Commits · c4cc5c74a74bf50f38afecee613f2a766bbfe0c1 · ensembl-gh-mirror / ensembl

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Nov 06, 2009
- example of how to use the farm options in the config file · c4cc5c74
  Ian Longden authored 15 years ago
  
  c4cc5c74
- config file can now take the exonerate executable to use and the queue to be used by the farm · 63b1a507
  Ian Longden authored 15 years ago
  
  63b1a507
- added turkey specific analyses · a902ab5a
  Magali Ruffier authored 15 years ago
  
  a902ab5a
Nov 05, 2009
- fixed typo · a7974c01
  Steve Trevanion authored 15 years ago
  
  a7974c01
Nov 04, 2009
- Updated the script for new gene.biotype values processed_transcript and lincRNA. · 581f7c2b
  Michael Schuster authored 15 years ago
  
  581f7c2b
- fixed attrib code which was longer than allowed. · 629d0ede
  Julio Fernandez Banet authored 15 years ago
```
Add attrib for gene count of lincRNAs
```
  629d0ede
- Modifications made to allow xref projections to run across multiple servers. · 98230184
  Rhoda Kinsella authored 15 years ago
```
Addition of human and mouse projection to turkey plus human, mouse and danio to
stickleback.
```
  98230184
- Modifications made to allow xref projections to run across multiple database servers. · 260bbf82
  Rhoda Kinsella authored 15 years ago
  
  260bbf82
- supposed to be on branch so removing last update · 77b8fe0b
  Ian Longden authored 15 years ago
  
  77b8fe0b
- New order fro prioritys · 6546fb88
  Ian Longden authored 15 years ago
  
  6546fb88
- Updated test database to release 57. · b5a96250
  Andreas Kusalananda Kähäri authored 15 years ago
  
  b5a96250
- Changed query_identity to xref_identity and target_identity to ensembl_identity · 7398663b
  Rhoda Kinsella authored 15 years ago
  
  7398663b
- moved to funcgen · b64a3b84
  Rhoda Kinsella authored 15 years ago
  
  b64a3b84
- test · 64f0cebb
  Ian Longden authored 15 years ago
  
  64f0cebb
- module to control LRG Slices · 745adb29
  Ian Longden authored 15 years ago
  
  745adb29
- update staging databases etc · adf5748a
  Ian Longden authored 15 years ago
  
  adf5748a
- set ignore correctly dependong on the mode · 3b363ab2
  Ian Longden authored 15 years ago
  
  3b363ab2
- remove print statement that swamps the output · baab5fc7
  Ian Longden authored 15 years ago
  
  baab5fc7
- Do not get HGNC from Uniprot anymore as this makes it circular · aa6d0d24
  Ian Longden authored 15 years ago
  
  aa6d0d24
- get the refseq data from the normal ccds database rather than the tracker ccds database · 0323765d
  Ian Longden authored 15 years ago
  
  0323765d
Oct 30, 2009
- changed rcp to scp · 4ca48827
  Nathan Johnson authored 15 years ago
  
  4ca48827
- Uses DBI to attain persistant session READ lock · 310a3a8e
  Nathan Johnson authored 15 years ago
```
removed -probe_mapping options as this is obsolete
Still needs tweaking for ens-genomics2 as we're not picking up the hostname alias
```
  310a3a8e
Oct 29, 2009
- Be more straight-forward. · ca188a21
  Andreas Kusalananda Kähäri authored 15 years ago
  
  ca188a21
- Deprecated the following three methods: · e2a0c596
  Andreas Kusalananda Kähäri authored 15 years ago
```
  - get_all_AffyFeatures()
  - get_all_OligoFeatures()
  - get_all_OligoFeatures_by_type()

Functionality is instead provided by the Ensembl Functional Genomics
API.
```
  e2a0c596
- Added mysql dirs for ens-staging1&2 · 1a94b667
  Nathan Johnson authored 15 years ago
  
  1a94b667
Oct 28, 2009
- Remove excessive tabs. · 9df42048
  Andreas Kusalananda Kähäri authored 15 years ago
  
  9df42048
- Sort a list and outdent one of the items. · 93023fe7
  Andreas Kusalananda Kähäri authored 15 years ago
  
  93023fe7
- Use CORE::length() rather than just length() to disambiguate. · 316e66b5
  Andreas Kusalananda Kähäri authored 15 years ago
  
  316e66b5
- added ncbigene · aac80749
  Bronwen Aken authored 15 years ago
  
  aac80749
- *** empty log message *** · e15f6d4c
  William McLaren authored 15 years ago
  
  e15f6d4c
- Removed references to Oligo and Affy as now in efg · d1a7d97d
  Nathan Johnson authored 15 years ago
  
  d1a7d97d
- removed old Affy classes modules as these are now in efg · a3d4c21a
  Nathan Johnson authored 15 years ago
  
  a3d4c21a
- The list of command line switches was inconsistent. · 2a6eee42
  Andreas Kusalananda Kähäri authored 15 years ago
  
  2a6eee42
Oct 27, 2009
- Removed Oligo Classes and Adaptors · ce87f468
  Nathan Johnson authored 15 years ago
  
  ce87f468
- Removed old probe mapping scripts · 9072f20c
  Nathan Johnson authored 15 years ago
  
  9072f20c
- Changed StructuralVariationFeature to StructuralVariation · 830757f3
  William McLaren authored 15 years ago
  
  830757f3
- removed data patches · 69be0ab2
  Nathan Johnson authored 15 years ago
  
  69be0ab2
- Added patch_56_57c, which adds ALT_GENE to the external_db.type enumeration. · 105a0526
  Michael Schuster authored 15 years ago
  
  105a0526
- updated with affy tidy patch details · b9dc5742
  Nathan Johnson authored 15 years ago
  
  b9dc5742
- added affy tidy patch · cec0e1af
  Nathan Johnson authored 15 years ago
  
  cec0e1af