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.
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
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