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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Pangenome Pipeline, cactus_convertAlignmentsToInternalNames out of date #431

Open SimonaSecomandi opened 3 years ago

SimonaSecomandi commented 3 years ago

Hi all,

I'm running the Pangenome Pipeline using the latest Cactus binary realease (cactus-bin-v1.3.0.tar.gz). The first two steps went well, while the last one, cactus-align, returned me an error regarding cactus_convertAlignmentsToInternalNames (log from cactus-align Cactus-align_log.txt. It seems that the binary is out of date. How can I update it? As already said, I'm using the lastest cactus precompiled binary..

Many thanks,

Simona

glennhickey commented 3 years ago

To check if you have the latest binary, run cactus_convertAlignmentsToInternalNames --workDir. If it's the latest, you will get this message

cactus_convertAlignmentsToInternalNames: option '--workDir' requires an argument

If it's not the latest, you will get the message from your log

cactus_convertAlignmentsToInternalNames: unrecognized option '--workDir'

To install the latest, download the binaries and follow the install instructions here: https://github.com/ComparativeGenomicsToolkit/cactus/releases/tag/v1.3.0