Hi Greg,
Regarding the tools contained in fml_gff_converter_programs.tar.bz2, the
following xml files are not well formed due to the malformed ! -- TODO
EDIT HERE tag:
fml_gff_converter_programs/galaxy/bed_to_gff3.xml
fml_gff_converter_programs/galaxy/gff3_to_bed.xml
Hi all,
I'm working on a tool where the repeat tag looks like an elegant
solution - however I want to limit the number of repeats to be 1, 2 or 3.
i.e. I want to set min=1 and max=3 attributes for the repeat,
based on analogy to the param tag.
Is this possible, but not documented here?
Hi Peter,
Yes, setting min and max values in the repeat tag should work as you need. As
you point out, it is probably not well documented, so please let us know if it
isn't working as you imagine it should.
Thanks for using Galaxy,
Dan
On Apr 19, 2011, at 6:47 AM, Peter Cock wrote:
Hi
On Tue, Apr 19, 2011 at 1:46 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Peter,
Yes, setting min and max values in the repeat tag should work as you need.
As you point out, it is probably not well documented, so please let us know
if it isn't working as you imagine it should.
Thanks
To be clear, you were able to connect to the galaxy server using WinSCP in
plain FTP mode, and had no errors uploading the files?
-Dannon
On Apr 19, 2011, at 9:37 AM, vasu punj wrote:
Dannon,
I used winSCP to upload the files but dont see in Galaxy in history of
uploaded files or even
Ok, great.
Please do remember to reply-all and include the list in the future. Among
other things, it helps us immensely in keeping track of what has and has not
been answered.
-Dannon
On Apr 19, 2011, at 9:43 AM, vasu punj wrote:
I figured out and find files. Thanks.
--- On Tue,
Hello,
I have a question regarding execution of workflows using API
(workflow_execute.py).
I am writing a script to automate file uploading and workflow
execution using API.
I was able to upload files and the response gave me ids for each file
with 32 characters although the README
Hi Kanwei,
I noticed that the BLAST+ output options for HTML are not working,
a side effect of my recent refactoring. Could you transplant/merge this
fix and test please:
https://bitbucket.org/peterjc/galaxy-central/changeset/e1e6f92e07bf
Taka,
Would you mind sharing the exact command you used to call
workflow_execute.py?
It does sound like you're doing something very similar to what
scripts/api/example_watch_folder.py does. That script also uploads from
the file system to a data library and subsequently executes a workflow
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,
I'm getting inconsistent behavior when I run a workflow.
I have one workflow,that when I run it, the green box indicating my workflow
has been submitted shows up in the middle panel with Tools to the left,
histories to the right, and menu above.
For another workflow, I submit it successfully,
Dave,
What revision of galaxy are you running (hg tip)? We've made a few
changes quite recently to running workflows, though I haven't seen any
errors like this yet.
Also, what's different about the two workflows (history destinations,
multiple-inputs, rename actions, etc.)?
-Dannon
On
ca0c4ad2bb39 is the last upstream change set in our fork (Glen is planning
to update our fork with the latest dist later this week).
Neither workflow does history destinations.
Both histories have multiple inputs going to varying tools in the workflow.
Both histories rename outputs.
One workflow
K
On Tue, Apr 19, 2011 at 11:22 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Kanwei,
I noticed that the BLAST+ output options for HTML are not working,
a side effect of my recent refactoring. Could you transplant/merge this
fix and test please:
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