Hi Luobin,
You can first delete the dataset from the history by clicking the 'X'.
After that, in the history menu you can find 'Purge Deleted Datasets'.
You're question might me more appropriate for the Galaxy users email
list galaxy-u...@lists.bx.psu.edu mailto:galaxy-u...@lists.bx.psu.edu.
Hi all,
After upgrading to the latest galaxy-dist, Trackster does not behave.
Nearly all saved viz's just show a blank main window, while just
displaying the Galaxy header and the trackster header bar.
In contrast, one visualisation gives this error:
ConverterDependencyException: 'A
Hemant,
The BWA index format was changed in 0.6.0 to integrate the BWT and
reverse BWT into the same file. I would recommend using BWA 0.5.9 to
generate the index, which does still create .bwt and .rbwt files.
--Dave B.
On 11/7/12 14:32:15.000, Kelkar, Hemant wrote:
We recently upgraded
Hello Derrick,
Your message discusses 2 separate issues:
1. When you install your meme_chip repository from the tool shed, the file
named tool_data_table_conf.xml.sample contained in the repository is copied to
the ~/tool-data directory in the local Galaxy instance. This issue has been
Try clearing your browser cache and see if that does the trick.
If not, please open your JavaScript console and report the errors that you're
seeing.
Thanks,
J.
On Nov 8, 2012, at 4:56 AM, Joachim Jacob wrote:
Hi all,
After upgrading to the latest galaxy-dist, Trackster does not behave.
Clearing cache did not solve it.
The Js console reports (when trying to visualize an short-read alignment):
Uncaught ReferenceError: Dataset is not defined visualization.js:1
Uncaught ReferenceError: Dataset is not defined tracks.js:1
Uncaught ReferenceError: Dataset is not defined
Running a CloudMan created instance on Amazon.
Updated using cloudman from http://bitbucket.org/galaxy/galaxy-central to
version 8167:b0c916349070
Tried to run bowtie and get the following error. Searched the message archives
an someone else reported the same problem but thought it was related
Unfortunately the cloud instance upgrade path requires some manual intervention
here due to tool migrations. SSH in to your instance, edit
/mnt/galaxyTools/galaxy-central/datatypes_conf.xml removing any references to
BlastXML. Save the file, restart galaxy, and you should be good to go.
Hi Joachim
This might be completely unrelated, but your situation reminds me of our
case when we did the last update (to Oct 5th release):
All previously stored visualizations didn't work any more a first. I had
to modify the datatypes_conf.xml file by adding
the following line:
datatype
Ok that fixed Bowtie.
Any thoughts on expected state of installing Abyss from toolshed. It
indicates no requirements so my expectation is that installing from
toolshed should install the appropriate abyss package in a location the
tool is expecting to find it.
In looking at the toolshed looks
I removed two BlastXML references and restarted galaxy and a new compute
node.
This problem still exists and is found at stdout.
Sequence file aligned.
ERROR: Unable to read builds file: [Errno 2] No such file or directory:
Neither abyss wrapper in the toolshed installs binaries (you'd see a
tool_dependencies.xml in the repository), that's left up to the end user. You
might contact the authors of the wrappers via the toolshed to see if they were
going to add dependency management and had a newer version, but
Dannon
If I install abyss to the galaxy tools volume and use cloud admin to do a
snapshot I assume I then need to remove and then add compute nodes? From
the EC2 management console I see two 15GiB EBS volumes from the same
snapshot and I have a master and one compute node running. The other
You do not need to restart or add/remove worker nodes, the master's tool and
data volumes are shared via NFS.
The easiest way to make this work for you in the cloud is probably going to be
installing the version of the Abyss binaries you'd like to use manually in
Thanks! That was the explanation I was looking for and the link for how to
Do you have any suggestions for fixing the error that are still occurring
after running Bowtie?
Sequence file aligned.
ERROR: Unable to read builds file: [Errno 2] No such file or directory:
Glad to help. The first step would be to check and see if those files actually
exist (and they should).
If those messages are occurring on stdout and not stderr though, they shouldn't
be causing failed jobs and something else might be wrong.
-Dannon
On Nov 8, 2012, at 1:27 PM, Scooter
Errors are being output to stdout
The files don't exist and complicated by the /../../ where I don't know
which subdirectory to follow. Attached screen shot of job failing giving
the ERROR message in the web gui. I also get the same errors when
attempting to run Abys which doesn't run because it
Ok that directory exists but public builds.txt has a .sample at the end.
ubuntu@ip-10-110-143-10:/mnt/galaxyTools/galaxy-central/tool-data/shared/ucsc$
ls
builds.txt builds.txt.sample publicbuilds.txt.sample ucsc_build_sites.txt.new
builds.txt.buildbot manual_builds.txt ucsc_build_sites.txt
Ah ha! This is the problem -- your run.sh is incorrect due to what I'm
assuming was a failed merge. Here's a correct copy, note the inclusion of the
extra .sample files.
Modify or replace your run.sh with this (which is from the most recent cloud
images), restart galaxy, and you're good to
Hi,I always see this error pop up in the logs when one of the steps failed...It seems to have a problem deleting the working directory since it claims they are not empty.Ofcourse when I check, the directory is empty, but I am left with a gazilion empty working directories, alhtough no problems
Hi Philipe,
Unfortunately, the velvet wrappers in the toolshed seem to be very specific
to a certain compilation of velvet. You'll need to recompile Velvet locally
with the same settings. I think it needs CATEGORIES=5 in the make command
for velvet.
Hope this helps,
Simon Gladman
VBC - Monash
Hi all,
Have looked through the list archives regarding this without much luck.
I have a repeat parameter which contains a boolean based conditional. I
wrote a simple test case for it but I think the test keeps failing at the
boolean parameter..
input section looks like:
repeat
Hi dev,
I have written a perl script to perform some complex demultiplexing of
reads. It works well on my computer but the integration to Galaxy is a bit
tricky since it's the first time for me.
At one point my perl script generates a bunch of fasta files, I want all
this fasta files to be
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