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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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required fastafrombed to install phyloFlash #159

Open SumTot opened 2 years ago

SumTot commented 2 years ago

Hello, I am trying to install PhyloFlash but when I check for dependencies with: phyloFlash.pl -check_env

I get this message: Unable to find all required tools. These are missing: [11:48:47] fastaFromBed (fastaFromBed) [11:48:47] FATAL: Please make sure these are installed and in your PATH. Aborting.

I have install bedtools and it includes FastafromBed. In addition I have moved the command fastafromBed to the phyloFlash folder but it is not recognized. How can I fix the problem? Thank you in advance for your help!

HRGV commented 2 years ago

Hi, the tool calls are case sensitive. Could you please check that you can access fastaFromBed from the environment you are running phyloFlash in. Simply type it in at the command line. If you can not execute it, you need to fix this prior to running phyloFlash. fastaFromBed needs to be accessible in the folders that are given by $PATH.