So I have finally determined the cause and found a resolution. The issue was the fact that the version of Java on the Ubuntu linux VM from AWS is 1.6.x. GATK2 requires version 1.7.0 or higher. This is fine, but you will need to manually upgrade the java version. To do so you will need to complete the following: SSH to the VM sudo su - root CD to /mnt/galaxy/ Complete the following steps: 1. sudo apt-get purge openjdk* (This removes java 1.6 completely) 2. Modify this file: vi /etc/apt/sources.list.d/cloudbiolinux.list (Remove the leading section of line 11) 3. sudo add-apt-repository ppa:webupd8team/java 4. sudo apt-get update 5. sudo apt-get install oracle-java7-installer 6. java -version Now if you plan to add nodes via the Cloudman Console you will need to perform these tasks for each node you install. I worked with AWS Support to setup an "Auto Scaling Group" to accommodate this process. This required getting my Master instance upgraded and creating an AMI from it.

From that point you can build the group based on the following: http://docs.aws.amazon.com/AutoScaling/latest/DeveloperGuide/creating-your- auto-scaling-groups.html

This was, in theory, a great idea. However, it did not work for me. Each of the node that were generated by this tool had Java version 1.6.x and this caused GATK2 to fail. My recommendation is that if you have time you should paly around with this more, but I did not have that luxury for this project. Iry On 10/11/14 12:00 PM, "galaxy-dev-request@lists.bx.psu.edu" <galaxy-dev-request@lists.bx.psu.edu> wrote:

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Today's Topics:

1. Re: Tool development: Is it possible to pass a user's id in dynamic_options() parameter? (Dooley, Damion) 2. Re: Tool development: Is it possible to pass a user's id in dynamic_options() parameter? (Daniel Blankenberg) 3. Anyone else having issues with cloudman cloudlaunch? (Chris Dagdigian) 4. Re: Anyone else having issues with cloudman cloudlaunch? (Dannon Baker) 5. Re: Anyone else having issues with cloudman cloudlaunch? (Dannon Baker) 6. Re: Anyone else having issues with cloudman cloudlaunch? (Chris Dagdigian) 7. Re: Anyone else having issues with cloudman cloudlaunch? (Dannon Baker) 8. Re: Anyone else having issues with cloudman cloudlaunch? (Chris Dagdigian) 9. GATK2 java version related issues (Iry Witham) 10. Why does Galaxy CloudMan 2.3 (ami-a7dbf6ce) run the boinc client? (Chris Dagdigian) 11. Re: GATK2 java version related issues (Daniel Blankenberg) 12. Re: Why does Galaxy CloudMan 2.3 (ami-a7dbf6ce) run the boinc client? (Dannon Baker) 13. Re: GATK2 java version related issues (Iry Witham)

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Message: 1 Date: Fri, 10 Oct 2014 09:02:50 -0700 From: "Dooley, Damion" <Damion.Dooley@bccdc.ca> To: Daniel Blankenberg <dan@bx.psu.edu> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a user's id in dynamic_options() parameter? Message-ID: <7891813F3C8F424B97D8BF2E5600E51903302322C5B5@VEXCCR02.phsabc.ehcnet.ca>

Content-Type: text/plain; charset="Windows-1252"

Hi Dan,

I'd like to get the user's galaxy user name directly - but the <code file="..."> that drives my dynamic_options select list has no access to any information in a galaxy's user session, right? (Ultimately I'm trying to get the dynamic_options code to make galaxy api calls using the user's api key.) I saw the GenomeSpace tool earlier - but got the impression that a user was entering their genome login in the tool form. I was hoping just to get a user's galaxy id without any re-entry of it.

p.s. Its been really great getting advice from all of you; I hope to contribute likewise.

d.

Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ________________________________________ From: Daniel Blankenberg [dan@bx.psu.edu] Sent: Friday, October 10, 2014 8:08 AM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a user's id in dynamic_options() parameter?

Hi Damion,

Text fields are not currently able to be populated by dynamic_options, but in a dynamic_options select list you could access the user?s username directly. If you want the user to be able to override it, you could have a conditionally used empty text box that your tool defaults to using when it is populated.

An example that you might want to look at could be the GenomeSpace Export tool (tools/genomespace/genomespace_exporter.*), which queries the GenomeSpace API to get a list of available folders for export for a specific user using attributes of the current user?s preferences (GenomeSpace username and token). It generates a drill_down type select parameter, but the same can be done for a standard select list.

Thanks for using Galaxy,

Dan

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Message: 2 Date: Fri, 10 Oct 2014 12:59:06 -0400 From: Daniel Blankenberg <dan@bx.psu.edu> To: "Dooley, Damion" <Damion.Dooley@bccdc.ca> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a user's id in dynamic_options() parameter? Message-ID: <1A8CFB92-0432-4FAC-B139-84E05F0EDE57@bx.psu.edu> Content-Type: text/plain; charset="windows-1252"

Hi Damion,

In the genomespace exporter case, the call to ?dynamic_options="galaxy_code_get_genomespace_folders( genomespace_site = 'prod', trans=__trans__, value=__value__, input_dataset=input1, base_url=base_url )?? is passing in trans, which it is using to determine user and an attribute of the user. You could then check to see if trans.user is not None, and then get trans.user.username.

You may be able to access user or username here by the more recently added ?__user__? or even ?__user_name__? / ?__user_id__? / ?__user_email__" variables directly, but I didn?t test that they were available in this dynamic_options context example (if they are available, they would be preferred over accessing trans).

For accessing a user?s API key, this trello card is of interest: https://trello.com/c/hL4NYsSp/2108-request-from-jxtx-provide-consistent-in terface-to-tools-for-communicating-with-the-api. Of course the Key can be obtained directly from the user object as well.

Hope this helps,

Dan

On Oct 10, 2014, at 12:02 PM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:

...

Hi Dan,

I'd like to get the user's galaxy user name directly - but the <code file="..."> that drives my dynamic_options select list has no access to any information in a galaxy's user session, right? (Ultimately I'm trying to get the dynamic_options code to make galaxy api calls using the user's api key.) I saw the GenomeSpace tool earlier - but got the impression that a user was entering their genome login in the tool form. I was hoping just to get a user's galaxy id without any re-entry of it.

p.s. Its been really great getting advice from all of you; I hope to contribute likewise.

d.

Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ________________________________________ From: Daniel Blankenberg [dan@bx.psu.edu] Sent: Friday, October 10, 2014 8:08 AM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a user's id in dynamic_options() parameter?

Hi Damion,

Text fields are not currently able to be populated by dynamic_options, but in a dynamic_options select list you could access the user?s username directly. If you want the user to be able to override it, you could have a conditionally used empty text box that your tool defaults to using when it is populated.

An example that you might want to look at could be the GenomeSpace Export tool (tools/genomespace/genomespace_exporter.*), which queries the GenomeSpace API to get a list of available folders for export for a specific user using attributes of the current user?s preferences (GenomeSpace username and token). It generates a drill_down type select parameter, but the same can be done for a standard select list.

Thanks for using Galaxy,

Dan