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Search: Posts Made By: Sisi_ieo
Forum: Bioinformatics 02-06-2019, 10:15 PM
Replies: 347
Views: 185,363
Posted By Sisi_ieo
Thanks for the patience, answering your...

Thanks for the patience, answering your questions:
1. If I run "bbmap.sh" or "bbduck.sh" for instance the content of the file is shown (parameters, flags, etc).

If I run the command with the...
Forum: Bioinformatics 02-06-2019, 05:55 AM
Replies: 347
Views: 185,363
Posted By Sisi_ieo
Yes, that is what I've done. the path to...

Yes, that is what I've done.

the path to bbmap is --> /Users/owner/bbmap and it is included in the $PATH

I think that the problem is related to the way the script searches the classes. None of...
Forum: Bioinformatics 02-06-2019, 04:38 AM
Replies: 347
Views: 185,363
Posted By Sisi_ieo
Hi, sorry, I come back with this. I have: ...

Hi, sorry, I come back with this. I have:
/Users/owner/bbmap/current/jgi/BBDuk.class
/Users/owner/bbmap/current/jgi/BBDuk2.class
but any file with the name BBDukF.class

The bbduk.sh, which is...
Forum: Bioinformatics 01-19-2019, 11:44 AM
Replies: 347
Views: 185,363
Posted By Sisi_ieo
Problems running BBDuk with class path

Hi all,

I'm trying to run bbduk.sh on mac os High Sierra 10.13.1, and it is stuck with some issue with classpath. I've already included the path to the bbduk.sh file in the path and the...
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