Basic functionality achieved
Added color class, renamed some variables
Added new GATK server and example_bam resource
Handle update command
Merge branch 'feature/update' into develop
Resources save in their folder, bam auto recognized as binary, multiple file names, only warn if invalid resource id
Added ucsc and ensembl servers
Added 3 resources, corrected ensembl login
Added three resources: 1000G, NCBI assembly, UCSC assembly
Loop over resources to return key and doctoring
Added messenger module
Renamed module: yaml_reader -> yaml
New class: Registry
- get a resource
- list all resources
- search (fuzzy) resources
- fuzzy matchOne
Renamed class: YamlReader -> DefaultReader
- get -> find
New class: HistoryReader
- return resources to update
Documentation and generalised variable names
Merge branch 'feature/search' into develop
- Removed bcolors class (magic…)
+ Added docs
Merge branch 'feature/color-cli' into develop
* Changed order of arguments for send method
* Changed structure for cosmid script
+ Added resource.id attr
* Started including Registry in cosmid cli
+ Added ghost printing (messenger)
+ Added goahead method to Registry
* Changed name of YAML module (yaml -> yml) due to conflict
* Moved a lot of the logic to Registry
+ New 'grab' method in Registry
* YAML readers no longer complain directly about not finding files
+ cosmic exec handles file creation etc.
- Not changing work dir but appending to path names
* Fixed some bugs
+ Added dependencies