I am launching instances with the brand new AMI, ami-118bfc78. The symlinks are 
broken for me.  Is there an additional step I need to take after launching the 
instances? I feel like I am overlooking something.

Also, fixing bow tie along with top-hat did not fix the error. I will look into 
this further.

Thanks for any suggestions.

From: Enis Afgan <eaf...@emory.edu<mailto:eaf...@emory.edu>>
Date: Fri, 12 Jul 2013 18:02:30 +0200
To: Microsoft Office User 
<ravpreet.se...@oicr.on.ca<mailto:ravpreet.se...@oicr.on.ca>>
Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
<galaxy-dev@lists.bx.psu.edu<mailto: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.

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 as well and 
see if that fixes the issue.


On Fri, Jul 12, 2013 at 5:26 PM, Ravpreet Setia 
<ravpreet.se...@oicr.on.ca<mailto:ravpreet.se...@oicr.on.ca>> wrote:
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 /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 may be an issue with tophat's XML or 
python script though, since I fixed Velvet's symlink and env.sh and it worked 
perfectly.

This document explains how the default symlink and env.sh are used by Galaxy:
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

Thanks for any suggestions.

___________________________________________________________
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/

Reply via email to