On Wed, Sep 12, 2012 at 12:16 AM, Kenneth R. Auerbach
kauerb...@comcast.net 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
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
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
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.
?xml version=1.0?
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:
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.sh,
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
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 python
Hi David,
With the exception of requiring versions strings in requirement tags in the
tool config in order to enable versioned tool dependency installation (which is
documented in the tool shed wiki at
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
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
11 matches
Mail list logo
