-05 12:13:39 +00:00
Nicola Soranzo f32ece1e8d Faster and cleaner set creation 2020-02-03 15:42:09 +00:00
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
M Bernt fc58fd082a properly quote paths in upload script 2020-01-15 21:46:24 +01:00
xgaia 099da43ce8 upgrade tool to 3.2.1 2020-01-07 16:57:17 -05:00
xgaia 6ba2fafa5e add missing env 2020-01-07 16:57:10 -05:00
xgaia 5f15d5caa4 upgrade tool to 3.2.1 2020-01-06 15:17:06 +01:00
xgaia 3626950f6e add missing env 2020-01-06 15:13:15 +01:00
Marius van den Beek 9d1c6cad3b Merge pull request #8517 from xgaia/dev 
Upgrade askomics interactive tool
 2019-12-19 18:09:28 +01:00
Martin Cech 02d869bc62 drop duplicated env var 2019-12-19 10:53:19 -05:00
Martin Cech d835b6c572 bump image version 2019-12-19 10:52:05 -05:00
Martin Cech fd1367f3ed fix env name per @abretaud 2019-12-19 10:29:00 -05:00
Martin Cech 6a9df22287 adjust new ITs to newly available properties 2019-12-18 14:41:15 -05:00
Bjoern Gruening 278e25fc24 add 3 new ITs 2019-12-18 14:38:55 -05:00
Martin Cech 6f044b6a67 fix ITs: jupyter, iobio, phinch; commit author: @bgruening 2019-12-18 14:37:59 -05:00
Martin Cech 3727bd0404 Merge branch 'dev' into dev 2019-12-18 14:30:20 -05:00
M Bernt 2ea05e81f8 grouping: redecided for the less intrusive rstrip 2019-11-11 11:17:20 +01:00
M Bernt 3a0d9325a6 grouping: strip newlines 
fixes https://github.com/galaxyproject/galaxy/issues/8383

more generally: if grouping is done on the last column then the newline
was retained and contained in the output.
 2019-11-10 22:16:00 +01:00
Martin Cech 67a3950c27 Merge branch 'release_19.09' into dev 2019-11-08 12:55:24 -05:00
John Chilton 4ccef702be Cleanup structured IT internals access commit. 
- Unit test fixes and added tests.
- Change __history_id to __history_id__ per comment from @bgruening
 2019-10-30 09:59:55 -04:00
John Chilton 2e7a0720e7 Structured access to Galaxy internals for ITs. 2019-10-30 09:59:55 -04:00
John Chilton 94e19d7098 Merge pull request #8888 from nsoranzo/shebangs 
Fix script shebangs
 2019-10-27 13:22:16 -04:00