Commits · baca69ba39b151fce564ce4afad676c0afd97e37 · ensembl-gh-mirror / ensembl-hive

This project is mirrored from https://:*****@github.com/Ensembl/ensembl-hive.git. Pull mirroring updated 26 minutes ago.

Nov 05, 2014
- hide the password previously passed to the schema patcher and potentially shown by die() · baca69ba
  Leo Gordon authored 10 years ago
  
  baca69ba
- bugfix [to ee51e74e] : restore the password-hiding functionality between... · e6712560
  Leo Gordon authored 10 years ago
```
bugfix [to ee51e74e] : restore the password-hiding functionality between beekeeper.pl and runWorker.pl
```
  e6712560
Oct 29, 2014
- The main index is docs/index.html · 3f785d09
  Matthieu Muffato authored 10 years ago
  
  3f785d09
Oct 27, 2014
- fix warning "Use of uninitialized value in subroutine entry" · 9da22407
  Matthieu Muffato authored 10 years ago
```
PR #5
```
  9da22407
- always write the sequence to the current seqio - fix for creating lots of empty output files · f7fe4373
  Roy Storey authored 10 years ago
  
  f7fe4373
- setting to 0 as per POD and Leo's request · d9045a10
  Roy Storey authored 10 years ago
  
  d9045a10
- fix warning "Use of uninitialized value in subroutine entry" · c2d46aef
  Roy Storey authored 10 years ago
  
  c2d46aef
Oct 16, 2014
- bugfix: prevent scheduling a negative number of Workers · c0381e5c
  Leo Gordon authored 10 years ago
  
  c0381e5c
Sep 02, 2014
- Added a link to the schema diagram in PNG · 4d5985df
  Matthieu Muffato authored 10 years ago
  
  4d5985df
- Added an HTML index for the workshop · ce381371
  Matthieu Muffato authored 10 years ago
  
  ce381371
Sep 01, 2014
- 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

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
- bugfix: be more conservative in rebalancing semaphore counters - Thanks to Irina for reporting · 2050dd61
  Leo Gordon authored 10 years ago
  
  2050dd61
May 15, 2014

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
- 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
- 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
- bugfix: added CLAIMED state to log_message.status to capture parameter parsing problems · 01bc9d89
  Leo Gordon authored 10 years ago
  
  01bc9d89
Mar 10, 2014
- 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
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
- added SGE and CONDOR configuration sections for future plugins · 1d099c6a
  Leo Gordon authored 11 years ago
  
  1d099c6a
Feb 10, 2014
- bugfix: stop printing diagnostic information on STDOUT · d15ca8f8
  Leo Gordon authored 11 years ago
  
  d15ca8f8
Feb 07, 2014
- Minutes should be displayed on the x axis (not 00) · 51b4c7ef
  Matthieu Muffato authored 11 years ago
  
  51b4c7ef
Jan 31, 2014
- cosmetic: added deprecated message to CreateNewJob() and some documentation to... · 13b19b79
  Leo Gordon authored 11 years ago
```
cosmetic: added deprecated message to CreateNewJob() and some documentation to store_jobs_and_adjust_counters()
```
  base/version/2.0
  
  13b19b79
Jan 30, 2014
- store_jobs_and_adjust_counters() now also deals with semaphore_count... · 1b89a412
  Leo Gordon authored 11 years ago
```
store_jobs_and_adjust_counters() now also deals with semaphore_count corrections. It is now the preferred job-creation interface.
```
  1b89a412
- a more straightforward storing method for an AnalysisJob · 6f8ef59b
  Leo Gordon authored 11 years ago
  
  6f8ef59b
Jan 28, 2014
- bugfix: no hope for other DBD drivers to support detection of... · e45199af
  Leo Gordon authored 11 years ago
```
bugfix: no hope for other DBD drivers to support detection of auto-incrementing fields => use our inernal fixed rule
```
  e45199af
- store a Job using BaseAdaptor's store() method · 95b1f35f
  Leo Gordon authored 11 years ago
  
  95b1f35f
- ObjectAdaptor is now overflow-aware and can store longer blobs transparently · 412da5f6
  Leo Gordon authored 11 years ago
  
  412da5f6
- let Job.input_id stringify itself · 93da7196
  Leo Gordon authored 11 years ago
  
  93da7196
- bugfix: stop printing overflow-related debug output to STDOUT; interface with... · 7ab1f0cb
  Leo Gordon authored 11 years ago
```
bugfix: stop printing overflow-related debug output to STDOUT; interface with overflow adaptor simplified
```
  7ab1f0cb