Commits · 0b16a1cd432913c838810bbd227cd5a49435ffe4 · ensembl-gh-mirror / ensembl

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Sep 26, 2013
- Updated for farm3 (unit for bsub's -M switch was changed for new farm). · 0b16a1cd
  Andreas Kusalananda Kähäri authored 11 years ago
  
  0b16a1cd
Jan 16, 2013
- Removed commas that shouldn't be before "rusage" in mem reqs. It used to work with those · 9a3942f0
  ens-carlos authored 12 years ago
```
commas though.
```
  9a3942f0
May 22, 2012
- ENSCORESW-156 . Fixing the memory requirements · 3ace762f
  Andy Yates authored 12 years ago
  
  3ace762f
Mar 20, 2012
- Use 'biotypes_include' (same as 'biotypes') and 'biotypes_exclude' · 92e9f90d
  Andreas Kusalananda Kähäri authored 13 years ago
```
(rather than 'not_biotypes'), for cleaner looking configuration.
```
  92e9f90d
Mar 19, 2012
- Include example of new 'not_biotypes' option. · b39b1228
  Andreas Kusalananda Kähäri authored 13 years ago
  
  b39b1228
Nov 10, 2011
- Use latest exonerate. · b955105f
  Andreas Kusalananda Kähäri authored 13 years ago
  
  b955105f
Oct 27, 2011
- · 3d7248c0
  Andreas Kusalananda Kähäri authored 13 years ago
```
Add gene_score_threshold (0.125).
```
  3d7248c0
Oct 05, 2011
- Remove the options for turning off exonerate and for not doing the · fa606048
  Andreas Kusalananda Kähäri authored 13 years ago
```
projection to highest common coordinate system.  Recent bugfix makes
these unneccesary.
```
  fa606048
Oct 03, 2011
- The synteny framework only needs 10 minutes, not 30. · 0691fb46
  Andreas Kusalananda Kähäri authored 13 years ago
  
  0691fb46
Sep 29, 2011
- Set default for do_similarity_scoring to '1'. · 910855cd
  Andreas Kusalananda Kähäri authored 13 years ago
  
  910855cd
Sep 27, 2011
- New options now implemented. · e6dc6dec
  Andreas Kusalananda Kähäri authored 13 years ago
  
  e6dc6dec
Sep 26, 2011
- New options (still to be implemented): · 0469ef29
  Andreas Kusalananda Kähäri authored 13 years ago
```
; TODO ; do_similarity_scoring      = 0
; TODO ; do_project_to_common_cs    = 0
```
  0469ef29
Sep 22, 2011
- Added "run_similarity_scoring" (defaults to '1' for the time being). · 8a619148
  Andreas Kusalananda Kähäri authored 13 years ago
```
This is an option for turning on or off exonerate.  You might want to do
this if the assembly hasn't changed.
```
  8a619148
Aug 30, 2011
- Estimate 90 minutes over all rather than 180. · e050a84d
  Andreas Kusalananda Kähäri authored 13 years ago
  
  e050a84d
- Remove unused "exonerate_jobs" parameter. · 4cc96770
  Andreas Kusalananda Kähäri authored 13 years ago
```
Add new "lsf_opt_exonerate" parameter.

Add running time estimates (not hard limits) for the various jobs.
```
  4cc96770
Mar 09, 2011
- Raise the transcript score threshold from zero to 0.25. This will in · 32996166
  Andreas Kusalananda Kähäri authored 14 years ago
```
the future prevent some of the worst transcript stable ID mappings to go
through.
```
  32996166
Mar 02, 2011
- Remove unused options. · da95416e
  Andreas Kusalananda Kähäri authored 14 years ago
```
Add options for separate DNA database (commented out).
```
  da95416e
Feb 24, 2011
- Updated. · cd8e33d8
  Andreas Kusalananda Kähäri authored 14 years ago
  
  cd8e33d8
Feb 11, 2009
- *** empty log message *** · cf398b08
  Glenn Proctor authored 16 years ago
  
  cf398b08
Apr 28, 2008
- plugin architecture for InternalIdMapper · ce19e680
  Patrick Meidl authored 16 years ago
  
  ce19e680
Apr 23, 2008
- added mapping_types and plugin_stable_id_gererator · 93ce6af7
  Patrick Meidl authored 16 years ago
  
  93ce6af7
Apr 22, 2008
- added --cache_method=build_cache_auto implementation · 2a60002d
  Patrick Meidl authored 16 years ago
  
  2a60002d
Apr 17, 2008
- new parameters to limit concurrent lsf jobs · 18fdc081
  Patrick Meidl authored 16 years ago
  
  18fdc081
Apr 04, 2008
- changed param dumppath to basedir · 23c5faec
  Patrick Meidl authored 16 years ago
  
  23c5faec
- changed LINUX86 to X86_64 lsf host type · ab711d25
  Patrick Meidl authored 16 years ago
  
  ab711d25
Oct 09, 2007
- latest config · 72dfae42
  Patrick Meidl authored 17 years ago
  
  72dfae42
Sep 14, 2007
- more configurable options · f1d581ea
  Patrick Meidl authored 17 years ago
  
  f1d581ea
Aug 27, 2007
- added "upload_*" and "urlprefix · 5f7e9882
  Patrick Meidl authored 17 years ago
  
  5f7e9882
Jun 29, 2007
- latest state of the code (mostly adaptations due to changes in ConfParser and Logger) · 649a4c36
  Patrick Meidl authored 17 years ago
  
  649a4c36
Oct 26, 2006
- score building, first full draft · b17d8adb
  Patrick Meidl authored 18 years ago
  
  b17d8adb
Jul 04, 2006
- stable Id mapping ported to perl · 687ad4c2
  Patrick Meidl authored 18 years ago
  
  687ad4c2