This may be a problem with the latest Galaxy Cloudman AMI.
Some tools (tophat is one) are failing to run because they cannot be found. I
have noticed that after launching a new instance with the latest AMI, the
package/version/default sym-links under /mnt/galaxy/tools point to a
directory in
Is this a migrated cluster or a brand new one? I'm guessing you're using
the new AMI?
The migration process supposed to have updated those env.sh paths.
More to the point, is your tophat job failing due to bowtie not being
found? Try adding the path to bowtie executables to tophat's env.sh file
@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman - Software does not work due to broken
symlinks
Is this a migrated cluster or a brand new one? I'm guessing you're using the
new AMI?
The migration process supposed to have updated those env.sh paths.
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