Install/command not found?

broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool

GNU General Public License v2.0

338 stars 60 forks source link

Install/command not found? #100

Closed Firedrops closed 5 years ago

Firedrops commented 5 years ago

I have downloaded the .jar release, and java -jar pilon.jar returns

Pilon version 1.23 Mon Nov 26 16:04:05 2018 -0500

    Usage: pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam]
                 [...other options...]
           pilon --help for option details

but pilon --help or pilon anything returns bash: pilon: command not found.

Am I still missing a step to correct usage?

Firedrops commented 5 years ago

Circumvented by installing via conda instead. Really should be in official documentation, only found this method from Googling.