Commits · 5583e54ed4f95f4cd4d8e954c553f86c8be1bdc2 · deep_genome / cedalion

08 Mar, 2017 19 commits
- Change: chicken_turtle_util.cli renamed to click · 5583e54e
  timdiels authored Oct 24, 2016
  
  5583e54e
- Doc: click help message · 82ba2dca
  timdiels authored Oct 24, 2016
  
  82ba2dca
- Change: no nul chars in pipeline name · 823c0733
  timdiels authored Oct 24, 2016
  
  823c0733
- Change: core.Context no longer requires cache/data directory · 33aa37ce
  timdiels authored Oct 24, 2016
  
  33aa37ce
- Enhance: Prevent release to PyPI · de397686
  timdiels authored Oct 24, 2016
  
  de397686
- Doc: * in middle of protein sequence is an error · 2c4ccc8f
  timdiels authored Oct 14, 2016
  
  2c4ccc8f
- Change: result directory: organise into input/output directory · 60edb7e9
  timdiels authored Oct 14, 2016
  
  60edb7e9
- Fix: replace fernproject fasta headers with a kind of gene id · b92b9a94
  timdiels authored Oct 14, 2016
  
  b92b9a94
- Fix Blast2GO. Decypher instead. Result directory: · eabcc2fe
  timdiels authored Oct 12, 2016
```
- Fixed and manually tested Blast2GO
- Decypher Blast instead of NCBI Blast
- Organise result into single directory of symlinks.
```
  eabcc2fe
- OrthoMCL: use decypher instead of ncbi blast · adbb22dc
  timdiels authored Sep 25, 2016
  
  adbb22dc
- Config file: rename 'general' section to 'pipeline' · 4beb6d3a
  timdiels authored Sep 25, 2016
  
  4beb6d3a
- Create core database if missing (instead of failing) · 6e5b2093
  timdiels authored Sep 25, 2016
  
  6e5b2093
- Replace test_run by gitignored deploy script · 1511fc61
  timdiels authored Sep 25, 2016
  
  1511fc61
- Blast2GO with Decypher Blast (nearly works) · 8189eb26
  timdiels authored Sep 25, 2016
  
  8189eb26
- Blast2GO attempt with blastp · 4a6c2436
  timdiels authored Sep 24, 2016
  
  4a6c2436
- Use redesigned core.pipeline. PhyML works now. · 1c5642a2
  timdiels authored Sep 20, 2016
  
  1c5642a2
- Refactor: remove old scripts and configuration files · b771ebc1
  timdiels authored Mar 08, 2017
  
  b771ebc1
- Apply chicken turtle project structure. Rename deep_blue_genome ->... · 4c9f7b0d
  timdiels authored Sep 20, 2016
```
Apply chicken turtle project structure. Rename deep_blue_genome -> deep_genome. Refactor up to PhyML and Blast2GO (exclusive)
```
  4c9f7b0d
- Initial commit · 363906b4
  timdiels authored May 02, 2016
```
The pipeline code written by Jan Deneweth, with passwords replaced by
TODO_* as the repository will be made public.
```
  363906b4