Dannon Baker
8b9e91310f
Merge branch 'release_17.05' into dev
2017-09-14 15:17:10 -04:00
Dannon Baker
a6acf116cd
Merge pull request #4607 from natefoo/py3-set-meta
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Python 3 fixes for set_metadata.py
2017-09-13 17:22:56 -04:00
John Chilton
52436aa4f9
Merge pull request #4600 from mvdbeek/datatypes_registroy_in_working_directory
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Write datatypes registry xml to working directory
2017-09-13 14:57:30 -04:00
Nate Coraor
b442113e76
Don't use + on iterators.
2017-09-13 13:45:29 -04:00
Nate Coraor
191d11c4a0
Python 3 fixes for set_metadata.py
2017-09-13 13:27:56 -04:00
Eric Rasche
11d4380d2b
Merge pull request #4599 from mvdbeek/make_qsub_submissions_more_robust
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Retry job submissions in ShellJobRunner
2017-09-13 14:39:53 +02:00
mvdbeek
ecd8b90e44
Decrease log-level for resubmission msg
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and specifiy log level directly in if/else clause. Thx @erasche.
2017-09-13 13:44:20 +02:00
E Rasche
61e05670c2
now unused imports
2017-09-13 07:53:41 +00:00
E Rasche
60dd7306d0
Remove unreachable statements
2017-09-13 05:59:03 +00:00
mvdbeek
194b249e1d
Fix import order
2017-09-12 21:08:35 +02:00
mvdbeek
49884cdfa3
Remove references to integrated_datatypes_config
2017-09-12 19:44:02 +02:00
mvdbeek
51f2ecf857
Use a string template to write registry xml
2017-09-12 19:15:12 +02:00
mvdbeek
b3b71343c1
Write out registry once per job
2017-09-12 19:15:12 +02:00
Marius van den Beek
36a3a6b3d9
Merge pull request #4569 from jvolkening/fast5
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fast5_archive datatype
2017-09-12 15:47:55 +02:00
mvdbeek
c5a08186b7
Retry job submissions in ShellJobRunner
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If I submit a large amount of jobs in a very short time I sometimes see
```
galaxy.jobs.runners.cli ERROR 2017-09-11 05:03:02,404 (17633) submission
failed (stderr): qsub: submit error (Invalid credential)
```
in my logs for a minor subset of jobs (2 out of 120 in the last instance
that this happened).
In this case waiting a little while and trying again solves the problem.
By default we will try submitting the job 3 times, and sleep 10 seconds
before trying again.
2017-09-12 15:14:42 +02:00
mvdbeek
7e2727bc0a
Remove bam to bai converter
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This converter served no real purpose (you can download bam index files
by clicking on the floppy icon, and we never had a bai datatype).
2017-09-12 14:04:41 +02:00
John Chilton
5da62ca264
Cancel workflow invocations when histories are deleted.
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With test case, rebased with spelling fixes thanks to @nsoranzo.
xref #3555 (third point)
2017-09-11 16:07:37 -04:00
jvolkening
08b5a47c39
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fast5
2017-09-08 08:52:50 -05:00
jvolkening
49258a7df8
fixed sniff order and misc linting errors
2017-09-08 08:48:52 -05:00
Dannon Baker
a8df8729b8
Merge pull request #4519 from shiltemann/biom2_datatype
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add biom2 datatype
2017-09-07 15:42:54 -04:00
jvolkening
297d2353ce
add datatype tests
2017-09-07 13:24:05 -05:00
jvolkening
f07c6a9843
optimized sniffing, subclassed different tarball types
2017-09-07 12:04:33 -05:00
shiltemann
2615094597
Revert "remove unused variable"
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This reverts commit 4119caf9b7
2017-09-07 18:22:58 +02:00
shiltemann
d4cf4bff4f
PEP8 fix
2017-09-07 18:11:00 +02:00
Saskia Hiltemann
8f3c65c59e
use version 2.7.1 of h5py
2017-09-07 17:39:01 +02:00
E Rasche
618d89b972
lint-import-order
2017-09-07 16:31:32 +02:00
E Rasche
cb41639078
flake8
2017-09-07 16:31:32 +02:00
E Rasche
36758478d5
non-URL things get passed to this function
2017-09-07 16:31:21 +02:00
E Rasche
d1892fc444
the library prefers unicode stuff
2017-09-07 16:31:21 +02:00
E Rasche
e50e7239b5
Implement IP address whitelisting
2017-09-07 16:31:20 +02:00
Nate Coraor
74f7181eaf
Merge pull request #4503 from mvdbeek/paramiko_long_running
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Allow paramiko cli to recover from ssh timeout
2017-09-07 10:19:04 -04:00
John Chilton
57ff68edd0
Merge pull request #4539 from mvdbeek/purge_source
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Prevent in-place editing of uploaded files if files are imported from the FTP folder
2017-09-07 10:11:04 -04:00
jvolkening
2fc60430a1
fix formatting to make tox happy
2017-09-07 08:24:19 -05:00
mvdbeek
b17fbfb968
Fix startup of galaxy when wehbooks dir is empty
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Reported by @alpapan on gitter.
2017-09-07 13:57:50 +02:00
jvolkening
9e6cb13e31
Merge remote-tracking branch 'upstream/dev' into fast5
2017-09-06 19:34:49 -05:00
Nicola Soranzo
37802abee2
Merge pull request #4560 from martenson/improving-datalibraries
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improve docs and access checks in datalibs manager/api
2017-09-06 09:11:15 +01:00
Nicola Soranzo
486f436e76
Merge pull request #4559 from mvdbeek/use_bzip2file
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Allow working with pbzip2 compressed files
2017-09-06 01:32:26 +01:00
Martin Cech
f78eca8912
remove unused import
2017-09-05 14:28:21 -04:00
mvdbeek
8c4716e71d
Use environment markers to select bz2file when python is < 3.3
2017-09-05 19:32:37 +02:00
Dannon Baker
7db47e7e3c
Merge pull request #4557 from jmchilton/shared_histories_unbound
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Prevent unbound variable error history controller.
2017-09-05 13:27:51 -04:00
mvdbeek
cccf79ac5f
Make bz2file dependency conditional on python being below version 3.3
2017-09-05 18:30:25 +02:00
Nicola Soranzo
235bdca1eb
Merge pull request #4556 from jmchilton/conditional_chronos
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Make chronos dependency conditional.
2017-09-05 17:26:05 +01:00
jvolkening
87b798d40a
FAST5 archive support
2017-09-05 11:08:54 -05:00
mvdbeek
4de0ec59f3
Add bz2file to list of requirements
2017-09-05 17:54:24 +02:00
Martin Cech
b12d29d14b
improve docs and access checks
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thanks @nsoranzo
2017-09-05 11:50:33 -04:00
John Chilton
65b86e3eb0
Merge pull request #4553 from mvdbeek/allow_exporting_workflow_with_uninstalled_tools
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Allow exporting workflows when tool is uninstalled
2017-09-05 11:04:59 -04:00
mvdbeek
46c85ffa98
Allow working with pbzip2 compressed files
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This adds supprt for uploading and uncompressing pbzip2 compressed
files by exchanging the bz2 module with bz2file (recommended as workaround in
https://docs.python.org/2/library/bz2.html ). The problem was reported by
@alpapan in #4538 and this commit should fix #4538 .
Depends on https://github.com/galaxyproject/starforge/pull/147 for the
bz2file wheel.
2017-09-05 16:54:34 +02:00
John Chilton
338b0c994c
Merge pull request #4511 from FredericBGA/import_history_and_symlink
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import of history works even if we use symlink in database directory
2017-09-05 10:53:44 -04:00
John Chilton
c671581900
Prevent unbound variable error history controller.
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Fixes #4423 I suppose - thanks @erasche.
2017-09-05 10:39:42 -04:00
John Chilton
932a3aa3be
Make chronos dependency conditional.
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Fixes #4085 .
2017-09-05 10:28:16 -04:00
Dannon Baker