Commits · 5215a997cd90cab054aa0ef691b97c6d380acdbf · ensembl-gh-mirror / ensembl-hive

This project is mirrored from https://:*****@github.com/Ensembl/ensembl-hive.git. Pull mirroring updated 9 minutes ago.

Mar 05, 2013
- extend a method in JobAdaptor to return a limited number of jobs (for use in generate_graph) · 5215a997
  Leo Gordon authored 12 years ago
  
  5215a997
Mar 01, 2013
- Fixed a memory leak in data_dbc() · f44ec5cb
  Matthieu Muffato authored 12 years ago
  
  f44ec5cb
Feb 28, 2013
- cosmetic: renamed README.txt back to README to retain an unbroken history in CVS · a2735bba
  Leo Gordon authored 12 years ago
  
  a2735bba
- cosmetic: added new commits to README and renamed it Changelog; split out the... · c22c76e5
  Leo Gordon authored 12 years ago
```
cosmetic:  added new commits to README and renamed it Changelog; split out the old README.txt (non-Changelog part)
```
  c22c76e5
- avoid having beekeeper run in submitted-to-the-farm state - detect it, report and quit · b57d7d04
  Leo Gordon authored 12 years ago
  
  b57d7d04
- param_substitution is now default everywhere, no need to call it explicitly · e31f86dd
  Leo Gordon authored 12 years ago
  
  e31f86dd
- added param_required() and param_is_defined() interfaces to Process · 9911fc95
  Leo Gordon authored 12 years ago
  
  9911fc95
Feb 27, 2013
- bugfix: updated examples of how to use JobFactory without and with input_id_template · eec01bfd
  Leo Gordon authored 12 years ago
  
  eec01bfd
- bugfix: changed implementation of data_dbc() to correctly compare things before caching · 040f6dc6
  Leo Gordon authored 12 years ago
  
  040f6dc6
- Clone::clone is no longer used, so dependency has been removed · 01186efa
  Leo Gordon authored 12 years ago
  
  01186efa
Feb 25, 2013
- It is more efficient to give MySQL a LIMIT clause · 97ef20de
  Matthieu Muffato authored 12 years ago
  
  97ef20de
Feb 23, 2013

JobFactory uses $overriding_hash to create jobs/rows from input_id_template;... · e2ac50d8

Leo Gordon authored 12 years ago

JobFactory uses $overriding_hash to create jobs/rows from input_id_template; 'input_id' parameter deprecated; standaloneJob supports templates.

e2ac50d8

Substitution machinery now supports an extra $overriding_hash that contains... · ee740713

Leo Gordon authored 12 years ago

Substitution machinery now supports an extra $overriding_hash that contains parameters with higher precedence than the whole of param() structure

ee740713

Feb 22, 2013
- fixed several problems with parameter substitution and detection of undefs;... · 24ccc976
  Leo Gordon authored 12 years ago
```
fixed several problems with parameter substitution and detection of undefs; added param_required() and param_is_defined()
```
  24ccc976
- reload the cached data_dbc() value on change of param('db_conn') · a63e0880
  Leo Gordon authored 12 years ago
  
  a63e0880
Feb 21, 2013
- The modules of the analyses must be accessible · 163f7250
  emepyc authored 12 years ago
  
  163f7250
Feb 20, 2013
- New runnable to check the size of the resultset of any SQL query · 11e97693
  Matthieu Muffato authored 12 years ago
  
  11e97693
Feb 19, 2013
- removed param_substitute() call from Runnables -- no longer needed, as substitution is automatic · 466eff91
  Leo Gordon authored 12 years ago
  
  466eff91
- a "total" (anything-to-anything) substitution mechanism has been implemented in Hive::Params · 4738451a
  Leo Gordon authored 12 years ago
  
  4738451a
Feb 18, 2013
- The preferred meadow type must be registered · ac43d03d
  Matthieu Muffato authored 12 years ago
  
  ac43d03d
- The modules of the analysis must be loadable · 7f7a24f7
  Matthieu Muffato authored 12 years ago
  
  7f7a24f7
- In dataflow rules within the same database, the destination analysis must exist · 30dbffd3
  Matthieu Muffato authored 12 years ago
  
  30dbffd3
- In control rules within the same database, the condition analysis must exist · c40028e3
  Matthieu Muffato authored 12 years ago
  
  c40028e3
Feb 15, 2013
- make sure all LSF pids are quoted, to protect them from tcsh interpretation of square brackets · ab023be5
  Leo Gordon authored 12 years ago
  
  ab023be5
Feb 14, 2013
- a new script to remove old "DONE" jobs and associated job_file and log_message entries · 1b5487c4
  Leo Gordon authored 12 years ago
  
  1b5487c4
- seed_pipeline.pl now shows examples of input_ids of seedable analyses · db583ef6
  Leo Gordon authored 12 years ago
  
  db583ef6
- Made $final_clause a parameter of _generic_fetch() & removed default ORDER-BY; hopefully faster · 0534027c
  Leo Gordon authored 12 years ago
  
  0534027c
Feb 13, 2013
- In case no -logic_name/-analysis_id was supplied, show the list of analyses... · e0b9856f
  Leo Gordon authored 12 years ago
```
In case no -logic_name/-analysis_id was supplied, show the list of analyses that have no incoming dataflow (and so are candidates for seeding)
```
  e0b9856f
- Added perldoc to seed_pipeline.pl script · c5ad3d59
  Leo Gordon authored 12 years ago
  
  c5ad3d59
- A new script to quickly seed any analysis of any pipeline. · 51b175d8
  Leo Gordon authored 12 years ago
  
  51b175d8
- hide the calls to URLFactory into the DBAdaptor's constructor · f174a05a
  Leo Gordon authored 12 years ago
  
  f174a05a
Feb 12, 2013
- hash of resources no longer depends on default_meadow (bugfix) · 969061b9
  Leo Gordon authored 12 years ago
  
  969061b9
Feb 07, 2013
- Updated to release 71 · 756de99d
  Kathryn Beal authored 12 years ago
  
  756de99d
Feb 06, 2013
- Tables must be in the right order. Otherwise, the foreign key checks complain · c47dc9bf
  Matthieu Muffato authored 12 years ago
  
  c47dc9bf
Jan 25, 2013
- resolving conflict: using mine · 4ac338e1
  Leo Gordon authored 12 years ago
  
  4ac338e1
- diagram improvement: (1) no more "empty boxes" and (2) tables dataflown from a... · 50066325
  Leo Gordon authored 12 years ago
```
diagram improvement: (1) no more "empty boxes" and (2) tables dataflown from a box are shown in their boxes
```
  50066325
Jan 15, 2013
- Table dataflows are now included into semaphore boxes (bugfix: wrong internal name) · 924d002d
  Matthieu Muffato authored 12 years ago
  
  924d002d
Jan 14, 2013
- Added a new presentation, moved presentations into a separate folder. · af7da3a7
  Leo Gordon authored 12 years ago
  
  af7da3a7
Jan 11, 2013
- cosmetic fix: commented back the debug output that was left uncommented by mistake · c643f1ca
  Leo Gordon authored 12 years ago
  
  c643f1ca
- Added coloured barchart display option and jobs/data display option (no big... · 2796654c
  Leo Gordon authored 12 years ago
```
Added coloured barchart display option and jobs/data display option (no big data checks, use with care on small examples).
'Pad' is now configurable from JSON.
Beware: JSON config options have moved around!
```
  2796654c