Re: galaxy-dev Digest, Vol 100, Issue 10

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Re: galaxy-dev Digest, Vol 100, Issue 10

Iry Witham
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, "[hidden email]"
<[hidden email]> 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)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Fri, 10 Oct 2014 09:02:50 -0700
>From: "Dooley, Damion" <[hidden email]>
>To: Daniel Blankenberg <[hidden email]>
>Cc: "[hidden email]" <[hidden email]>
>Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a
> user's id in dynamic_options() parameter?
>Message-ID:
> <[hidden email]>
>
>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 [[hidden email]]
>Sent: Friday, October 10, 2014 8:08 AM
>To: Dooley, Damion
>Cc: [hidden email]
>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
>
>
>------------------------------
>
>Message: 2
>Date: Fri, 10 Oct 2014 12:59:06 -0400
>From: Daniel Blankenberg <[hidden email]>
>To: "Dooley, Damion" <[hidden email]>
>Cc: "[hidden email]" <[hidden email]>
>Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a
> user's id in dynamic_options() parameter?
>Message-ID: <[hidden email]>
>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 <[hidden email]>
>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 [[hidden email]]
>> Sent: Friday, October 10, 2014 8:08 AM
>> To: Dooley, Damion
>> Cc: [hidden email]
>> 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: 3
>Date: Fri, 10 Oct 2014 13:24:30 -0400
>From: Chris Dagdigian <[hidden email]>
>To: "[hidden email]" <[hidden email]>
>Subject: [galaxy-dev] Anyone else having issues with cloudman
> cloudlaunch?
>Message-ID: <[hidden email]>
>Content-Type: text/plain; charset=ISO-8859-1
>
>
>Anyone else having issues using cloudman version of galaxy?
>
>No matter what set of AWS keys I use to try to start a new galaxy
>cluster I always get the vague
>
>"Bad Request : Instance failure, but no specific error was detected.
>Please check your AWS Console."
>
>... error on the launch screen. Nothing obvious in the AWS console. I'm
>using both my root AWS keys as well as IAM generated keys with full
>admin rights and no love.
>
>I do have one running cluster; does that need to be stopped or paused
>before I try to launch more?
>
>Regards,
>Chris
>
>
>
>
>------------------------------
>
>Message: 4
>Date: Fri, 10 Oct 2014 13:27:07 -0400
>From: Dannon Baker <[hidden email]>
>To: [hidden email]
>Cc: "[hidden email]" <[hidden email]>
>Subject: Re: [galaxy-dev] Anyone else having issues with cloudman
> cloudlaunch?
>Message-ID:
> <CAGn_WZn4c-QAWGdQ8Ad2tJ727C=[hidden email]>
>Content-Type: text/plain; charset="utf-8"
>
>Hi Chris,
>
>How are you trying to start these clusters?
>
>And, the one you started successfully, how did you start it?
>
>-Dannon
>
>On Fri, Oct 10, 2014 at 1:24 PM, Chris Dagdigian <[hidden email]> wrote:
>
>>
>> Anyone else having issues using cloudman version of galaxy?
>>
>> No matter what set of AWS keys I use to try to start a new galaxy
>> cluster I always get the vague
>>
>> "Bad Request : Instance failure, but no specific error was detected.
>> Please check your AWS Console."
>>
>> ... error on the launch screen. Nothing obvious in the AWS console. I'm
>> using both my root AWS keys as well as IAM generated keys with full
>> admin rights and no love.
>>
>> I do have one running cluster; does that need to be stopped or paused
>> before I try to launch more?
>>
>> Regards,
>> Chris
>>
>>
>> ___________________________________________________________
>> 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/
>>
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>------------------------------
>
>Message: 5
>Date: Fri, 10 Oct 2014 13:30:35 -0400
>From: Dannon Baker <[hidden email]>
>To: [hidden email]
>Cc: "[hidden email]" <[hidden email]>
>Subject: Re: [galaxy-dev] Anyone else having issues with cloudman
> cloudlaunch?
>Message-ID:
> <CAGn_WZmPxHuqeEWQmUsEXCXSqF+Up1Tpx=u=[hidden email]>
>Content-Type: text/plain; charset="utf-8"
>
>Just realized you said cloudlaunch in the subject there, so I'm assuming
>that's what you used.  For both working and non-working clusters?  And
>this
>is cloudlaunch on usegalaxy.org?  I can check the logs for more detailed
>launch failures, if so.
>
>On Fri, Oct 10, 2014 at 1:27 PM, Dannon Baker <[hidden email]>
>wrote:
>
>> Hi Chris,
>>
>> How are you trying to start these clusters?
>>
>> And, the one you started successfully, how did you start it?
>>
>> -Dannon
>>
>> On Fri, Oct 10, 2014 at 1:24 PM, Chris Dagdigian <[hidden email]>
>>wrote:
>>
>>>
>>> Anyone else having issues using cloudman version of galaxy?
>>>
>>> No matter what set of AWS keys I use to try to start a new galaxy
>>> cluster I always get the vague
>>>
>>> "Bad Request : Instance failure, but no specific error was detected.
>>> Please check your AWS Console."
>>>
>>> ... error on the launch screen. Nothing obvious in the AWS console. I'm
>>> using both my root AWS keys as well as IAM generated keys with full
>>> admin rights and no love.
>>>
>>> I do have one running cluster; does that need to be stopped or paused
>>> before I try to launch more?
>>>
>>> Regards,
>>> Chris
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>>>
>>
>>
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>------------------------------
>
>Message: 6
>Date: Fri, 10 Oct 2014 13:35:41 -0400
>From: Chris Dagdigian <[hidden email]>
>To: Dannon Baker <[hidden email]>
>Cc: "[hidden email]" <[hidden email]>
>Subject: Re: [galaxy-dev] Anyone else having issues with cloudman
> cloudlaunch?
>Message-ID: <[hidden email]>
>Content-Type: text/plain; charset=UTF-8
>
>
>Appreciate the fast reply! I'm at a training session where I hope to
>spin up 24 cloudman managed galaxy instances so each student can have a
>1:1 ownership of their own cluster
>
>I used this URL to fire up my test cluster:
>
>https://usegalaxy.org/cloudlaunch
>
>... but the test cluster is running out of RAM building bowtie2 index
>files so I was trying to start a new cluster based on the currently
>running system but started on an instance type with more memory.
>
>And today when I go back to the https://usegalaxy.org/cloudlaunch I'm
>getting  the errors I posted
>
>If there is anything in the logs I'd appreciate it. Not sure if I'm
>doing anything wrong on my end.
>
>Currently launching the pure base AMI without the cloudlaunch interface
>to see if I get further ...
>
>Regards,
>Chris
>
>
>Dannon Baker wrote:
>> Just realized you said cloudlaunch in the subject there, so I'm assuming
>> that's what you used.  For both working and non-working clusters?  And
>> this is cloudlaunch on usegalaxy.org <http://usegalaxy.org>?  I can
>> check the logs for more detailed launch failures, if so.
>
>
>------------------------------
>
>Message: 7
>Date: Fri, 10 Oct 2014 13:56:27 -0400
>From: Dannon Baker <[hidden email]>
>To: [hidden email]
>Cc: "[hidden email]" <[hidden email]>
>Subject: Re: [galaxy-dev] Anyone else having issues with cloudman
> cloudlaunch?
>Message-ID:
> <CAGn_WZmk2wotibgJA8JJJwhhD+CScJ0tR5aU-zP=DmeSw=[hidden email]>
>Content-Type: text/plain; charset="utf-8"
>
>The errors I'm seeing in the logs relate to virtualization required baked
>into the AMI for the large memory instances.  This is an error on our side
>related to new instance types.
>
>What I'd recommend to get off the ground immediately (with reasonable
>memory on a node) would be to use the c3.8xlarge instance type (compute
>optimized 8x, 60GB memory), which will launch successfully.
>
>On Fri, Oct 10, 2014 at 1:35 PM, Chris Dagdigian <[hidden email]> wrote:
>
>>
>> Appreciate the fast reply! I'm at a training session where I hope to
>> spin up 24 cloudman managed galaxy instances so each student can have a
>> 1:1 ownership of their own cluster
>>
>> I used this URL to fire up my test cluster:
>>
>> https://usegalaxy.org/cloudlaunch
>>
>> ... but the test cluster is running out of RAM building bowtie2 index
>> files so I was trying to start a new cluster based on the currently
>> running system but started on an instance type with more memory.
>>
>> And today when I go back to the https://usegalaxy.org/cloudlaunch I'm
>> getting  the errors I posted
>>
>> If there is anything in the logs I'd appreciate it. Not sure if I'm
>> doing anything wrong on my end.
>>
>> Currently launching the pure base AMI without the cloudlaunch interface
>> to see if I get further ...
>>
>> Regards,
>> Chris
>>
>>
>> Dannon Baker wrote:
>> > Just realized you said cloudlaunch in the subject there, so I'm
>>assuming
>> > that's what you used.  For both working and non-working clusters?  And
>> > this is cloudlaunch on usegalaxy.org <http://usegalaxy.org>?  I can
>> > check the logs for more detailed launch failures, if so.
>>
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>------------------------------
>
>Message: 8
>Date: Fri, 10 Oct 2014 14:07:13 -0400
>From: Chris Dagdigian <[hidden email]>
>To: Dannon Baker <[hidden email]>
>Cc: "[hidden email]" <[hidden email]>
>Subject: Re: [galaxy-dev] Anyone else having issues with cloudman
> cloudlaunch?
>Message-ID: <[hidden email]>
>Content-Type: text/plain; charset=UTF-8
>
>
>Much appreciated - thanks again for the diagnosis and helping me confirm
>that I was not fat-fingering anything on my end!
>
>Currently I have a c3.4xlarge instance that booted directly from the AWS
>console using the current AMI referenced on the cloudlaunch page. It's
>waiting at the cloudman admin interface for my currently running cluster
>to finish the EBS snapshot process needed to instantiate a shared
>cluster. I just need to feed it the shared cluster string but the EBS
>snapshot is going pretty slowly.
>
>If I run into issues I'll tear down my hand-launched version and will go
>back to cloudlaunch and c3.8xlarge. Thanks!
>
>Regards,
>Chris
>
>
>
>Dannon Baker wrote:
>> The errors I'm seeing in the logs relate to virtualization required
>> baked into the AMI for the large memory instances.  This is an error on
>> our side related to new instance types.
>>
>> What I'd recommend to get off the ground immediately (with reasonable
>> memory on a node) would be to use the c3.8xlarge instance type (compute
>> optimized 8x, 60GB memory), which will launch successfully.
>
>
>------------------------------
>
>Message: 9
>Date: Fri, 10 Oct 2014 19:04:53 +0000
>From: Iry Witham <[hidden email]>
>To: "[hidden email]" <[hidden email]>
>Subject: [galaxy-dev] GATK2 java version related issues
>Message-ID: <D05DA613.38CD5%[hidden email]>
>Content-Type: text/plain; charset="us-ascii"
>
>Hi Team,
>
>I am sorry to be a pest, but I am under-the-gun to get this resolved.  I
>have followed the instructions for installing GATK2 on my cloud VM.
>After doing that I discovered that the version of java running on the VM
>was v1.6.x and GATK2 required v1.7.0x.  I removed version 6 and installed
>version 7, uninstalled GATK2 and reinstalled it and reset all of the
>settings that may have reverted with the uninstalls/reinstalls.  Now when
>I run Unified Genotyper I get the following error:
>
>Exception in thread "main" java.lang.UnsupportedClassVersionError:
>org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported major.minor
>version 51.0
>at java.lang.ClassLoader.defineClass1(Native Method)
>at java.lang.ClassLoader.defineClass(ClassLoader.java:643)
>at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
>at java.net.URLClassLoader.defineClass(URLClassLoader.java:277)
>at java.net.URLClassLoader.access$000(URLClassLoader.java:73)
>at java.net.URLClassLoader$1.run(URLClassLoader.java:212)
>at java.security.AccessController.doPrivileged(Native Method)
>at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
>at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
>at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
>at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
>Could not find the main class:
>org.broadinstitute.gatk.engine.CommandLineGATK. Program will exit.
>
>Researching this I found a post at
>http://gatkforums.broadinstitute.org/discussion/3378/gatk2-error-when-i-te
>sted-it-after-installing that refers to upgrading java as the solution.
>However, that did not fix the issue.  In addition I copied the jar file
>to a temp directory and unzipped it to examine the MANAFEST.MF file for
>versioning issues.  This is what I found:
>
>Manifest-Version: 1.0
>Build-Jdk: 1.7.0_51
>Built-By: gsa-engineering
>Created-By: Apache Maven
>Main-Class: org.broadinstitute.gatk.engine.CommandLineGATK
>Archiver-Version: Plexus Archiver
>
>          This tells me that there is something else causing the problem.
> Does anyone have an idea where to look now?
>
>Regards,Iry
>
>The information in this email, including attachments, may be confidential
>and is intended solely for the addressee(s). If you believe you received
>this email by mistake, please notify the sender by return email as soon
>as possible.
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>------------------------------
>
>Message: 10
>Date: Fri, 10 Oct 2014 15:15:53 -0400
>From: Chris Dagdigian <[hidden email]>
>To: "[hidden email]" <[hidden email]>
>Subject: [galaxy-dev] Why does Galaxy CloudMan 2.3 (ami-a7dbf6ce) run
> the boinc client?
>Message-ID: <[hidden email]>
>Content-Type: text/plain; charset=UTF-8
>
>
>Just a paranoia check ...
>
>I manually started the cloudman galaxy AMI (ami-a7dbf6ce) and noticed
>that it is configured and running a boinc client
>
>Just wanted to check if this was legit and expected ...
>
>Regards,
>Chris
>
>
>
>------------------------------
>
>Message: 11
>Date: Fri, 10 Oct 2014 15:16:14 -0400
>From: Daniel Blankenberg <[hidden email]>
>To: Iry Witham <[hidden email]>
>Cc: "[hidden email]" <[hidden email]>
>Subject: Re: [galaxy-dev] GATK2 java version related issues
>Message-ID: <[hidden email]>
>Content-Type: text/plain; charset="windows-1252"
>
>First guess is that perhaps the system is still defaulting to using java
>1.6 and not 1.7. What happens if you run ?java -version? as the Galaxy
>system user? Perhaps try a reboot of the vm as well to make sure that the
>Galaxy app is running with java 1.7.
>
>Also, is this a custom vm? If it using running things on different
>cluster nodes, you?ll need to make sure the java version on those nodes
>are 1.7 as well.
>
>Thanks,
>
>Dan
>
>
>On Oct 10, 2014, at 3:04 PM, Iry Witham <[hidden email]> wrote:
>
>> Hi Team,
>>
>> I am sorry to be a pest, but I am under-the-gun to get this resolved.
>>I have followed the instructions for installing GATK2 on my cloud VM.
>>After doing that I discovered that the version of java running on the VM
>>was v1.6.x and GATK2 required v1.7.0x.  I removed version 6 and
>>installed version 7, uninstalled GATK2 and reinstalled it and reset all
>>of the settings that may have reverted with the uninstalls/reinstalls.
>>Now when I run Unified Genotyper I get the following error:
>>
>> Exception in thread "main" java.lang.UnsupportedClassVersionError:
>>org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported major.minor
>>version 51.0
>> at java.lang.ClassLoader.defineClass1(Native Method)
>> at java.lang.ClassLoader.defineClass(ClassLoader.java:643)
>> at
>>java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
>> at java.net.URLClassLoader.defineClass(URLClassLoader.java:277)
>> at java.net.URLClassLoader.access$000(URLClassLoader.java:73)
>> at java.net.URLClassLoader$1.run(URLClassLoader.java:212)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
>> Could not find the main class:
>>org.broadinstitute.gatk.engine.CommandLineGATK. Program will exit.
>>
>> Researching this I found a post at
>>http://gatkforums.broadinstitute.org/discussion/3378/gatk2-error-when-i-t
>>ested-it-after-installing that refers to upgrading java as the solution.
>> However, that did not fix the issue.  In addition I copied the jar file
>>to a temp directory and unzipped it to examine the MANAFEST.MF file for
>>versioning issues.  This is what I found:
>>
>> Manifest-Version: 1.0
>> Build-Jdk: 1.7.0_51
>> Built-By: gsa-engineering
>> Created-By: Apache Maven
>> Main-Class: org.broadinstitute.gatk.engine.CommandLineGATK
>> Archiver-Version: Plexus Archiver
>>  
>>           This tells me that there is something else causing the
>>problem.  Does anyone have an idea where to look now?
>>
>> Regards,Iry
>> The information in this email, including attachments, may be
>>confidential and is intended solely for the addressee(s). If you believe
>>you received this email by mistake, please notify the sender by return
>>email as soon as possible.
>> ___________________________________________________________
>> 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/
>
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>------------------------------
>
>Message: 12
>Date: Fri, 10 Oct 2014 15:25:06 -0400
>From: Dannon Baker <[hidden email]>
>To: Chris Dag <[hidden email]>
>Cc: "[hidden email]" <[hidden email]>
>Subject: Re: [galaxy-dev] Why does Galaxy CloudMan 2.3 (ami-a7dbf6ce)
> run the boinc client?
>Message-ID:
> <CAGn_WZ=[hidden email]>
>Content-Type: text/plain; charset="utf-8"
>
>Legit and expected, no craziness going on there.  I've never actually used
>it, but my guess is it got included on this AMI from the cloudbiolinux
>base
>we used.
>
>On Fri, Oct 10, 2014 at 3:15 PM, Chris Dagdigian <[hidden email]> wrote:
>
>>
>> Just a paranoia check ...
>>
>> I manually started the cloudman galaxy AMI (ami-a7dbf6ce) and noticed
>> that it is configured and running a boinc client
>>
>> Just wanted to check if this was legit and expected ...
>>
>> Regards,
>> Chris
>>
>> ___________________________________________________________
>> 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/
>>
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>
>------------------------------
>
>Message: 13
>Date: Fri, 10 Oct 2014 19:59:31 +0000
>From: Iry Witham <[hidden email]>
>To: Daniel Blankenberg <[hidden email]>
>Cc: "[hidden email]" <[hidden email]>
>Subject: Re: [galaxy-dev] GATK2 java version related issues
>Message-ID: <D05DB16A.38CDB%[hidden email]>
>Content-Type: text/plain; charset="windows-1252"
>
>Hi Dan,
>
>I had suspected that, but when I run java ?version I get the following:
>
>java version "1.7.0_65"
>OpenJDK Runtime Environment (IcedTea 2.5.1)
>(7u65-2.5.1-4ubuntu1~0.12.04.2)
>OpenJDK 64-Bit Server VM (build 24.65-b04, mixed mode)
>
>I have rebooted the VM and nothing has changed.  The VM is built on AWS
>cloud and is using the latest galaxy ami:
>
>
>  1.  AMI: ami-a7dbf6ce
>  2.  Name: Galaxy CloudMan<https://wiki.galaxyproject.org/CloudMan> 2.3
>
>The only difference is that I needed to upgrade the java version for
>GATK2 and snpEff.  I currently have just a single node running so there
>is no issue with the wrong java version running on additional nodes.
>
>Thanks,
>Iry
>
>From: Daniel Blankenberg <[hidden email]<mailto:[hidden email]>>
>Date: Friday, October 10, 2014 3:16 PM
>To: Iry Witham <[hidden email]<mailto:[hidden email]>>
>Cc: "[hidden email]<mailto:[hidden email]>"
><[hidden email]<mailto:[hidden email]>>
>Subject: Re: [galaxy-dev] GATK2 java version related issues
>
>First guess is that perhaps the system is still defaulting to using java
>1.6 and not 1.7. What happens if you run ?java -version? as the Galaxy
>system user? Perhaps try a reboot of the vm as well to make sure that the
>Galaxy app is running with java 1.7.
>
>Also, is this a custom vm? If it using running things on different
>cluster nodes, you?ll need to make sure the java version on those nodes
>are 1.7 as well.
>
>Thanks,
>
>Dan
>
>
>On Oct 10, 2014, at 3:04 PM, Iry Witham
><[hidden email]<mailto:[hidden email]>> wrote:
>
>Hi Team,
>
>I am sorry to be a pest, but I am under-the-gun to get this resolved.  I
>have followed the instructions for installing GATK2 on my cloud VM.
>After doing that I discovered that the version of java running on the VM
>was v1.6.x and GATK2 required v1.7.0x.  I removed version 6 and installed
>version 7, uninstalled GATK2 and reinstalled it and reset all of the
>settings that may have reverted with the uninstalls/reinstalls.  Now when
>I run Unified Genotyper I get the following error:
>
>Exception in thread "main" java.lang.UnsupportedClassVersionError:
>org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported major.minor
>version 51.0
>at java.lang.ClassLoader.defineClass1(Native Method)
>at java.lang.ClassLoader.defineClass(ClassLoader.java:643)
>at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
>at java.net.URLClassLoader.defineClass(URLClassLoader.java:277)
>at java.net.URLClassLoader.access$000(URLClassLoader.java:73)
>at java.net.URLClassLoader$1.run(URLClassLoader.java:212)
>at java.security.AccessController.doPrivileged(Native Method)
>at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
>at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
>at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
>at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
>Could not find the main class:
>org.broadinstitute.gatk.engine.CommandLineGATK. Program will exit.
>
>Researching this I found a post at
>http://gatkforums.broadinstitute.org/discussion/3378/gatk2-error-when-i-te
>sted-it-after-installing that refers to upgrading java as the solution.
>However, that did not fix the issue.  In addition I copied the jar file
>to a temp directory and unzipped it to examine the MANAFEST.MF file for
>versioning issues.  This is what I found:
>
>Manifest-Version: 1.0
>Build-Jdk: 1.7.0_51
>Built-By: gsa-engineering
>Created-By: Apache Maven
>Main-Class: org.broadinstitute.gatk.engine.CommandLineGATK
>Archiver-Version: Plexus Archiver
>
>          This tells me that there is something else causing the problem.
> Does anyone have an idea where to look now?
>
>Regards,Iry
>The information in this email, including attachments, may be confidential
>and is intended solely for the addressee(s). If you believe you received
>this email by mistake, please notify the sender by return email as soon
>as possible.
>___________________________________________________________
>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/
>
>
>The information in this email, including attachments, may be confidential
>and is intended solely for the addressee(s). If you believe you received
>this email by mistake, please notify the sender by return email as soon
>as possible.
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>
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>
>End of galaxy-dev Digest, Vol 100, Issue 10
>*******************************************


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___________________________________________________________
Please keep all replies on the list by using "reply all"
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