Re: [galaxy-dev] Galaxy on cloud config issues

8 Aug 2013

      Hello Dannon,

This bucket did not launch Galaxy properly. Here is the whole Cluster status log:

22:11:22 - Master starting
22:11:23 - Completed initial cluster configuration. This seems to be a new cluster; waiting to configure the type
22:11:27 - SGE prerequisites OK; starting the service
22:11:35 - Configuring SGE...
22:11:45 - Successfully setup SGE; configuring SGE
22:11:46 - Saved file 'persistent_data.yaml' to bucket 'cm-bcf1a9a44e022cfe983b8302199ed978'
22:11:46 - Saved file 'cm_boot.py' to bucket 'cm-bcf1a9a44e022cfe983b8302199ed978'
22:11:47 - Saved file 'cm.tar.gz' to bucket 'cm-bcf1a9a44e022cfe983b8302199ed978'
22:11:47 - Saved file 'EmptyGalaxy.clusterName' to bucket 'cm-bcf1a9a44e022cfe983b8302199ed978'

The "Access Galaxy" button on CloudMan Console stays gray and  the Services Control panel on Admin Console  shows that Galaxy and PostgreSQL are not running. Maybe the log file gives you a clue:

'pd.yaml' not found at paths.py load!
Set paths.P_GALAXY_HOME as '/mnt/galaxyTools/galaxy-central'
Python version:  (2, 6)
Image configuration suports: {'apps': ['cloudman', 'galaxy']}
[DEBUG] app:54 2013-08-08 22:11:22,729: Initializing app
[DEBUG] app:55 2013-08-08 22:11:22,729: Running on 'ec2' type of cloud.
[DEBUG] app:72 2013-08-08 22:11:22,729: Getting pd.yaml
[DEBUG] ec2:275 2013-08-08 22:11:22,730: No S3 Connection, creating a new one.
[DEBUG] ec2:278 2013-08-08 22:11:22,730: Got boto S3 connection.
[DEBUG] misc:113 2013-08-08 22:11:22,761: Checking if bucket 'cm-bcf1a9a44e022cfe983b8302199ed978' exists... it does not.
[DEBUG] misc:444 2013-08-08 22:11:22,761: Bucket 'cm-bcf1a9a44e022cfe983b8302199ed978' does not exist, did not get remote file 'persistent_data.yaml'
...

Thank you.

Best Regards,
Anatoly

From: Dannon Baker [mailto:dannon.baker@gmail.com]
Sent: Wednesday, August 07, 2013 5:01 PM
To: Ulyanov_Anatoly
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy on cloud config issues

A new tools volume will be released shortly.  For now, you can launch the previous cloudman release using the following:

https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop

On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly <Ulyanov_Anatoly@allergan.com<mailto:Ulyanov_Anatoly@allergan.com>> wrote:
Hello,

Does anybody use the last Galaxy image? I am running Galaxy image on EC2:

Instance ID         i-1b2d3773
Image ID (AMI) ami-118bfc78

It looks as those three tools have configuration problems:

EBOSS
Blast+
meme

For all three I am getting a message that looks  like that:

/mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found
Error invoking command: blastp

Is there a way to fix configuration files for those tools?

Thank you.

Best Regards,
Anatoly

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