thank you!
--
Dr. Ioana C. Chintauan-Marquier
Muséum National d'Histoire Naturelle
Institut de SYstématique Evolution Biodiversité (ISYEB)
UMR MNHN/CNRS/UPMC/EPHE 7205
57 Rue Cuvier, CP50 (Entomologie, équipe Phylevo)
F-75231 PARIS cedex 05
France
Tel: +33 (0)1 40 79 34 15/+33 (0)6 02 27 32 41
Hello John
Thanks for taking a look, and for the explanation. It's useful to know
that it's not something intrinsically wrong with what I've been doing,
and I'll work around it for now. It's good to know that it's targeted
for a fix at some point, even if it doesn't make it into the next
Thanks for the additional details - I am responding on list for people
who may encounter similar problems in the future.
The job running code will provide both core tools and tool shed tools
with the same PYTHONPATH - but some tools might setup a Python
virtualenv for instance which would replace
Thanks John -
Would it be more productive for us to port gsummary.py as a shed tool?
best -
david
On Oct 2, 2014, at 6:46 AM, John Chilton jmchil...@gmail.com wrote:
Thanks for the additional details - I am responding on list for people
who may encounter similar problems in the future.
Okay - revisiting this because I was not nearly cautious enough with
my previous response. A couple large caveats -
- Exposing the master key or any admin key on the command line will
make it available to everyone who has access to the tools- so if you
do so you either need to encode it some way,
Ok, thanks for the on-target info and organizing the Trello card solution.
So the configfiles construct lets us pass data that is available in the
cheeta template context into a temporary file which the tool then has access
to, thus avoiding exposing parameters in the command line execution
Hi Team,
I have a new instance of galaxy cloudman running and have added tools from the
toolshed to it. When I attempt to run tools like sam-to-bam or any gatk tool I
am prompted for a reference genome. However, indices/references not available
for these tools. I have added the following
Thanks, that was the first thing I checked. However, restarting the
handler didn't help. Downloading the offending data and re-uploading as
a new data set and then rerunning using the new dataset as input did
work. Also, all other jobs continued to run fine.
Lance
Kandalaft, Iyad wrote:
Hi Dan,
Thanks for pointing out the tab issue. However, I have made the modification
and restarted my instance, but still get no reference genome listed. It is
funny that there are a limited number of tools that have this issue. They are:
SAM Tools:
Generate pileup
SAM-to-BAM
Mpileup
I see Galaxy API has a feature to import a history dataset into the library (in
copy_hda_to_ldda() fn from GCC2013 training day course). Is this available as
well via Bioblend? Latest docs don't seem to include this feature. It would
be the opposite of Bioblend's
Thanks for responding, John.
Yes, you're right.. finally just struck me that the failure was due to my
compute nodes not having internet connection.
Unfortunately, we have to setup our cluster this way due to limited
resources and galaxy would submit jobs to it. I guess the other option that
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