I see you are experiencing the same problem as I am. The reason these programs cannot be found is because the "default" symlink is broken. The following page describes how the symlink is used by Galaxy: 

http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

Suppose you wish to fix Tophat, then you will need to go to /mnt/galaxy/tools/tophat. Type 'ls –l' and you will notice that the 'default' symlink points to a directory in "/mnt/galaxyTools". Recall that this update merged galaxyTools and galaxyData into a single volume – but the symlink was not modified to account for this. Therefore, the symlink should instead point to /mnt/galaxy/tools/tophat/<VERSION>. 

Then, go into the directory of the version you specified and modify the env.sh file so it also has the proper path. 

Let me know if Tophat works for you, even after doing this it fails to run properly for me. However, at least now Galaxy can find the programs. 


From: Mohammad Heydarian <mheydar1@jhmi.edu>
Date: Fri, 12 Jul 2013 14:21:23 -0400
To: Microsoft Office User <ravpreet.setia@oicr.on.ca>
Cc: Enis Afgan <afgane@gmail.com>, Galaxy-dev <galaxy-dev@bx.psu.edu>
Subject: Re: [galaxy-dev] Galaxy CloudMan release - Tophat does not work

Cufflinks, Cuffcompare, and Cuffdiff are also failing to run because they can not be found. I am using the newly released version of Cloudman 2.0 (ami-118bfc78).

Any help would be appreciated.
Cheers, 
Mo Heydarian
On Mon, Jul 8, 2013 at 5:02 PM, Ravpreet Setia <Ravpreet.Setia@oicr.on.ca> wrote:
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 /mnt/galaxyTools, which does not exist since this new AMI merged galaxyTools and galaxyData. 

Additionally, even after manually fixing the symlink and the path in the env.sh file (it also references galaxyTools), running tophat would fail, although now, at least, it can find the program. 

This document explains how the default symlink is used by Galaxy: 

Thanks for any suggestions. 



From: Enis Afgan <afgane@gmail.com>
Date: Sun, 30 Jun 2013 07:37:46 +0200
To: Galaxy-dev <galaxy-dev@bx.psu.edu>
Subject: [galaxy-dev] Galaxy CloudMan release

Last night, we released an update to Galaxy CloudMan. CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration.

IMPORTANT - please read
Any new cluster will automatically start using this version of CloudMan. Existing clusters will be given an option to do an automatic update once the main interface page is refreshed. Note that this upgrade is a major version upgrade and thus the migration is rather complicated. The migration process has been automated but will take a little while to complete. If you have made customizations to your cluster in terms of adding file systems, upgrading the database, or similar, we do not recommend you perform the upgrade. Note that this upgrade comes with (and requires) a new AMI (ami-118bfc78), which will be automatically used if starting an instance via CloudLaunch.

This update brings a large number of updates and new features, the most prominent ones being:
- Unification of galaxyTools and galaxyData file systems into a single galaxy filesystem. This change makes it possible to utilize the Galaxy Tool Shed when installing tools into Galaxy.
- Added initial support for Hadoop-type workloads
- Added initial support for cluster federation via HTCondor
- Added a new file system service for instance's transient storage, allowing it to be used across the cluster over NFS
- Added a service for Galaxy Reports webapp
- Added optional Loggly (loggly.com) based off-site logging support
- Added tags to all resources utilized by CloudMan

For more details on the new features, see the the CHANGELOG and for even more details see, all of 291 commit messages from 7 contributors.

Enjoy and please let us know what you think,
Enis


P.S. 
We also now have a logo for CloudMan
Inline image 2

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