Hi Anthony,
The line numbers for binary.py don't match the current
latest source, but I would bet this is due to the samtools
binary not being on the path of the cluster nodes. Note
Galaxy itself needs samtools for dealing with BAM files
and this is expected to be on the $PATH (and it not
Thanks Björn, no rush!
Is anyone here doing 16S on Galaxy? I've been looking into options, and
FastQC, Trimmomatic, PEAR and the MOTHUR tools seem to give a viable
workflow. Other options are QIIME or integrating the UPARSE pipeline as I
understand. Any comments appreciated!
Thanks,
Peter
On 3
I think newer versions of Galaxy give a better error message - I am
pretty sure the problem is you are missing samtools. It needs to be
available on the PATH for Galaxy if you use bam data.
-John
On Fri, Jun 3, 2016 at 1:00 PM, Anthony Underwood
wrote:
>
>
> Jobs
Jobs that I run on a local Galaxy install on a Fedora 23 machine are completing
but are erroring with the message below. Any idea why the metadata can not be
written?
Thanks
galaxy.jobs.runners.local DEBUG 2016-06-03 17:30:02,044 execution finished:
Don't know if this helps or not but here's the link to Novell's entry on LDAP
support for eDirectory
https://www.novell.com/documentation/edir873/?page=/documentation/edir873/edir873/data/h007.html
Mark Fernandes
T: +44 (0)1603 255000
Institute of Food Research,
Me finishing my re review and pressing the merge button.
I tend to merge as it is at the moment and do some small adjustments
afterwards ... This weekend Peter, this weekend! :)
Am 03.06.2016 um 13:37 schrieb Peter van Heusden:
> PR #429 on tools-iuc contains the updated MOTHUR toolsuite for
PR #429 on tools-iuc contains the updated MOTHUR toolsuite for Galaxy.
https://github.com/galaxyproject/tools-iuc/pull/429
It *looks* like it is ready to merge - what is still needed before it
merges into tools-iuc?
Thanks!
Peter
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