Hi Edward
Select 'view' instead of 'run' in your workflow list. This will give you
a nice (human readable) overview of all the steps, or select the
download option to get an xml describing your workflow.
Regards, Hans
On 09/13/2012 03:20 AM, Edward Hills wrote:
Hi Galaxy team,
I am wanti
Hi Galaxy team,
I am wanting to know where to find the queue that stores all tool's that
are going to be executed in the pipeline.
For example, I am running a workflow of 5 tools all linked together (the
details are not important). Programatically I wish to know the names of the
tools that are go
Hi guys,
Just a quick question about the total size of the genome indexes just made
available via rsync server?
Cheers,
Derrick
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Hi Lance,
What is the changeset revision that you installed? It looks like you could
only have installed one of the following 3 revisions:
1:14e18dc9ed13
2:f5d08224af89
4:14bec14f4290
Since you could not have installed 3:f7a5b54a8d4f, I'm not quite sure how you
could be trying to update to 4.
Hi David,
With the exception of requiring versions strings in tags in the
tool config in order to enable versioned tool dependency installation (which is
documented in the tool shed wiki at
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_third-party_tool_dependency_installation_and_compilation
Hi David,
Can you send me your tarball?
Thanks,
Greg Von Kuster
On Sep 12, 2012, at 6:16 PM, David Hoover wrote:
> I've created a repository in the test toolshed and tried uploading gzipped
> tarballs with all files required. I have several tool config files (.xml)
> wrapping a single pyth
I've created a repository in the test toolshed and tried uploading gzipped
tarballs with all files required. I have several tool config files (.xml)
wrapping a single python script with some tool-data dependencies.
If I upload a single tool config file with the dependencies, everything is ok.
Hi Lance,
Thank you for finding this issue and a bigger thanks for the patch. We've
updated FreeBayes in the toolshed with your patch. Please let us know if you
encounter further issues.
Thanks!
Dan
On Sep 11, 2012, at 5:08 PM, Lance Parsons wrote:
> Today I ran into a new issues with inst
On Sep 12, 2012, at 1:09 PM, Fields, Christopher J wrote:
> Simple question: is there a way within universe_wsgi.ini to point to a
> specific location where Galaxy log (and possibly PID) files can be dropped?
> I've searched for this but couldn't find an answer beyond locally modifying
> run.s
Hello everyone,
I am comparing two samples (control and treated) paired end RNA Seq data. I
am getting different FPKM values on my cufflinks output of 2 samples when
compared to the 2 values that cuffdiff..
Below is the snap shot of a gene with different FPKM values. (I am not
displaying the gene
I've updated my development system now, and when I try to get updates
for that particular tool (htseq_count) I run into the following error.
Any ideas on how I can/should fix this? Thanks.
URL:
http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://t
Hello David,
This is not currently possible, but will be available in the next Galaxy
distribution release, currently scheduled for about 10 days from now. You will
include a tool_dependencies.xml file in your tool shed repository that looks
something like the following.
$INSTA
Simple question: is there a way within universe_wsgi.ini to point to a specific
location where Galaxy log (and possibly PID) files can be dropped? I've
searched for this but couldn't find an answer beyond locally modifying run.sh,
but it's entirely possible I'm missing something obvious.
We wa
Are there any environment variables that are honored by toolshed installed
tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or
$GALAXY_HOME, then uploaded it the test toolshed, then installed it
automatically. Neither of these resolved to what I expected. I don't want to
har
Hi Alex,
Assuming the installed repository is stuck in a "Cloning" state (you can see
this by clicking the Admin menu link "Manage installed tool shed
repositories"), you can fix it by manually running the following sql command in
your db environment (string case is required).
update tool_shed
On Wed, Sep 12, 2012 at 12:16 AM, Kenneth R. Auerbach
wrote:
> Hello,
>
> Can anyone tell me why I keep getting this error when I try to do a blast
> search in Galaxy? I checked that the nr database file was there and had the
> right permissions. Does this error mean that Galaxy can't find the nr
16 matches
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