Commits · c8555886eab12d419d4f21df4d70aa6d95dc45f1 · ensembl-gh-mirror / ensembl-hive

This project is mirrored from https://:*****@github.com/Ensembl/ensembl-hive.git. Pull mirroring updated Aug 08, 2022.

18 Mar, 2016 3 commits
- made most of the tests in t/ runnable as standalone scripts · c8555886
  Matthieu Muffato authored Mar 18, 2016
  
  c8555886
- Copied and adapted the test-suite from 2.3 · 409f0181
  Matthieu Muffato authored Mar 18, 2016
  
  409f0181
- PostgreSQL doesn't know GROUP_CONCAT() · fda33dbd
  Matthieu Muffato authored Mar 18, 2016
  
  fda33dbd
17 Mar, 2016 1 commit
- bugfix [pgsql]: "argument of AND must be type boolean, not type integer" · e257b7de
  Matthieu Muffato authored Mar 17, 2016
  
  e257b7de
10 Mar, 2016 1 commit

bugfix: make sure the outer pair of quotes is removed as per bash rules (using... · 9d7edf37

Leo Gordon authored Mar 10, 2016

bugfix: make sure the outer pair of quotes is removed as per bash rules (using a new function) -- thanks to Harpreet for reporting

9d7edf37

08 Mar, 2016 1 commit
- bugfix: hide the URL password in LSF output (again) · c863467f
  Leo Gordon authored Mar 08, 2016
  
  c863467f
02 Feb, 2016 1 commit

compatibility fix: in LSF since version 9.1.2 job array index seems to be... · a34c8d96

Leo Gordon authored Feb 02, 2016

compatibility fix: in LSF since version 9.1.2 job array index seems to be appended to the first column of bjobs output - thanks to Jan Vogel for reporting

a34c8d96

29 Jan, 2016 1 commit
- Updated the copyright year --> 2016 · 758dbbd1
  Leo Gordon authored Jan 29, 2016
  
  758dbbd1
20 Jan, 2016 1 commit
- Capture errors from reading files / running commands in JobFactory · b937bc71
  Matthieu Muffato authored Jan 20, 2016
  
  b937bc71
11 Jan, 2016 1 commit
- bugfix: return binds stronger than "and" and "or" · 62caed79
  Leo Gordon authored Jan 11, 2016
  
  62caed79
08 Dec, 2015 1 commit
- bugfix: protect the specific quoting of the command from shell interpolation · 4f1bb003
  Leo Gordon authored Dec 08, 2015
  
  4f1bb003
23 Nov, 2015 7 commits
- Better way of sharing the "take_time" parameter · fe2a9468
  Matthieu Muffato authored Nov 23, 2015
  
  fe2a9468
- Made _add_together() a method so that we can die if input data are missing · 39a9b86b
  Matthieu Muffato authored Nov 23, 2015
  
  39a9b86b
- Renamed AnalysisStats::update() to update_stats_and_monitor() in order to... · db9be104
  Matthieu Muffato authored Nov 23, 2015
```
Renamed AnalysisStats::update() to update_stats_and_monitor() in order to restore the inherited update() method
```
  db9be104
- Added an option to accurately catch errors in pipes (needs bash to work) · 3bfa527e
  Matthieu Muffato authored Nov 16, 2015
  
  3bfa527e
- Use "bash -o pipefail" to make sure we catch errors on both sides of the pipe · cbeda052
  Matthieu Muffato authored Nov 15, 2015
  
  cbeda052
- Explain that is in minutes (but stored in secs) · 170af2c2
  Javier Herrero authored Nov 25, 2014
  
  170af2c2
- Set (cause_of_death) to 'UNKNOWN' when not defined · 96b7d55e
  Javier Herrero authored Nov 25, 2014
  
  96b7d55e
13 Nov, 2015 2 commits
- The batch-size is not set by the workers, so they shouldn't update it · 3024d0b7
  Matthieu Muffato authored Sep 28, 2015
  
  3024d0b7
- Only update hive_capacity in analysis_stats when in DYNAMIC mode · a22a4e4b
  Matthieu Muffato authored Sep 28, 2015
```
This way, we avoid overriding values set by an external source (a human,
for instance)
```
  a22a4e4b
27 Aug, 2015 1 commit
- bugfix: chunk_length and chunk_size must be updated at the same time the... · 2c545d12
  Matthieu Muffato authored Aug 27, 2015
```
bugfix: chunk_length and chunk_size must be updated at the same time the sequences are written (thank you @mn1 !)
```
  2c545d12
25 Aug, 2015 1 commit
- New option in FastaFactory to put the chunks in hashed directories · ce1cf0ec
  Matthieu Muffato authored Aug 25, 2015
  
  ce1cf0ec
18 Aug, 2015 1 commit
- bugfix: do not show the database password in the graph title · b19f06c6
  Matthieu Muffato authored Aug 18, 2015
  
  b19f06c6
13 Aug, 2015 1 commit
- Declare all the variables to avoid ParamWarning messages · 1a0cb137
  Matthieu Muffato authored Aug 13, 2015
  
  1a0cb137
18 Jun, 2015 1 commit
- bugfix: correctly identify situations where bkill-r was used · 047997a6
  Leo Gordon authored Jun 18, 2015
  
  047997a6
27 Mar, 2015 1 commit
- bugfix: prevent PostgreSQL from padding the test numbers with spaces · 69155d85
  Leo Gordon authored Mar 27, 2015
  
  69155d85
24 Feb, 2015 2 commits
- bugfix: be more specific when counting locally-running workers · 635dd4f3
  Leo Gordon authored Feb 24, 2015
  
  635dd4f3
- bugfix: leave quoting of strings to the DBI and switch to using placeholders · d9d2c7c6
  Leo Gordon authored Mar 17, 2014
```
(cherry-picked from version/2.1 branch)
```
  d9d2c7c6
16 Jan, 2015 1 commit
- bugfix: specialization failures should not be considered critical · 051fa22e
  Leo Gordon authored Jan 16, 2015
```
Conflicts:
	modules/Bio/EnsEMBL/Hive/Worker.pm
```
  051fa22e
05 Nov, 2014 2 commits
- hide the password previously passed to the schema patcher and potentially shown by die() · baca69ba
  Leo Gordon authored Nov 05, 2014
  
  baca69ba
- bugfix [to ee51e74e] : restore the password-hiding functionality between... · e6712560
  Leo Gordon authored Nov 05, 2014
```
bugfix [to ee51e74e] : restore the password-hiding functionality between beekeeper.pl and runWorker.pl
```
  e6712560
29 Oct, 2014 1 commit
- The main index is docs/index.html · 3f785d09
  Matthieu Muffato authored Oct 29, 2014
  
  3f785d09
27 Oct, 2014 4 commits
- fix warning "Use of uninitialized value in subroutine entry" · 9da22407
  Matthieu Muffato authored Oct 27, 2014
```
PR #5
```
  9da22407
- always write the sequence to the current seqio - fix for creating lots of empty output files · f7fe4373
  Roy Storey authored Oct 17, 2014
  
  f7fe4373
- setting to 0 as per POD and Leo's request · d9045a10
  Roy Storey authored Oct 26, 2014
  
  d9045a10
- fix warning "Use of uninitialized value in subroutine entry" · c2d46aef
  Roy Storey authored Oct 24, 2014
  
  c2d46aef
16 Oct, 2014 1 commit
- bugfix: prevent scheduling a negative number of Workers · c0381e5c
  Leo Gordon authored Oct 16, 2014
  
  c0381e5c
02 Sep, 2014 2 commits
- Added a link to the schema diagram in PNG · 4d5985df
  Matthieu Muffato authored Sep 02, 2014
  
  4d5985df
- Added an HTML index for the workshop · ce381371
  Matthieu Muffato authored Sep 02, 2014
  
  ce381371
01 Sep, 2014 1 commit
- Added the Doxygen documentation · 41c8920f
  Matthieu Muffato authored Aug 14, 2014
  
  41c8920f