Merge sge-patch into dev-master - Githubissues

datasnakes / OrthoEvolution

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

https://orthoevolution.readthedocs.io/en/master/

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Merge sge-patch into dev-master #110

Closed sdhutchins closed 6 years ago

sdhutchins commented 6 years ago

Features Added

Improved SGE submodule
- Added SGEPipelineTask based on luigi and @jfeala's SGEJobTask
- Added a pipeline test to the Pipeline module
- Added sgeconfig
- Started on BaseJob and SGEJob
Improved gi_list_config
- Works on Linux but not windows. Needs speed improvement.
Nearly completed NCBIFtpClient
- Currently, works; Tested functions to download and update databases.
- Needs an archive function.

Features Deprecated

Qsub was replaced by sge
Qstatxml
- Needs replacing; Qstat class is intact but needs parsing function.