The documentation for the API is looking real nice...Great...
I do have some trouble finding how I move a history item into a data
library...
Could you give me a few pointers which API call to make for that?
We can assume I have the HDA indentifiers for those objects, just need to
know the
Right.
I will convert it to text, allowing only simple links (a with href only)
to be shown.
Thanks,
Hagai
On Wed, Jan 30, 2013 at 8:03 PM, James Taylor ja...@jamestaylor.org wrote:
You may want to be careful with this solution because it allows script
injection, any HTML including javascript
Hey Dannon
Thanks, the web page I was finding earlier was mostly just an outline. This is
much better. At this point I'm just interested in learning what general
capabilities the API can provide. I'm sure after I read this and think more
about it I'll have questions. One thing I am thinking
Thon,
Without getting my hands on it, my hunch is that this isn't directly possible
out of the box as a 'copy' type operation. That said, it's a fairly
straightforward (and sensible) addition if not. Contributions would be
welcome, as always. I've added a Trello card for this here:
Sure, automated data import and workflow execution is certainly possible. In
addition to the documentation there are several example scripts in the
/scripts/api directory of your galaxy install. In particular, for your use
case, you may want to have a look at example_watch_folder.py. This
Hi,
There are couple of Linux shells: bash, sh, zsh, csh. etc
I would like to know if Galaxy is written to be supported on a specific one
or it is written to support any linux shell?
I'm asking this, because I want to add some features and I want to know
what shell should I support?
Or should
Command lines inside tool configs are assumed to be 'sh' (posix bourne
shell). If you are extending one of the runners, definitely stick to
pure 'sh'.
However, once your command is run, there is no reason you can't use
any shell of your choice.
--
James Taylor, Assistant Professor, Biology/CS,
Hi Dina,
Cat files into one and convert into bigWig. UCSC has a tool
wigToBigWig on this same downloads area available (see section Source).
Or, in this case, you can grab our version of the data via rsync. We
have the file for hg18 and for hg19 - I should have mentioned this
originally! If
We also have a python library for dealing with the API, the documentation
is available at http://bioblend.readthedocs.org/
The library source code also contains an example very similar to what
you're trying to achieve: imports a workflow, imports data, and runs the
workflow. Here's that script:
I just wanted to follow up on this and make sure everything was now working as
expected. I've tried to reproduce the original issue and have thus far been
unsuccessful in doing so with a fresh instance. Is the configuration of your
Galaxy instance special in any way? Did you notice any
All works great, but I was hoping that there's an easy way to remove the
preview text box from the resulting History pane item (it currently shows
the unrendered html tags)?
This should not be happening. If your tool's output dataset has type HTML,
the peek (preview) should say 'HTML file'
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