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.se...@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: > http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies > > Thanks for any suggestions. > > > > From: Enis Afgan <afg...@gmail.com> > Date: Sun, 30 Jun 2013 07:37:46 +0200 > To: Galaxy-dev <galaxy-...@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 <http://usegalaxy.org/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<https://bitbucket.org/galaxy/cloudman/src/tip/CHANGELOG.md?at=default>and > for even more details see, all of 291 > commit > messages<https://bitbucket.org/galaxy/cloudman/commits/all?search=35baec1%3A8bbae3f> > from > 7 contributors. > > Enjoy and please let us know what you think, > Enis > > > P.S. > We also now have a logo for CloudMan > [image: Inline image 2] > > ___________________________________________________________ Please keep > all replies on the list by using "reply all" in your mail client. To manage > your subscriptions to this and other Galaxy lists, please use the interface > at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the > unified search at: http://galaxyproject.org/search/mailinglists/ > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/