Re: [galaxy-dev] setting metadata externally failed for HistoryDatasetAssociation

2016-06-03 Thread Peter Cock
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

Re: [galaxy-dev] The state of the MOTHUR merge?

2016-06-03 Thread Peter van Heusden
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

Re: [galaxy-dev] setting metadata externally failed for HistoryDatasetAssociation

2016-06-03 Thread John Chilton
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

[galaxy-dev] setting metadata externally failed for HistoryDatasetAssociation

2016-06-03 Thread Anthony Underwood
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:

Re: [galaxy-dev] LDAP authentication

2016-06-03 Thread mark fernandes (IFR)
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,

Re: [galaxy-dev] The state of the MOTHUR merge?

2016-06-03 Thread Björn Grüning
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

[galaxy-dev] The state of the MOTHUR merge?

2016-06-03 Thread Peter van Heusden
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 ___