Hi Dave,
on IRC we had a small discussion how we can make the progress easier for
you to collect this information. The idea was to create automatically
Trello cards for IUC and devteam tools and maybe a summary page in the
Tool Shed.
Cheers,
Bjoern
Am 15.10.2014 um 06:52 schrieb Dave Clements:
Hi all,
I'm trying to set the dbkey of an output file from the value (text) of
a parameter.
The parameter I want to use is genome.
conditional name=bedgraph
param name=check type=select label=Produce BedGraph
output help=Can be displayed directly on UCSC browser. One file
I believe there is a fix in the latest update to Galaxy for this thanks to Nate.
https://bitbucket.org/galaxy/galaxy-central/commits/579d211
The previous change to that file was in 2011 - so you are likely to be
able to apply the commit to any release of Galaxy you may be running.
-John
On
JJ,
Arg this is a mess. I am very sorry about this - I still don't
understand extra_files_path versus files_path myself. There are open
questions on Peter's blast repo and no one ever followed up on my
object store questions about this with Bjoern's issues a couple
release cycles ago. We need to
Okay - so this is what broke things:
https://bitbucket.org/galaxy/galaxy-central/commits/d781366bc120787e201b73a4dd99b56282169d86
My feeling with the commit was that wrappers and tools should never be
explicitly accessing paths explicitly through input.dataset.*. I think
this would circumvent
Hi Nikos,
In the very least, you’ll want to make sure that you have a bounding
actions/actions tag set around your actions. It is probably also advisable
to add a set of conditional/whens around the action, since you’re only setting
the dbkey under certain circumstances.
Thanks for using
Hi all,
I realize when you manually add a node you can request that it be a spot
instance. Is it also possible to use spot instances for auto-scaling?
Thank you very much,
Robert
This e-mail message (including any attachments) is for the sole use of
the
Hi Daniel,
Thanks for the response.
I've edited the output to:
data format=bedgraph name=bedgraph_slograt
label=${tool.name} on ${on_string}: Smoot Log2ratio (bedGraph)
from_work_dir=output_dir/slograt.bedgraph
filter bedgraph['check'] == 'yes' and slograt['check']
== 'yes'
I agree with you about the inadvisable use of: input.dataset.*.
I'm looking at:
lib/galaxy/model/__init__.py
class Dataset( object ):
...
def __init__( self, id=None, state=None, external_filename=None,
extra_files_path=None, file_size=None, purgable=True, uuid=None ):
...
Does removing the ‘param_attribute=“value' attribute help?
On Oct 15, 2014, at 11:23 AM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote:
Hi Daniel,
Thanks for the response.
I've edited the output to:
data format=bedgraph name=bedgraph_slograt
label=${tool.name} on
Yes!
Thank you very much Daniel.
On 15 October 2014 18:14, Daniel Blankenberg d...@bx.psu.edu wrote:
Does removing the ‘param_attribute=“value' attribute help?
On Oct 15, 2014, at 11:23 AM, Nikos Sidiropoulos nikos.sid...@gmail.com
wrote:
Hi Daniel,
Thanks for the response.
I've
Hey JJ,
Opened a pull request to stable with my best guess at the right to
proceed and hopefully a best practice recommendation we can all get
behind. Do you want to try it out and let me know if it fixes snpeff?
(It does fix the velvet datatypes you contributed to Galaxy.)
Hi John,
glad to see this gets some attention!
Am 15.10.2014 um 19:05 schrieb John Chilton:
Hey JJ,
Opened a pull request to stable with my best guess at the right to
proceed and hopefully a best practice recommendation we can all get
behind. Do you want to try it out and let me know if it
On Wed, Oct 15, 2014 at 1:47 PM, Björn Grüning
bjoern.gruen...@gmail.com wrote:
Hi John,
glad to see this gets some attention!
Am 15.10.2014 um 19:05 schrieb John Chilton:
Hey JJ,
Opened a pull request to stable with my best guess at the right to
proceed and hopefully a best practice
Looks good, John.
I tested with:
https://testtoolshed.g2.bx.psu.edu/view/jjohnson/snpsift_dbnsfp_datatypes
lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
reverting from hack:
command interpreter=pythontabular_to_dbnsfp.py $input
Hi Team,
I had manually installed the latest version of snpEff based on the
recommendation of Pablo and after modifying the XML files I had a working
version of snpEff that produced a vcf. However, this morning I reran my
workflow and it is failing again, but this time I am getting the
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