Branden,
Sorry for the delay in response. Have you gotten things working yet?
If not, what changeset are you on now? The data tables issue is what's
going on here. But it's odd that you're still seeing from_file in
BWA and Bowtie, because they (plus all NGS tools except the samtools
Hi Branden,
Vipin, thanks for the tip. I was not aware of data tables at all.
I checked bwa_wrapper.xml and it is still using the from_file attribute for
the reference genome parameter, not from_data_table. It would appear then
that BWA is not using data tables? Additionally, I have now
Does anybody have any idea why I would be getting this error before the
tool runs?
--
Branden Timm
Great Lakes Bioenergy Research Center
bt...@wisc.edu
On 4/19/2011 10:45 AM, Branden Timm wrote:
Hi All,
I'm having issues running BWA for Illumina with the latest version
of Galaxy
Hi Branden,
I find a wiki documentation here,
https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables
Hope this will help you to experiment a bit around.
regards, Vipin
Does anybody have any idea why I would be getting this error before the
tool runs?
--
Branden Timm
Great Lakes
Vipin, thanks for the tip. I was not aware of data tables at all.
I checked bwa_wrapper.xml and it is still using the from_file attribute
for the reference genome parameter, not from_data_table. It would
appear then that BWA is not using data tables? Additionally, I have now
noticed that
Hi All,
I'm having issues running BWA for Illumina with the latest version of
Galaxy (5433:c1aeb2f33b4a).
It seems that the error is a python list error while preparing the job:
Traceback (most recent call last):
File /home/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py, line 58,
