Suppress filenames in SAM merge using egrep #4
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Based on fix suggested by Roberto Alonso (at CIPF) on the mailing list, see: https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-February/021589.html
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+1 Option "-h" is supported also on OS X: https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man1/egrep.1.html I was also suggesting to Roberto to open a PR, but including also the changes to lib/galaxy/datatypes/sequence.py . |
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Fixing |
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If someone is going to be looking into this anyway, it might be nice to make sure that we are using a list of arguments instead of a string when calling the external command. And also probably not use os.system. But this change looks good to me. |
blankenberg
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Feb 25, 2015
Suppress filenames in SAM merge using egrep
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This is an automated message. Thanks for your contribution, a Trello card to track this issue has been created. Apply this patch for testing. |
jxtx
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Jun 16, 2015
Fix Guru's name in CONTRIBUTORS.md
bgruening
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Jul 11, 2015
Resolves the merge conflict, one minor whitespace fix.
jmchilton
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Jul 14, 2015
Update docs, re-instate backwards compatability
mvdbeek
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Mar 4, 2016
Fix execution order and short-circuit issue when installing tools
jmchilton
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Jun 15, 2016
Stays up-to-date with dev of galaxy project
dannon
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Aug 15, 2016
Force update repository manager to launch postfork.
martenson
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Sep 21, 2016
propagate allowed username changes to form hints
dannon
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Jan 31, 2017
I feel that mapping from
```
- from: blast+
to: blast
```
should be the same as
```
- from:
name: blast+
version: Null
to: blast
```
since it should just be syntatic sugar. And I think that second version reads like it should by default apply to all versions.
I feel therefore it is probably better to explicitly require stating that a mapping only applies to unversioned requirements. This commit does that by introducing the syntax:
```
- from:
name: blast+
unversioned: true
to:
name: blast
version: 1.3.4
```
It feels better to have strongly typed entities like this than to introduce magic constants such as:
```
- from:
name: blast+
version: __unversioned__
to:
name: blast
version: 1.3.4
```
which is another route this could have gone I guess.
mvdbeek
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Aug 1, 2024
Fixes #18633: ``` ValueError: dictionary update sequence element #4 has length 1; 2 is required File "galaxy/tools/__init__.py", line 1969, in handle_single_execution rval = self.execute( File "galaxy/tools/__init__.py", line 2066, in execute return self.tool_action.execute( File "galaxy/tools/actions/model_operations.py", line 89, in execute self._produce_outputs( File "galaxy/tools/actions/model_operations.py", line 120, in _produce_outputs tool.produce_outputs( File "galaxy/tools/__init__.py", line 3816, in produce_outputs new_labels_dict = dict(source_new_label) Exception caught while attempting to execute tool with id '__RELABEL_FROM_FILE__': ```
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Based on fix suggested by Roberto Alonso (at CIPF) on the mailing list, see:
https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-February/021589.html