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thkuo / seq2geno

Computational pipeline for genomic features of bacterial population
GNU General Public License v3.0
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the environment #16

Closed thkuo closed 5 years ago

thkuo commented 6 years ago

Use "script" function to execute python and r scripts instead of calling them with "shell". The scripts are thus need to be rewritten to fit the environment (eg. python and r versions) and variables inherits.

thkuo commented 6 years ago

Clean the main environment (currently phypal)

thkuo commented 6 years ago

The dependencies of perl environment has conflict wtih the R environment, causing problems when installing the environment. solution A: convert all the perl scripts to python (or r) solution B: solve the environment conflict

thkuo commented 5 years ago

also refer to #52