Commits · c90501546ad433802ab2ed4f18af64f2574031ed · ensembl-gh-mirror / ensembl-hive

This project is mirrored from https://:*****@github.com/Ensembl/ensembl-hive.git. Pull mirroring updated 24 minutes ago.

Sep 01, 2014

Merge branch 'version/1.9' into version/2.0 · c9050154

Matthieu Muffato authored 10 years ago

* version/1.9:
  Added the Doxygen documentation
  Added scripts documentation
  Added docs/index.html and use rawgit in README.md
  typo
  Include the CSS for the eHive HTML doc
  Doc update to please Doxygen
  bugfix: in each branch README.md will have to refer to its own version of docs
  adding reformatted install.html and README.md links to HTML documents (relying on htmlpreview functionality)

c9050154

Added the Doxygen documentation · 41c8920f
Matthieu Muffato authored 10 years ago

41c8920f
Added scripts documentation · 3172e1fd
Matthieu Muffato authored 10 years ago

3172e1fd
Added docs/index.html and use rawgit in README.md · 24a3a417
Matthieu Muffato authored 10 years ago

24a3a417
typo · 077c55dc
Matthieu Muffato authored 10 years ago

077c55dc

Include the CSS for the eHive HTML doc · 5da9608c

Matthieu Muffato authored 10 years ago

The CSS file is a copy from 00_general.css (in ensembl-webcode).
Variables have been replaced, and a few tweaks have been made:
 - global padding on <body>
 - font-size in the th/td elements

5da9608c

Doc update to please Doxygen · 16f33e19

Matthieu Muffato authored 10 years ago

Doxygen doesn't like when a =head2 section is not linked to a method.
We had to move the comments to #-prefixed lines.

16f33e19

Aug 04, 2014
- bugfix: in each branch README.md will have to refer to its own version of docs · 3cf8a95e
  Leo Gordon authored 10 years ago
  
  3cf8a95e
- adding reformatted install.html and README.md links to HTML documents (relying... · 7eb79753
  Leo Gordon authored 10 years ago
```
adding reformatted install.html and README.md links to HTML documents (relying on htmlpreview functionality)
```
  7eb79753
Jul 18, 2014
- pulling in the "pending independently" patch from version/1.9 · 7c15f499
  Leo Gordon authored 10 years ago
  
  7c15f499
- bugfix: make sure that when multiple users are running the same pipeline on... · 609fcc7f
  Leo Gordon authored 10 years ago
```
bugfix: make sure that when multiple users are running the same pipeline on LSF, the numbers of their pending jobs are computed independently -- thanks, Mateus!
```
  609fcc7f
Jun 05, 2014
- Pulling in the bugfix to rebalance semaphores more conservatively · 15926eb5
  Leo Gordon authored 10 years ago
  
  15926eb5
- bugfix: be more conservative in rebalancing semaphore counters - Thanks to Irina for reporting · 2050dd61
  Leo Gordon authored 10 years ago
  
  2050dd61
May 15, 2014

Pulling in the bugfix to distinguish /tmp directories of multiple local workers · ee990068
Leo Gordon authored 10 years ago

ee990068

Merge pull request #3 from jherrero/version/1.9 · ee9d4eec

Leo Gordon authored 10 years ago

bugfix: when using more than one standalone worker make sure their /tmp directories do not clash

ee9d4eec

Fix bug when using more than one standalone worker · eb3fbb00

Javier Herrero authored 10 years ago

The worker_temp_directory for standalone workers was set to
/tmp/worker_${USER}.standalone. If two standalone workers were running
on the machine, they could overwrite each other’s files.
The fix include the process ID ($$ in Perl) in the directory name.

eb3fbb00

Apr 23, 2014
- Pulling in the bugfix for jobs dying when parsing parameters · 658c9078
  Leo Gordon authored 10 years ago
  
  658c9078
- bugfix: make sure jobs that die while parsing parameters in CLAIMED state go directly to FAILED · 6eb4e142
  Leo Gordon authored 10 years ago
  
  6eb4e142
Apr 10, 2014
- Merge branch 'version/1.9' into version/2.0 · 6dc0d105
  Matthieu Muffato authored 10 years ago
```
* version/1.9:
  Really cleans-up the temp directory if it has been created by a previous worker
```
  6dc0d105
- Really cleans-up the temp directory if it has been created by a previous worker · fe8bef7c
  Matthieu Muffato authored 10 years ago
  
  fe8bef7c
Apr 04, 2014
- Pulling in the log_message.status U= { 'CLAIMED' } fix · 2311145f
  Leo Gordon authored 10 years ago
  
  2311145f
- bugfix: added CLAIMED state to log_message.status to capture parameter parsing problems · 01bc9d89
  Leo Gordon authored 10 years ago
  
  01bc9d89
Mar 25, 2014
- another version of LongMult pipeline to test -wait_for rules · cb3eb95f
  Leo Gordon authored 10 years ago
  
  cb3eb95f
Mar 18, 2014
- bugfix: do not crash when given full URL to analyses|tables · 5a3beced
  Leo Gordon authored 11 years ago
  
  5a3beced
Mar 12, 2014
- bugfix: even when given -url DBAdaptor should still be prepared to load registry. Thanks, Magali! · aa15abb8
  Leo Gordon authored 11 years ago
  
  aa15abb8
Mar 10, 2014
- Ported the versioning code to version/2.0 branch, added the branch description to Changelog · e3516eef
  Leo Gordon authored 11 years ago
  
  e3516eef
- Added a short description of changes for version 1.9 · 781ef4ae
  Leo Gordon authored 11 years ago
  
  781ef4ae
- The main scripts now report code and DB schema versions via calling a centralized Utils method · 611790a2
  Leo Gordon authored 11 years ago
  
  611790a2
- introducing code version that you can require via "use Bio::EnsEMBL::Hive::Version 2.0" · ef236a47
  Leo Gordon authored 11 years ago
  
  ef236a47
Mar 07, 2014
- incorporate the EHIVE_ROOT_DIR fix · 8c1bc771
  Leo Gordon authored 11 years ago
  
  8c1bc771
Feb 13, 2014
- hotfix: override automatic setting of EHIVE_ROOT_DIR to outwit unfriendly Meadows. Thanks, Lel! · 7f579a9e
  Leo Gordon authored 11 years ago
  
  7f579a9e
Feb 11, 2014
- bugfix: CoreDBConnection pretends to be a Bio::EnsEMBL::DBSQL::DBConnection when possible · 54ff3120
  Leo Gordon authored 11 years ago
  
  54ff3120
- merged-in: added SGE and CONDOR configuration sections for future plugins · 1785e9ed
  Leo Gordon authored 11 years ago
  
  1785e9ed
- added SGE and CONDOR configuration sections for future plugins · 1d099c6a
  Leo Gordon authored 11 years ago
  
  1d099c6a
Feb 10, 2014
- added two hotfixes from stable · b674bfe1
  Leo Gordon authored 11 years ago
  
  b674bfe1
- bugfix: stop printing diagnostic information on STDOUT · d15ca8f8
  Leo Gordon authored 11 years ago
  
  d15ca8f8
Feb 07, 2014
- simplify installation docs for coreless Hive · 2ff18a11
  Leo Gordon authored 11 years ago
  
  2ff18a11
- Minutes should be displayed on the x axis (not 00) · 51b4c7ef
  Matthieu Muffato authored 11 years ago
  
  51b4c7ef
- First attempt at coreless Hive code. Passes LongMult pipeline test. · 4910c5c3
  Leo Gordon authored 11 years ago
  
  4910c5c3
- removed an unused reference to Exception · 77fcf67d
  Leo Gordon authored 11 years ago
  
  77fcf67d