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cancerit / cgpCaVEManPostProcessing

Flagging add on to CaVEMan
http://cancerit.github.io/cgpCaVEManPostProcessing/
GNU Affero General Public License v3.0
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Add use of share dir to config files #17

Closed ghost closed 6 years ago

ghost commented 7 years ago

Ensure cgpCaVEManWrapper installs config ini files to a share dir rather than requiring them to be copied to a reference area.

ghost commented 6 years ago

Decided to provide appropriate error message to point to the shared area if the sharedir is to be used but species couldn't be resolved.

ghost commented 6 years ago

Given the species name passed is used to resolve the species in the file itself, we need to rename the directories to common names e.g. Human, rather than Homo_sapiens, have dual copies, one for each variant, or some sort of translation code. Any opinions @keiranmraine @AndyMenzies ?

ghost commented 6 years ago

Will add a new issue for the discussed changes #27

ghost commented 6 years ago

Merged into feature/overlapping_reads https://github.com/cancerit/cgpCaVEManPostProcessing/commit/289627c3500ee8d09bd2ed5695a4f367a37a7426