Hi,
I seem to have some problems with the visibility of tool outputs in my
workflows. When I flag any given output as visible, Galaxy sometimes
decides to hide it in the resulting history anyway. I can't find any
systematic behavior though. It seems to be rather arbitrary weather
Galaxy
Could you share an offending workflow with me? Or is it any workflow? I've
not seen this behavior before, but it definitely shouldn't be random. So in
your situation the same workflow run multiple times will not consistently hide
the same datasets?
-Dannon
On Mar 23, 2012, at 6:05 AM,
Hi Daniel,
On Mar 22, 2012, at 11:21 AM, Daniel Sobral wrote:
Hi Greg,
This is the output I get in the toolshed log:
Firefox/10.0.2
172.22.50.249 - - [22/Mar/2012:15:11:50 +0100] GET
On Mar 23, 2012, at 10:09 AM, Daniel Sobral wrote:
The path I defined on shed_tool_conf.xml should be writable. In fact, I
can install repositories from your toolsheds (galaxy main or galaxy
test) with no problems. I actually used the galaxy test toolshed to add
my own repositories as a
Hi all,
In order to ease sharing the developed Galaxy tools in our group, we
want to launch a private Toolshed.
However, upon running ./run_community.sh, I got following error.
Traceback (most recent call last):
File ./scripts/paster.py, line 34, in module
command.run()
File
Hi all,
is there some way I can allow datasets (specifically bam files) that are
annotated with a custom build to be displayed in a local IGV (assuming a
genome with the same name was generated for IGV)?
I tried some things with display_applications/igv/bam.xml, but I
couldn't get it to
You'll need to configure your Python 2.6 to include mercurial. You can do
something like
easy_install -U mercurial
but there are other approaches as well.
On Mar 23, 2012, at 10:33 AM, Joachim Jacob wrote:
Hi all,
In order to ease sharing the developed Galaxy tools in our group, we
Thanks for your fast reply! It did the trick and kept me going on a
sunny friday afternoon. :-)
# easy_install -U mercurial
Cheers,
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
Hi, all,
Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am
wondering if there is an update on megablast web interface and wrapper in
Galaxy?
Thanks,
Luobin
___
Please keep all replies on the list by using reply all
On Fri, Mar 23, 2012 at 4:22 PM, Luobin Yang yangl...@isu.edu wrote:
Hi, all,
Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am
wondering if there is an update on megablast web interface and wrapper in
Galaxy?
Yes, there are wrappers for the main tools from NCBI
Make sure that the Python you're running when you start the server is supported
by Galaxy (2.5+)
This will tell you what Python version you are using:
python -V
If that isn't the problem, try deleting the pysam egg and then re-fetching it:
python ./scripts/fetch_eggs.py
from your Galaxy
Yeah, that's what I was wondering: to update megablast tool to use NCBI
BLAST+ .
I revised megablast wrapper a bit to use the legacy_blast.pl from NCBI
BLAST+, but it seems the output format is not compatible with the tool
(Fetch taxonomic representation) in metagenomic analyses anymore.
So it
Looks like I'll have to try again. Maybe with a more general question (?)
When you're debugging tools, how do you get Galaxy to tell you what the
tool is doing? My tool doesn't work properly, but paster.log just shows
a line for the request. It doesn't say anything about what tool_runner
is
Hi,
I have just installed a Galaxy instance at my local machine and uploaded some
sequence data into it. But, when I tried to some NGS tools which need reference
genome, i found the selection window was empty. I wonder how to get a reference
genome data (e.g., hg19) incorporated into the
Hi Mark,
Try these changes:
tool id=sra-trace-download name=Download SRA data tool_type=data_source
and
param name=GALAXY_URL type=baseurl
value=/tool_runner?tool_id=sra-trace-download/
Although 'GALAXY_URL' should be generated automatically if it is not included
explicitly for
A final pointer: to see tools that use dynamic options, take a look at Extract
GFF features and Filter GFF dataset by feature count
Good luck,
J.
On Mar 22, 2012, at 12:15 PM, Greg Von Kuster wrote:
It's always best to look at examples in the code base for technical details
like this rather
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