search

xiezhq / ISEScan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Apache License 2.0
84 stars 16 forks source link

Remove hard coded 3rd party dependencies #32

Closed oschwengers closed 3 years ago

oschwengers commented 4 years ago

Hi @xiezhq , would it be possible to remove the hard coded paths in the constants.py to all 3rd party dependencies like FragGeneScan, Blast and HMMER?

This would make it easier to distribute and integrate ISEScan. For example, in BioConda the required patch file could be removed: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/isescan/constants.patch

For example: https://github.com/xiezhq/ISEScan/blob/38e37bc066108422ac6bd406df661cd855cc34f0/constants.py#L9

xiezhq commented 3 years ago

yes, it can be done. Again, I will implement your suggestions in new version of ISEScan.

xiezhq commented 3 years ago

Update, ISEScan v1.7.2.2 and later remove the hard coded 3rd party dependencies, see release history.