Re: [galaxy-dev] 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, galaxy-dev-requ...@lists.bx.psu.edu
galaxy-dev-requ...@lists.bx.psu.edu wrote:

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1. Change the subject of your response from Galaxy-dev Digest Vol ...
to the original subject for the thread.
2. Strip out everything else in the digest that is not part of the thread
you are responding to.

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2. Not doing this greatly increases the number of emails that match
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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'sid 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 damion.doo...@bccdc.ca
To: Daniel Blankenberg d...@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:
   7891813f3c8f424b97d8bf2e5600e51903302322c...@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

Re: [galaxy-dev] galaxy-dev Digest, Vol 100, Issue 15

[Iry Witham]

So Ihave finally determined the cause and found a resolution for the
snpEff/java problem.  The issue was the fact that the vrsion of Java on
the Ubuntu linux VM from AWS is 1.6.x  snpEff 4.0e requires version 1.7.0
or higher.  This is fine, but you willneed to manually upgrade the java
version.  To do so you will need to complete the following:

SSH to the VM

sdo 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/cloudbiolinu.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 installoracle-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 snpEff t 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 10/16/14 12:00 PM, galaxy-dev-requ...@lists.bx.psu.edu
galaxy-dev-requ...@lists.bx.psu.edu wrote:

Send galaxy-dev mailing list submissions to
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To subscribe or unsubscribe via the Worl Wide Web, visit
   http://lists.bx.psu.edu/listinfo/galaxy-dev
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   galaxy-ev-requ...@lists.bx.psu.edu

You can reach the person managing the list at
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When replying, please edit your Subjct line so it is more specific
than Re: Contents of galaxy-dev digest...


HEY!  This is important!  If you reply to a thread in a igest, please
1. Change the subject of your response from Galaxy-dev Digest Vol ...
to the original subject for the thread.
2. Strip out everything else in the dgest that is not part of the thread
you are responding to.

Why?
1. This will keep the subject meaningful.  People will have some ideafrom the 
subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match
search ueries, but that aren't actually informative.

Today's Topics:

   1. Re: Set output dbkey from parameter value (Daniel Blankenberg)   2. Re: 
 Set output dbkey from parameter value (Nikos Sidiropoulos)
   3. Re: snpeff tool for Galay extra_files_path (John Chilton)
   4. Re: snpeff tool for Galaxy extra_files_path (Bj?rn Gr?nng)
   5. Re: snpeff tool for Galaxy extra_files_path (John Chilton)
   6. Re: snpeff tool for Galaxy extra_files_path (Jim Johnson)
   7. snpEff and java issue(Iry Witham)
   8. Re: HOWTO share tool parameter settings? (Lukasse, Pieter)
   9.Help with Galaxy server migration (Sarah Diehl)
  10. Re: Help with Galaxy server migrtion (John Chilton)
  11. Login issue with a nginx proxy (Alexandre Loywick)
  12. Re: Help with Galaxy server migration (Sarah Diehl)


-

Message: 1
Date: Wed, 15 Oct 2014 12:14:28 -0400
From: Daniel Blankenberg d...@bx.psu.edu
To: Nikos Sidiropoulos nikos.sid...@gmail.com
Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Set output dbkey from parameter value
Message-ID: e77c8a92-617a-455e-b5eb-209f4505b...@bx.psu.edu
Content-Type: text/plain; charset=windows-1252

Does removing the ?param_attribute=?value' attribute help?


On Oct 15, 2014, at 11:23 AM, Nikos Sidiropoulos nikos.sid...@gmail.com
wrote:

 Hi Daniel,
 
 Thanks for the response.
 
 I've edited the output to:
 
data format=bedgraph name=bedgraph_slograt
 label=${tool.name} on ${on_string}: Smoot Log2ratio (bedGraph)
 from_work_dir=output_dir/slograt.bedgraph
filter bedgraph['check'] == 'yes' and slograt['check']
 == 'yes' /filter
actions
conditional name=bedgraph.check
when value=yes
action type=metadata name=dbkey
option type=from_param
 name=bedgraph.genome param_attribute=value /
   /action
/when
/conditional
/actions
/data
 
 Now I'm getting a tool execution error.
 
 Error executing tool: 'unicode' object has no attribute 'value'
 
 I've tried to change the param_attribute to ext, dbkey (ones that
 I know that exist) and got a similar error.
 
 Bests,
 Nikos
 
 On 15 October 2014 16:58, Daniel Blankenberg d...@bx.psu.edu wrote:
 Hi Nikos,
 
 In the very least, you?ll want to make sure

[galaxy-dev] snpEff and java issue

[Iry Witham]

Hi Team,

I had manually installed the latest version of snpEff based on the 
recommendation of Pablo and after modifying the XML files I had a working 
version of snpEff that produced a vcf.  However, this morning I reran my 
workflow and it is failing again, but this time I am getting the following 
error:

Fatal error: Exit code 1 (Error)
Exception in thread main java.lang.UnsupportedClassVersionError: 
ca/mcgill/mcb/pcingola/snpEffect/commandLine/SnpEff : 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: 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff. Program will exit.

Nothing has been changed since I had success.

Regards,
Iry


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[galaxy-dev] GATK2 java version related issues

[Iry Witham]

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-tested-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

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is intended solely for the addressee(s). If you believe you received this email 
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Re: [galaxy-dev] GATK2 java version related issues

[Iry Witham]

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 CloudManhttps://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 d...@bx.psu.edumailto:d...@bx.psu.edu
Date: Friday, October 10, 2014 3:16 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
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 
iry.wit...@jax.orgmailto:iry.wit...@jax.org 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-tested-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
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is intended solely for the addressee(s). If you believe you received this email 
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[galaxy-dev] GATK2 reporting Invalid argument value '/mnt/galaxy/tools/gatk2/bin/' at position 8.

[Iry Witham]

Hi Team,

I have installed GATK2 into a galaxy cloud instance to use the Unified 
Genotyper for our sequencing course. However, when I run the tool I get the 
following error message:

Dataset 41: Unified Genotyper on data 8 and data 13 (VCF)

Tool execution generated the following error message:

ERROR 
--
ERROR A USER ERROR has occurred (version 3.2-2-gec30cee):
ERROR
ERROR This means that one or more arguments or inputs in your command are 
incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online 
documentation guide
ERROR (or rerun your command with --help) to view allowable command-line 
arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really 
tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid argument value '/mnt/galaxy/tools/gatk2/bin/' at 
position 8.
ERROR 
--

The following is the command that is being invoked by galaxy:

python 
/mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/84584664264c/gatk2/gatk2_wrapper.py
 --stdout /mnt/galaxy/files/000/dataset_326.dat -d -I 
/mnt/galaxy/files/000/dataset_226.dat bam gatk_input_0 -d  
/mnt/galaxy/files/_metadata_files/000/metadata_13.dat bam_index 
gatk_input_0 -p ' java -jar $GATK2_PATH/GenomeAnalysisTK.jar -T 
UnifiedGenotyper --num_threads ${GALAXY_SLOTS:-4} --out 
/mnt/galaxy/files/000/dataset_324.dat --metrics_file 
/mnt/galaxy/files/000/dataset_325.dat $GATK2_SITE_OPTIONS 
--num_cpu_threads_per_data_thread 1 --genotype_likelihoods_model BOTH 
--standard_min_confidence_threshold_for_calling 30.0 
--standard_min_confidence_threshold_for_emitting 30.0 ' -d -R 
/mnt/galaxy/files/000/dataset_220.dat fasta gatk_input



I have reviewed my configuration files and cannot locate where the issue lies. 
I am also posting this with the GATK Forum to see if they have any ideas. 
Unfortunately I need to get this resolved ASAP since I need to complete my 
testing by tomorrow.

Thanks,

Iry

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[galaxy-dev] snpEf dataset generation errors

[Iry Witham]

I am trying to resolve an issue with snpEff 3.4 running on a cloudman instance 
of galaxy.  The instance is invoking the following command and failing:

java -Xmx6G -jar $SNPEFF_JAR_PATH/snpEff.jar eff -c 
$SNPEFF_JAR_PATH/snpEff.config -i vcf -o vcf -upDownStreamLen 5000 
-spliceSiteSize 1 -stats /mnt/galaxy/files/000/dataset_364.dat -noLog -download 
GRCh37.68 /mnt/galaxy/files/000/dataset_313.dat  
/mnt/galaxy/files/000/dataset_363.dat

The error it is reporting is:

Fatal error: Exit code 255 (Error)
java.lang.RuntimeException: java.lang.RuntimeException: File not found on the 
server. Make sure the database name is correct.
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.download(SnpEffCmdDownload.java:159)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:234)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:217)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1001)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
Caused by: java.lang.RuntimeException: File not found on the server. Make sure 
the database name is correct.
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.download(SnpEffCmdDownload.java:122)
... 8 more
java.lang.RuntimeException: Genome download failed!
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1002)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)

I have upgraded to java 1.7.0 due to an issue with GATK2.

In addition to this when I try to run snpEff I am unable to select a genome 
source unless I use the Named on demand option.  How do I get snpEff genome 
version data configured?  The snpEff_genomes.loc file lists all of the genomes 
I need and many more.  I appreciate the help.

Regards,
Iry

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is intended solely for the addressee(s). If you believe you received this email 
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Re: [galaxy-dev] Cloudman indices installation/configuration

[Iry Witham]

Hi Enis,

Thanks for that information.  Now I am getting an error with the 
Unified_Genotyper failing to locate the GenomeAnalysisTK.jar.  I discovered 
that gatk2 needs to be downloaded and installed.  I have done that, but can't 
seem to figure out where the env.sh file reference below exists.  Can you point 
me to the correct proximity of that file?  Or do I need to create the file and 
if so where?

Thanks,
Iry

Galaxy wrapper for GATK2

This wrapper is copyright 2013 by Björn Grüning, Jim Johnson  the Galaxy Team.

The Genome Analysis Toolkit or GATK is a software package developed at the 
Broad Institute to analyse next-generation resequencing data. The toolkit 
offers a wide variety of tools, with a primary focus on variant discovery and 
genotyping as well as strong emphasis on data quality assurance. Its robust 
architecture, powerful processing engine and high-performance computing 
features make it capable of taking on projects of any size.

http://www.broadinstitute.org/gatk 
http://www.broadinstitute.org/gatk/about/citing-gatk

GATK is Free for academics, and fee for commercial use. Please study the GATK 
licensing website: http://www.broadinstitute.org/gatk/about/#licensing

Installation

The recommended installation is by means of the 
toolshedhttp://toolshed.g2.bx.psu.edu/view/iuc/gatk2.

Galaxy should be able to install samtools dependencies automatically for you. 
GATK2, and its new licence model, does not allow us to distribute the GATK 
binaries. As a consequence you need to install GATK2 by your own, please see 
the GATK website for more information:

http://www.broadinstitute.org/gatk/download

Once you have installed GATK2, you need to edit the env.sh files that are 
installed together with the wrappers. You must edit the GATK2_PATH environment 
variable in the file:

tool_dependency_dir/environment_settings/GATK2_PATH/iuc/gatk2/hash_string/env.sh

to point to the folder where you have installed GATK2.

Optionally, you may also want to edit the GATK2_SITE_OPTIONS environment 
variable in the file:

tool_dependency_dir/environment_settings/GATK2_SITE_OPTIONS/iuc/gatk2/hash_string/env.sh

to deactivate the 'call home feature' of GATK with something like:

GATK2_SITE_OPTIONS='-et NO_ET -K /data/gatk2_key_file'

GATK2_SITE_OPTIONS can be also used to insert other specific options into every 
GATK2 wrapper at runtime, without changing the actual wrapper.

Read more about the Phone Home problem at: 
http://www.broadinstitute.org/gatk/guide/article?id=1250

Optionally, you may also want to add some commands to be executed before GATK 
(e.g. to load modules) to the file:

tool_dependency_dir/gatk2/default/env.sh

Finally, you should fill in additional information about your genomes and 
annotations in the gatk2_picard_index.loc and gatk2_annotations.txt. You can 
find them in the tool-data/ Galaxy directory.


From: Enis Afgan afg...@gmail.commailto:afg...@gmail.com
Date: Saturday, October 4, 2014 6:10 AM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman indices installation/configuration

Hi Iry,
Try adding the following to your 
/mnt/galaxy/galaxy-app/tool_data_table_conf.xml, populating the referenced 
files (tool-data/gatk2_picard_index.loc and tool-data/gatk2_annotations.txt) as 
desired and restarting Galaxy:

!-- Location of Picard dict files valid for GATK --
table name=gatk2_picard_indexes comment_char=#
columnsvalue, dbkey, name, path/columns
file path=tool-data/gatk2_picard_index.loc /
/table
!-- Available of GATK references --
table name=gatk2_annotations comment_char=#
columnsvalue, name, gatk_value, tools_valid_for/columns
file path=tool-data/gatk2_annotations.txt /
/table

Hope this gets you going. Let us know if it doesn't,
Enis

On Fri, Oct 3, 2014 at 1:36 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
It looks like I need to generate the dict file for the mm10 reference as well 
as add the reference to the srma_index.loc.  My question is where do these need 
to exist?  Do they belong in the repo directory structure or or in the primary 
tool-data directory?  The hg19.fa, hg19.fa.fia, hg19.dict as well as these same 
files for the mm9 GRCh37. However, the .dict does not exist for mm10.  Even 
though that is the case the references do not appear in the gatk2 tools.

Any ideas?

Thanks,
Iry

From: Daniel Blankenberg d...@bx.psu.edumailto:d...@bx.psu.edu
Date: Thursday, October 2, 2014 1:57 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman indices installation/configuration

Hi Iry,

First thing to check is that your fields are tab delimited — they appear

[galaxy-dev] Cloudman indices installation/configuration

[Iry Witham]

Hi Team,

I have a new instance of galaxy cloudman running and have added tools from the 
toolshed to it.  When I attempt to run tools like sam-to-bam or any gatk tool I 
am prompted for a reference genome.  However, indices/references not available 
for these tools.  I have added the following line to the sam_fa_indices.loc, 
but that did nothing:

index   hg19/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/gh19.fa

I have also added the following three lines to the gatk2_picard_index.loc:

hg19hg19Human (hg19)
/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
GRCh37  GRCh37  Human (GRCh37)  
/mnt/galaxyIndices/genomes/Hsapiens/GRCh37/seq/GRCh37.fa
mm10mm10Mouse (mm10)
/mnt/galaxyIndices/genomes/Mmusculus/mm10/seq/mm10.fa

I know I have missed something, but can't seem to figure it out.  Could someone 
point me in the right direction?

Regards,
__
Iry T. Witham
Scientific Applications Administrator
Computational Sciences Group
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609
Phone: 207-288-6744
email: iry.wit...@jax.org


[cid:A4FA2ADE-F7C3-4B38-851C-6FE20C32198B]


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Re: [galaxy-dev] Cloudman indices installation/configuration

[Iry Witham]

Hi Dan,

Thanks for pointing out the tab issue.  However, I have made the modification 
and restarted my instance, but still get no reference genome listed.  It is 
funny that there are a limited number of tools that have this issue.  They are:

SAM Tools:
Generate pileup
SAM-to-BAM
Mpileup
SNP/WGA: Data; Filters:
SnpEff
SnpEff Download (cannot select a genome version to download)
NGS: Picard:
SAM/BAM Alignment Summary
SAM/BAM GC Bias
NGS: GATK2 Tools: (All of the tools)

These are tools that I have installed via the toolshed.  Is there a different 
location for the .loc files that need modifying?

Thanks,
Iry

From: Daniel Blankenberg d...@bx.psu.edumailto:d...@bx.psu.edu
Date: Thursday, October 2, 2014 1:57 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman indices installation/configuration

Hi Iry,

First thing to check is that your fields are tab delimited — they appear to be 
spaces instead of tabs in this email, but copy and pasting into email can munge 
things sometimes (also “gh19.fa” is probably a typo, but that wouldn’t prevent 
the selection option from showing up).


Thanks for using Galaxy,

Dan


On Oct 2, 2014, at 1:49 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:

Hi Team,

I have a new instance of galaxy cloudman running and have added tools from the 
toolshed to it.  When I attempt to run tools like sam-to-bam or any gatk tool I 
am prompted for a reference genome.  However, indices/references not available 
for these tools.  I have added the following line to the sam_fa_indices.loc, 
but that did nothing:

index   hg19/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/gh19.fa

I have also added the following three lines to the gatk2_picard_index.loc:

hg19hg19Human (hg19)
/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
GRCh37  GRCh37  Human (GRCh37)  
/mnt/galaxyIndices/genomes/Hsapiens/GRCh37/seq/GRCh37.fa
mm10mm10Mouse (mm10)
/mnt/galaxyIndices/genomes/Mmusculus/mm10/seq/mm10.fa

I know I have missed something, but can't seem to figure it out.  Could someone 
point me in the right direction?

Regards,
__
Iry T. Witham
Scientific Applications Administrator
Computational Sciences Group
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609
Phone: 207-288-6744
email: iry.wit...@jax.orgx-msg://12/iry.wit...@jax.org


372D007A-1B00-4668-BA6B-F0527C1F24BE[34][3].png

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[galaxy-dev] Cloudman installed tools missing referneces

[Iry Witham]

Hi Team,

I have a new instance of galaxy cloudman running on AWS and when I go to run 
some of the tools I have installed like SAM-to-BAM it requires a reference 
genome, but none is available.  This is SAM-to-BAM version 1.1.4.  This is the 
first tool I have found this to be an issue so far.  Is there a loc file that 
needs modification?  I will need to add several references.

Thanks,
Iry

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[galaxy-dev] Join tool failure

[Iry Witham]

Hi Team,

I have upgraded to the latest galaxy distribution on my test server.  Now I am 
running into issues and can't figure this one out.  I am attempting to run the 
join.py tool to join two datasets at specified fields.  I am getting the 
following error:


Traceback (most recent call last):
  File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/tools/filters/join.py, 
line 18, in module
from galaxy.util.bunch import Bunch
  File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/__init__.py, 
line 95, in module
import galaxy.eggs
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/eggs/__init__.py, 
line 5, in module
import os, sys, shutil, glob, urllib, urllib2, ConfigParser, HTMLParser, 
zipimport, zipfile
  File /usr/lib64/python2.6/urllib2.py, line 93, in module
import hashlib
  File /usr/lib64/python2.6/hashlib.py, line 88, in module
import _hashlib
ImportError: /usr/lib64/libssl.so.10: symbol EC_KEY_get0_group, version 
OPENSSL_1.0.1_EC not defined in file libcrypto.so.10 with link time reference
Traceback (most recent call last):
  File ./scripts/set_metadata.py, line 29, in module
from galaxy import eggs
  File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/__init__.py, 
line 95, in module
import galaxy.eggs
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/eggs/__init__.py, 
line 5, in module
import os, sys, shutil, glob, urllib, urllib2, ConfigParser, HTMLParser, 
zipimport, zipfile
  File /usr/lib64/python2.6/urllib2.py, line 93, in module
import hashlib
  File /usr/lib64/python2.6/hashlib.py, line 88, in module
import _hashlib
ImportError: /usr/lib64/libssl.so.10: symbol EC_KEY_get0_group, version 
OPENSSL_1.0.1_EC not defined in file libcrypto.so.10 with link time reference

I am at a loss on the resolution for this.

Thanks,
Iry




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Re: [galaxy-dev] Upload file not working with new install

[Iry Witham]

Hi Nate,

We were able to get upgraded to pbs-python 4.4.0 after having to modify some 
c++ code that was causing errors with the _py.so.  We now have it running, but 
I am trying to get the references to work for the tools I have installed from 
the tool shed.  They can't seem to find the correct path.

Thanks,
Iry

Sent from my iPhone

On Aug 18, 2014, at 5:08 PM, Nate Coraor 
n...@bx.psu.edumailto:n...@bx.psu.edu wrote:

On Aug 18, 2014, at 9:55 AM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:

Hi John,

I was able to work through this since it was related to pbs on the
cluster.  However, I am still having issues.  This is the error I am
getting:

galaxy.tools.genome_index DEBUG 2014-08-18 09:31:56,819 Loaded genome
index tool: __GENOME_INDEX__
galaxy.jobs.manager DEBUG 2014-08-18 09:31:56,825 Starting job handler
galaxy.jobs INFO 2014-08-18 09:31:56,825 Handler 'handler1' will load all
configured runner plugins
galaxy.jobs.runners DEBUG 2014-08-18 09:31:56,829 Starting 5 LocalRunner
workers
galaxy.jobs DEBUG 2014-08-18 09:31:57,073 Loaded job runner
'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.runners DEBUG 2014-08-18 09:31:57,104 Starting 3 LWRRunner
workers
galaxy.jobs.runners.lwr_client.manager INFO 2014-08-18 09:31:57,197
Setting LWR client class to standard, non-caching variant.
galaxy.jobs DEBUG 2014-08-18 09:31:57,228 Loaded job runner
'galaxy.jobs.runners.lwr:LwrJobRunner' as 'lwr'
Traceback (most recent call last):
 File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/webapps/galaxy/bu
ildapp.py, line 39, in app_factory
   app = UniverseApplication( global_conf = global_conf, **kwargs )
 File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py,
line 144, in __init__
   self.job_manager = manager.JobManager( self )
 File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/manager.py,
line 23, in __init__
   self.job_handler = handler.JobHandler( app )
 File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py,
line 31, in __init__
   self.dispatcher = DefaultJobDispatcher( app )
 File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py,
line 583, in __init__
   self.job_runners = self.app.job_config.get_job_runner_plugins(
self.app.config.server_name )
 File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/__init__.py
, line 496, in get_job_runner_plugins
   module = __import__( module_name )
 File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/runners/pbs.
py, line 32, in module
   raise Exception( egg_message % str( e ) )
Exception:

The 'pbs' runner depends on 'pbs_python' which is not installed or not
configured properly.  Galaxy's scramble system should make this
installation
simple, please follow the instructions found at:

   http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster

Additional errors may follow:
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pbs_python-4.3.5-py2.6-l
inux-x86_64-ucs4.egg/_pbs.so: undefined symbol: log_record

Hi Iry,

It looks like we need to upgrade to pbs_python 4.4.0: 
https://oss.trac.surfsara.nl/pbs_python/ticket/34

The pbs_python 4.4.0 source is on our eggs server - could you update the 
version to 4.4.0 in /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs.ini and 
re-scramble the egg and let us know if this fixes it?

Thanks,
--nate



Removing PID file handler1.pid


I am running the following:

galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist qsub --about
HomeDir:   /var/spool/torque  InstallDir: /usr/local  Server: rockhopper
BuildDir:  /root/torque-4.2.5
BuildUser: root
BuildHost: galaxy2
BuildDate: Sat Aug 16 11:17:00 EDT 2014
Version:   4.2.5
Commit:  39f78e588b3a47a6c7bed1004ec7b5d0ccf24288


The handler.pid are being removed.

Thanks,
Iry

On 8/18/14 9:16 AM, John Chilton 
jmchil...@gmail.commailto:jmchil...@gmail.com wrote:

I have not seen this before - are you able to submit things as your
Galaxy user from the command line? Are their logs on the PBS side that
give any more clues?

-John

On Fri, Aug 15, 2014 at 2:01 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
Hi John,

   It looks like it may be related to PBS and Torque.  I am
currently
running torque-4.2.5.  I scrambled the pbs-python eggs and it is now
running pbs-python 4.3.5.  The good thing is I am now getting an attempt
to submit to pbs, but all jobs are failing.  This is the error:

galaxy.jobs.handler DEBUG 2014-08-15 13:10:37,822 (16) Dispatching to
pbs
runner
galaxy.jobs DEBUG 2014-08-15 13:10:41,110 (16) Persisting job
destination
(destination id: pbs:-l nodes=1:ppn=1,walltime=20:00:00)
galaxy.jobs.handler INFO 2014-08-15 13:10:41,145 (16) Job dispatched
galaxy.tools.deps DEBUG 2014-08-15 13:10:42,338 Building dependency
shell
command for dependency 'samtools'
galaxy.tools.deps WARNING 2014-08-15 13:10:42,339 Failed to resolve
dependency on 'samtools', ignoring
galaxy.jobs.runners.pbs

Re: [galaxy-dev] Upload file not working with new install

[Iry Witham]

I have checked and everything appears correct.  I did notice that in the 
/database/tmp/upload_store/ there are files that when I cat them they are the 
files I am/have attempted to upload.  However, they do not get moved to the 
/ftp directory.  I am wondering if this is due to a misconfiguration in the 
universe.wsgi.ini or if it could be related to proftpd or postgres.  
Unfortunately I am under a very tight deadline and need to figure this out.  
Any assistance will be appreciated.

Thanks,
Iry

From: Michael Mason 
mma...@benaroyaresearch.orgmailto:mma...@benaroyaresearch.org
Date: Thursday, August 14, 2014 12:48 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org, 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Upload file not working with new install

No sure if this will help but you may want to check this. We just fixed a 
problem from uploading small files via the ftp directory. Our nfs mount was set 
to cache file meta data about every 30 sec. This proved problematic when 
uploading a small fasta file that previously uploaded.  Every time we tried 
uploading, it finished with no errors but was empty. Turning the nfs caching 
off fixed this.

From: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Date: Thursday, August 14, 2014 9:34 AM
To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Upload file not working with new install

Hi Team,

I have installed a fresh version of Galaxy and am having an issue with the 
'Upload File' tool.  When I attempt to use it it just sits and spins.  No data 
gets uploaded.  I have looked through the universe.wsgi.ini file and cannot 
find anything there that stands out.  Can you point me to a possible solution?

Thanks,
Iry

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Re: [galaxy-dev] Upload file not working with new install

[Iry Witham]

Hi John,

It looks like it may be related to PBS and Torque.  I am currently
running torque-4.2.5.  I scrambled the pbs-python eggs and it is now
running pbs-python 4.3.5.  The good thing is I am now getting an attempt
to submit to pbs, but all jobs are failing.  This is the error:

galaxy.jobs.handler DEBUG 2014-08-15 13:10:37,822 (16) Dispatching to pbs
runner
galaxy.jobs DEBUG 2014-08-15 13:10:41,110 (16) Persisting job destination
(destination id: pbs:-l nodes=1:ppn=1,walltime=20:00:00)
galaxy.jobs.handler INFO 2014-08-15 13:10:41,145 (16) Job dispatched
galaxy.tools.deps DEBUG 2014-08-15 13:10:42,338 Building dependency shell
command for dependency 'samtools'
galaxy.tools.deps WARNING 2014-08-15 13:10:42,339 Failed to resolve
dependency on 'samtools', ignoring
galaxy.jobs.runners.pbs ERROR 2014-08-15 13:11:33,507 Connection to PBS
server for submit failed: 15007: No permission


Iry

On 8/15/14 12:11 PM, John Chilton jmchil...@gmail.com wrote:

Okay - I just checked out a clean Galaxy without modifications and I
don't see any problems with uploads. So this is likely something to do
with your setup - if I had to guess I would guess that your
job_conf.xml configuration is somehow incorrect - the job is getting
creating but nothing is running it. Can you verify this by looking in
the logs? I would imagine you do see lines like:

galaxy.tools.actions.upload_common INFO 2014-08-15 12:04:04,306 tool
upload1 created job id 2

for the uploads but nothing like:

galaxy.jobs.runners DEBUG 2014-08-15 12:04:05,119 (2) command is:
python 
/home/john/workspace/galaxy-central-fresh/tools/data_source/upload.py


You could also verify this is the problem by doing something other
than uploading - maybe a data source tool? I have attached a tool that
doesn't require any existing files or external data sources that I use
for testing stuff like this - maybe see if it runs?

If no jobs run - can you attach your job_conf.xml and we can try to
debug the problem from there.

If other tools run than it is likely not a job related problem - in
that case can you answer some questions - Are you using a proxy - if
so which one? Can you attach the configuration? Is the upload.xml tool
in your tool_conf.xml? Have you made modifications to it?

-John

On Fri, Aug 15, 2014 at 10:47 AM, Iry Witham iry.wit...@jax.org wrote:
 I have checked and everything appears correct.  I did notice that in the
 /database/tmp/upload_store/ there are files that when I cat them they
are
 the files I am/have attempted to upload.  However, they do not get
moved to
 the /ftp directory.  I am wondering if this is due to a
misconfiguration in
 the universe.wsgi.ini or if it could be related to proftpd or postgres.
 Unfortunately I am under a very tight deadline and need to figure this
out.
 Any assistance will be appreciated.

 Thanks,
 Iry

 From: Michael Mason mma...@benaroyaresearch.org
 Date: Thursday, August 14, 2014 12:48 PM
 To: Iry Witham iry.wit...@jax.org, galaxy-dev@lists.bx.psu.edu
 galaxy-dev@lists.bx.psu.edu
 Subject: Re: [galaxy-dev] Upload file not working with new install

 No sure if this will help but you may want to check this. We just fixed
a
 problem from uploading small files via the ftp directory. Our nfs mount
was
 set to cache file meta data about every 30 sec. This proved problematic
when
 uploading a small fasta file that previously uploaded.  Every time we
tried
 uploading, it finished with no errors but was empty. Turning the nfs
caching
 off fixed this.

 From: Iry Witham iry.wit...@jax.org
 Date: Thursday, August 14, 2014 9:34 AM
 To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
 Subject: [galaxy-dev] Upload file not working with new install

 Hi Team,

 I have installed a fresh version of Galaxy and am having an issue with
the
 'Upload File' tool.  When I attempt to use it it just sits and spins.
No
 data gets uploaded.  I have looked through the universe.wsgi.ini file
and
 cannot find anything there that stands out.  Can you point me to a
possible
 solution?

 Thanks,
 Iry

 The information in this email, including attachments, may be
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 this email by mistake, please notify the sender by return email as soon
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 --CONFIDENTIALITY NOTICE--: The information contained in this email is
 intended for the exclusive use of the addressee and may contain
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 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
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 Please keep all replies on the list

[galaxy-dev] Upload file not working with new install

[Iry Witham]

Hi Team,

I have installed a fresh version of Galaxy and am having an issue with the 
'Upload File' tool.  When I attempt to use it it just sits and spins.  No data 
gets uploaded.  I have looked through the universe.wsgi.ini file and cannot 
find anything there that stands out.  Can you point me to a possible solution?

Thanks,
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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[galaxy-dev] Issues with dependencies for toolshed packages

[Iry Witham]

Hi Team,

I have been trying to install package_snpEff_3_5 from the Galaxy main tool shed 
and package_snpEff_3_6 from the Galaxy test tool shed and have the same issue.  
Once the installer completes it shows that the dependency snpEff.x.x was not 
installed.  When I try to install the dependency it reports that the directory 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmp-toolshed-mtdi48tQV/snpEff
 does not exist.  I have checked to confirm that this is true and discovered 
that rather then a directory I find a null file named snpEff and the 
snpEff_v3.x_core.zip file.  I checked my shedtool dependencies folder and the 
directory for these tools are empty.  I have since uninstalled the package.  I 
just tried again to install the snpEff tool and am getting the followig error 
message:

Internal Server Error
Galaxy was unable to successfully complete your request

URL: 
http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413
Module galaxy.web.framework.middleware.error:149 in __call__
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  body = method( trans, **kwargs )
Module galaxy.web.framework:377 in decorator
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:1035 in 
prepare_for_install
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
Module tool_shed.util.common_util:310 in tool_shed_get
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  response = urlopener.open( uri )
Module urllib2:395 in open
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  response = meth(req, response)
Module urllib2:508 in http_response
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  'http', request, response, code, msg, hdrs)
Module urllib2:427 in error
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  result = self._call_chain(*args)
Module urllib2:367 in _call_chain
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  result = func(*args)
Module urllib2:603 in http_error_302
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  return self.parent.open(new)
Module urllib2:395 in open
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  response = meth(req, response)
Module urllib2:508 in http_response
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  'http', request, response, code, msg, hdrs)
Module urllib2:433 in error
  
 

Re: [galaxy-dev] Issues with dependencies for toolshed packages

[Iry Witham]

Hi Greg,

That resolved the internal server error issue.  Now I need to figure out the 
issue with the dependencies.  I was unable to post the actual error message 
previously, but am doing so now.  Here is the error I get for the dependency 
installation:

NameVersion TypeStatus  Error
snpEff 
http://galaxy2/admin_toolshed/manage_repository_tool_dependencies?repository_id=b1254334b8763c9coperation=browsetool_dependency_ids=81424a9b99396c5a
 3.6 package Error File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py,
 line 110, in install_and_build_package_via_fabric
tool_dependency = self.install_and_build_package( app, 
tool_shed_repository, tool_dependency, actions_dict )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py,
 line 103, in install_and_build_package
dir = tmp_dir
  File /usr/lib64/python2.6/contextlib.py, line 34, in __exit__
self.gen.throw(type, value, traceback)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py,
 line 142, in _setenv
yield
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py,
 line 68, in install_and_build_package
initial_download=True )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py,
 line 32, in execute_step
initial_download=initial_download )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py,
 line 397, in execute_step
dir = td_common_util.url_download( work_dir, downloaded_filename, url, 
extract=True )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py,
 line 560, in url_download
extraction_path = archive.extract( install_dir )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py,
 line 60, in extract
self.archive.extractall( os.path.join( path ) )
  File /usr/lib64/python2.6/zipfile.py, line 940, in extractall
self.extract(zipinfo, path, pwd)
  File /usr/lib64/python2.6/zipfile.py, line 928, in extract
return self._extract_member(member, path, pwd)
  File /usr/lib64/python2.6/zipfile.py, line 965, in _extract_member
target = file(targetpath, wb)

[Errno 20] Not a directory: 
'database/tmp/tmp-toolshed-mtdCAL19a/snpEff/snpEff.config'



This current package is owned by jjohnson and is located in the test toolshed.

Thanks,
Iry



From: Greg Von Kuster g...@bx.psu.edumailto:g...@bx.psu.edu
Date: Wednesday, August 6, 2014 12:34 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Issues with dependencies for toolshed packages

Hi Iry,

Sorry for the inconvenience.  The tool shed server was out of space - I've 
corrected the problem and have successfully installed repositories.  Please try 
again and let us know if you encounter problems.

Thanks!

Greg Von Kuster


On Aug 6, 2014, at 12:20 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:

Hi Team,

I have been trying to install package_snpEff_3_5 from the Galaxy main tool shed 
and package_snpEff_3_6 from the Galaxy test tool shed and have the same issue.  
Once the installer completes it shows that the dependency snpEff.x.x was not 
installed.  When I try to install the dependency it reports that the directory 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmp-toolshed-mtdi48tQV/snpEff
 does not exist.  I have checked to confirm that this is true and discovered 
that rather then a directory I find a null file named snpEff and the 
snpEff_v3.x_core.zip file.  I checked my shedtool dependencies folder and the 
directory for these tools are empty.  I have since uninstalled the package.  I 
just tried again to install the snpEff tool and am getting the followig error 
message:

Internal Server Error
Galaxy was unable to successfully complete your request
URL: 
http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413
Module galaxy.web.framework.middleware.error:149 in __call__
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  app_iter = self.application(environ,sr_checker)
Module paste.recursive:84 in __call__
  
 http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413#
  return self.application(environ,start_response)
Module paste.httpexceptions:633 in __call__

Re: [galaxy-dev] Issues with dependencies for toolshed packages

[Iry Witham]

Bjoern,

I am not getting the same error.  However, it is still failing.  I get the 
following banner:

This tool dependency is not installed correctly (see the Tool dependency 
installation error below). Choose Uninstall this tool dependency from the 
Repository Actions menu, correct problems if necessary, and try installing the 
dependency again.

And the following information is listed:

Tool shed repository: snpeff
Tool shed repository changeset revision: e8adfc4c0a6b
Tool dependency status: Error
Tool dependency installation error: This tool dependency's required tool 
dependency snpEff version 3.4 has status Error.
Tool dependency installation directory: 
./../shed_tools/tool_dependencies/snpEff/3.4/iuc/snpeff/e8adfc4c0a6b
Contents:
snpEffhttp://galaxy2/admin_toolshed/browse_tool_dependency?repository_id=0dd27a44d4d97a53operation=browsetool_dependency_ids=53b036f027c29984#
env.shhttp://galaxy2/admin_toolshed/browse_tool_dependency?repository_id=0dd27a44d4d97a53operation=browsetool_dependency_ids=53b036f027c29984#
if [ -f 
/hpcdata/galaxy-test/galaxy-setup/shed_tools/tool_dependencies/snpEff/3.4/iuc/package_snpeff_3_4/af7ff8187d09/env.sh
 ] ; then . 
/hpcdata/galaxy-test/galaxy-setup/shed_tools/tool_dependencies/snpEff/3.4/iuc/package_snpeff_3_4/af7ff8187d09/env.sh
 ; fi

Thanks,
Iry

From: bjoern.gruen...@googlemail.commailto:bjoern.gruen...@googlemail.com 
bjoern.gruen...@gmail.commailto:bjoern.gruen...@gmail.com
Date: Wednesday, August 6, 2014 1:16 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: Greg Von Kuster g...@bx.psu.edumailto:g...@bx.psu.edu, 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Issues with dependencies for toolshed packages

Iry,

are you seeing the same error with:
 https://toolshed.g2.bx.psu.edu/view/iuc/snpeff

Cheers,
Bjoern



2014-08-06 19:12 GMT+02:00 Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org:
Hi Greg,

That resolved the internal server error issue.  Now I need to figure out the 
issue with the dependencies.  I was unable to post the actual error message 
previously, but am doing so now.  Here is the error I get for the dependency 
installation:

NameVersion TypeStatus  Error
snpEff 
http://galaxy2/admin_toolshed/manage_repository_tool_dependencies?repository_id=b1254334b8763c9coperation=browsetool_dependency_ids=81424a9b99396c5a
 3.6 package Error File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py,
 line 110, in install_and_build_package_via_fabric
tool_dependency = self.install_and_build_package( app, 
tool_shed_repository, tool_dependency, actions_dict )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py,
 line 103, in install_and_build_package
dir = tmp_dir
  File /usr/lib64/python2.6/contextlib.py, line 34, in __exit__
self.gen.throw(type, value, traceback)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py,
 line 142, in _setenv
yield
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py,
 line 68, in install_and_build_package
initial_download=True )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py,
 line 32, in execute_step
initial_download=initial_download )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py,
 line 397, in execute_step
dir = td_common_util.url_download( work_dir, downloaded_filename, url, 
extract=True )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py,
 line 560, in url_download
extraction_path = archive.extract( install_dir )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py,
 line 60, in extract
self.archive.extractall( os.path.join( path ) )
  File /usr/lib64/python2.6/zipfile.py, line 940, in extractall
self.extract(zipinfo, path, pwd)
  File /usr/lib64/python2.6/zipfile.py, line 928, in extract
return self._extract_member(member, path, pwd)
  File /usr/lib64/python2.6/zipfile.py, line 965, in _extract_member
target = file(targetpath, wb)

[Errno 20] Not a directory: 
'database/tmp/tmp-toolshed-mtdCAL19a/snpEff/snpEff.config'



This current package is owned by jjohnson and is located in the test toolshed.

Thanks,
Iry



From: Greg Von Kuster g...@bx.psu.edumailto:g...@bx.psu.edu
Date: Wednesday, August 6, 2014 12:34 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Issues

[galaxy-dev] Fresh galaxy install fails to start

[Iry Witham]

Hi Dev Team,

I am attempting to get a new/clean installation running and am having 
difficulty.  I did a clone from https://bitbucket.org/galaxy/galaxy-dist and 
made my needed configuration changes for my environment.  I attempted to start 
it and needed to do the database upgrade via sh manage_db.sh upgrade.  That 
went just fine.  I tried another start and got the following error:

migrate.versioning.repository DEBUG 2014-07-17 13:07:56,566 Config: 
{'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 
'version_table': 'migrate_tools', 'repository_id': 'GalaxyTools'}}
tool_shed.galaxy_install.migrate.check DEBUG 2014-07-17 13:07:56,571 psycopg2 
egg successfully loaded for postgres dialect
Traceback (most recent call last):
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py,
 line 39, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
  File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py, line 
46, in __init__
self._configure_models( check_migrate_databases=True, 
check_migrate_tools=check_migrate_tools, config_file=config_file )
  File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/config.py, 
line 656, in _configure_models
verify_tools( self, install_db_url, config_file, install_database_options )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/migrate/check.py,
 line 150, in verify_tools
raise Exception( msg )
Exception:


The list of files at the end of this message refers to tools that are 
configured to load into the tool panel for
this Galaxy instance, but have been removed from the Galaxy distribution.  
These tools and their dependencies can be
automatically installed from the Galaxy tool shed at 
http://toolshed.g2.bx.psu.edu.

To skip this process, attempt to start your Galaxy server again (e.g., sh 
run.sh or whatever you use).  If you do this,
be aware that these tools will no longer be available in your Galaxy tool 
panel, and entries for each of them should
be removed from your file named ./tool_conf.xml.

CRITICAL NOTE IF YOU PLAN TO INSTALL
The location in which the tool repositories will be installed is the value of 
the 'tool_path' attribute in the tool
tag of the file named ./migrated_tool_conf.xml (i.e., toolbox 
tool_path=../shed_tools).  The default location
setting is '../shed_tools', which may be problematic for some cluster 
environments, so make sure to change it before
you execute the installation process if appropriate.  The configured location 
must be outside of the Galaxy installation
directory or it must be in a sub-directory protected by a properly configured 
.hgignore file if the directory is within
the Galaxy installation directory hierarchy.  This is because tool shed 
repositories will be installed using mercurial's
clone feature, which creates .hg directories and associated mercurial 
repository files.  Not having .hgignore properly
configured could result in undesired behavior when modifying or updating your 
local Galaxy instance or the tool shed
repositories if they are in directories that pose conflicts.  See mercurial's 
.hgignore documentation at the following
URL for details.

http://mercurial.selenic.com/wiki/.hgignore

The following tool dependencies can also optionally be installed (see the 
option flag in the command below).  If you
choose to install them (recommended), they will be installed within the 
location specified by the 'tool_dependency_dir'
setting in your main Galaxy configuration file (e.g., uninverse_wsgi.ini).

Tool Dependency

Name: bx-python, Version: 0.7.1, Type: package



Tool Dependency

Name: R, Version: 2.11.0, Type: package



Tool Dependency

Name: rpy, Version: 1.0.3, Type: package



Tool Dependency

Name: numpy, Version: 1.7.1, Type: package



Tool Dependency

Name: yacca, Version: 1.0, Type: package



Tool Dependency

Name: kernlab, Version: 0.1-4, Type: package



Tool Dependency

Name: libxml2, Version: 2.9.1, Type: package



Tool Dependency

Name: libpng, Version: 1.6.7, Type: package

[galaxy-dev] Continued issue fetching eggs

[Iry Witham]

Hi Team,

Quite some time back I posted that I was unable to upgrade my local galaxy 
instance due to issues fetching eggs.  I have not been able to get this 
resolved and was wondering if I could get some help.  The error I get is:

python scripts/fetch_eggs.py
Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched

Thanks,

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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[galaxy-dev] Egg distribution issue

[Iry Witham]

Hi Dev Team,

I have run into an egg distribution issue.  I had performed an upgrade late 
last month and am experiencing issues fetching eggs.  I am getting the 
following error message:

galaxy@jaxgalaxydev01:/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist python 
./scripts/fetch_eggs.py
Fetched 
http://eggs.galaxyproject.org/sqlalchemy_migrate/sqlalchemy_migrate-0.7.2-py2.6.egg
One of Galaxy's managed eggs depends on something which is missing, this is 
almost certainly a bug in the egg distribution.
Dependency sqlalchemy-migrate requires setuptools
Traceback (most recent call last):
  File ./scripts/fetch_eggs.py, line 37, in module
c.resolve() # Only fetch eggs required by the config
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/lib/galaxy/eggs/__init__.py, 
line 345, in resolve
egg.resolve()
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/lib/galaxy/eggs/__init__.py, 
line 168, in resolve
dists = pkg_resources.working_set.resolve( ( 
self.distribution.as_requirement(), ), env, self.fetch )
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/galaxy-dist-jax/lib/pkg_resources.py,
 line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (sqlalchemy-migrate 0.7.2 
(/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg),
 Requirement.parse('setuptools'))

Could someone point me in the right direction?

Thanks,

Iry
__
Iry T. Witham
Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609
Phone: 207-288-6744
email: iry.wit...@jax.org


[cid:3302E28C-F24A-4AF1-97B8-A33A6CD618F6]


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Re: [galaxy-dev] configuring auth_ldap for galaxy

[Iry Witham]

I think I am nearly there with the auth_ldap, but when I attempt to
access the site I get the following message:

Access to Galaxy is denied

Galaxy is configured to authenticate users via an external method (such as
HTTP authentication in Apache), but a username was not provided by the
upstream (proxy) server.  This is generally due to a misconfiguration in
the upstream server.

Please contact your local Galaxy administrator.

I am using a service account in the configuration and wonder if this
could be a permissions issue.

Thanks,
Iry


On 9/18/13 10:10 AM, Maddhi, Srinivas srinivas-mad...@uiowa.edu wrote:

Another galaxy + nginx + LDAP user here.


Iry,

I have it working as well with help from Galaxy Wiki docs and mailing list
archives. The configure options that were used to compile nginx:
--add-module=../nginx-auth-ldap.20130823
--add-module=../nginx-upload-module-2.2 --with-pcre=../pcre-8.33
--with-http_ssl_module --conf-path=/usr/local/etc/nginx/nginx.conf
--pid-path=/var/run/nginx.pid --error-log-path=/var/log/nginx/error.log
--http-log-path=/var/log/nginx/access.log --user=galaxy-qa
--group=galaxy-qa --with-debug

I also supplied the proxy_set_header X-URL-SCHEME https; directive in
the / and /api location blocks.

Good luck!


John,

Thanks for the detailed response to Iry's question, and docs for this
setup.

Related question: Are you aware of a mechanism that would transmit LDAP
attributes, say mail for example, to downstream apps ?  I have that
question in to the author of that module and haven't heard back.

The need for that: in my use case, the email address associated with
remote_user is not remote_u...@example.com but rather
first_name-last_n...@example.com.  As such, I am stuck, less than
ideally, with requiring users to use first_name-last_n...@example.com as
their username instead of just short_name. Our previous solution to this
was to hack galaxy-dist/lib/galaxy/web/framework/__init__.py which I would
like to avoid for ease of maintainability purposes.

Thank you.


-Original Message-
From: John Chilton chil...@msi.umn.edu
Date: Wednesday, September 18, 2013 7:49 AM
To: Iry Witham iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] configuring auth_ldap for galaxy

You have to compile nginx with the auth-ldap module. Have you done
this? I am doing using CloudBioLinux and here is how it is being done
in that context, but it would probably be easier just doing it by
hand:

https://github.com/chapmanb/cloudbiolinux/blob/master/cloudbio/galaxy/__i
n
it__.py

I have posted my information on configuring CloudMan's nginx for LDAP
auth, but you can ignore the CloudMan stuff:

https://production-galaxy-instances-with-cloudman-and-cloudbiolinux.readt
h
edocs.org/en/latest/#configuring-nginx-conf

http {

auth_ldap_url
ldap://ldap.example.com/dc=example,dc=com?uid?sub?(objectClass=person);
#auth_ldap_binddn cn=nginx,ou=service,dc=example,dc=com;
#auth_ldap_binddn_passwd mYsUperPas55W0Rd
#auth_ldap_group_attribute uniquemember; # default 'member'
#auth_ldap_group_attribute_is_dn on; # default on

...

}

location / {
auth_ldap_require valid_user;
auth_ldap LDAP Auth Source Description;
proxy_set_header REMOTE_USER $remote_user;


proxy_pass  http://galaxy_app;
proxy_set_header   X-Forwarded-Host $host;
proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
proxy_set_header   X-URL-SCHEME https;

  ...
}

# For API access, set REMOTE_USER if available so Galaxy
# session based requests are let through, if REMOTE_USER is not
# available pass the request through and let Galaxy determine
# if a key is present and valid.
location  /api {
proxy_set_header REMOTE_USER $remote_user;
proxy_pass  http://galaxy_app;
proxy_set_header   X-Forwarded-Host $host;
proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
}

-John

On Wed, Sep 18, 2013 at 7:37 AM, Iry Witham iry.wit...@jax.org wrote:
 Hi Team,

 Has anyone had any experience with setting up auth_ldap for nginx?  I
am
 attempting to make this work, but nginx fails to start with the
following
 message:

 Starting nginx nginx: [emerg] unknown directive auth_ldap_url in
 /usr/local/nginx/conf/nginx.conf:48
 startproc:  exit status of parent of /usr/local/nginx/sbin/nginx: 1

 failed

 Any help would be appreciated.

 Thanks,

 Iry Witham

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 and is intended solely for the addressee(s). If you believe you
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 this email by mistake, please notify the sender by return email as soon
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 possible.


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[galaxy-dev] configuring auth_ldap for galaxy

[Iry Witham]

Hi Team,

Has anyone had any experience with setting up auth_ldap for nginx?  I am 
attempting to make this work, but nginx fails to start with the following 
message:

Starting nginx nginx: [emerg] unknown directive auth_ldap_url in 
/usr/local/nginx/conf/nginx.conf:48
startproc:  exit status of parent of /usr/local/nginx/sbin/nginx: 1

  failed

Any help would be appreciated.

Thanks,

Iry Witham

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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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[galaxy-dev] Galaxy ego fetching error (Mac OS X 10.8)

[Iry Witham]

://eggs.galaxyproject.org/pexpect/pexpect-2.4-py2.7.egg
Fetched http://eggs.galaxyproject.org/amqplib/amqplib-0.6.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/PasteDeploy/PasteDeploy-1.5.0-py2.7.egg
Fetched http://eggs.galaxyproject.org/WebHelpers/WebHelpers-0.2-py2.7.egg
Fetched http://eggs.galaxyproject.org/docutils/docutils-0.7-py2.7.egg
Fetched http://eggs.galaxyproject.org/raven/raven-3.1.8-py2.7.egg
Fetched http://eggs.galaxyproject.org/Beaker/Beaker-1.4-py2.7.egg
Fetched http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg
Fetched http://eggs.galaxyproject.org/NoseTestDiff/NoseTestDiff-0.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/wchartype/wchartype-0.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/Tempita/Tempita-0.5.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg
Fetched http://eggs.galaxyproject.org/Routes/Routes-1.12.3-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/elementtree/elementtree-1.2.6_20050316-py2.7.egg
Fetched http://eggs.galaxyproject.org/decorator/decorator-3.1.2-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998f0caf01c5be731e926f4b0481f658f0-py2.7.egg
Fetched http://eggs.galaxyproject.org/WebOb/WebOb-0.8.5-py2.7.egg
Fetched http://eggs.galaxyproject.org/boto/boto-2.5.2-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/python_daemon/python_daemon-1.5.5-py2.7.egg
Traceback (most recent call last):
  File ./scripts/fetch_eggs.py, line 37, in module
c.resolve() # Only fetch eggs required by the config
  File /Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 
345, in resolve
egg.resolve()
  File /Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 
195, in resolve
return self.version_conflict( e.args[0], e.args[1] )
  File /Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 
226, in version_conflict
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, 
egg.fetch )
  File /Users/itw/work/Galaxy/galaxy-dist/lib/pkg_resources.py, line 565, in 
resolve
raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: mercurial==2.2.3
Fetch failed.

I have also tried to run python ./scripts/fetch_eggs.py and get the following:

milkyway:galaxy-dist itw$ python ./scripts/fetch_eggs.py
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched
Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is 
almost certainly a bug in the egg distribution.
Dependency ssh requires pycrypto=2.1,!=2.4
Traceback (most recent call last):
  File ./scripts/fetch_eggs.py, line 37, in module
c.resolve() # Only fetch eggs required by the config
  File /Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 
345, in resolve
egg.resolve()
  File /Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 
168, in resolve
dists = pkg_resources.working_set.resolve( ( 
self.distribution.as_requirement(), ), env, self.fetch )
  File /Users/itw/work/Galaxy/galaxy-dist/lib/pkg_resources.py, line 569, in 
resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (ssh 1.7.14 
(/Users/itw/work/Galaxy/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg), 
Requirement.parse('pycrypto=2.1,!=2.4'))


I have looked through the Dev site and have found nothing that helps.  Any 
ideas are welcome.

Thanks,

Iry Witham

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[galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

[Iry Witham]

Hi Team,

I urgently need to resize the data partition on my galaxy cloudman instance 
without loosing anything.  I notice that there a gui on the cloudman admin page 
that will allow me to increase it to 1000GB.  If I use that will it restart all 
of the processes?  I need to maintain this as a functional instance since it 
needs to be available for use tomorrow at 8:00 AM and I do not have the time to 
rebuild it.  The gui says it will create a snapshot.  The following is what it 
says:

Expand Disk Space
Through this form you may increase the disk space available to Galaxy. All of 
the cluster services (but not the cluster) WILL BE STOPPED until the new disk 
is ready, at which point they will all be restarted. This may result in Galaxy 
jobs that are currently running to fail. Note that the new disk size must be 
larger than the current disk size.

During this process, a snapshot of your data volume will be created, which can 
optionally be left in your account. If you decide to leave the snapshot for 
reference, you may also provide a brief note that will later be visible in the 
snapshot's description. New Disk Size (minimum 100GB, maximum 1000GB):

OK
Note (optional):

 or delete the created snapshot after filesystem resizing? If checked, the 
created snapshot will not be kept

What is the likelihood that this will be successful?  Has anyone utilized it?  
Is there another way to resize the /mnt/galaxyData/ and /mnt/galaxyIndices 
partitions that will allow me to do what I need to?

Thanks,

Iry Witham


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Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

[Iry Witham]

Hi Dannon,

I will give it a shot.  Are you familiar with the load balancer and how to make 
it work?  Or the auto scaling feature?

Thanks,

Iry

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 2:06 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

Hi Iry,

This should work, I use it regularly.  Just make sure you're not ssh'ed in and 
'in' /mnt/galaxyData or anything like that.  There's not really another way to 
do this that I'd recommend trying if you need the instance to continue working 
for something tomorrow.

Let me know if you have any issues and I can help.

-Dannon


On Mon, May 6, 2013 at 1:54 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
Hi Team,

I urgently need to resize the data partition on my galaxy cloudman instance 
without loosing anything.  I notice that there a gui on the cloudman admin page 
that will allow me to increase it to 1000GB.  If I use that will it restart all 
of the processes?  I need to maintain this as a functional instance since it 
needs to be available for use tomorrow at 8:00 AM and I do not have the time to 
rebuild it.  The gui says it will create a snapshot.  The following is what it 
says:

Expand Disk Space
Through this form you may increase the disk space available to Galaxy. All of 
the cluster services (but not the cluster) WILL BE STOPPED until the new disk 
is ready, at which point they will all be restarted. This may result in Galaxy 
jobs that are currently running to fail. Note that the new disk size must be 
larger than the current disk size.

During this process, a snapshot of your data volume will be created, which can 
optionally be left in your account. If you decide to leave the snapshot for 
reference, you may also provide a brief note that will later be visible in the 
snapshot's description. New Disk Size (minimum 100GB, maximum 1000GB):

OK
Note (optional):

 or delete the created snapshot after filesystem resizing? If checked, the 
created snapshot will not be kept

What is the likelihood that this will be successful?  Has anyone utilized it?  
Is there another way to resize the /mnt/galaxyData/ and /mnt/galaxyIndices 
partitions that will allow me to do what I need to?

Thanks,

Iry Witham


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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Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

[Iry Witham]

Hi Dannon,

I have attempted the resizing.  I clicked on the disk and set it for 1000GB.  
The instance restarted, but the volume remains at 100GB.  Is this due to the 
lack of disk space?  I don't see a snapshot when I look at the AWS console 
after the restart.  Any ideas?

Thanks,

IRy

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 2:06 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

Hi Iry,

This should work, I use it regularly.  Just make sure you're not ssh'ed in and 
'in' /mnt/galaxyData or anything like that.  There's not really another way to 
do this that I'd recommend trying if you need the instance to continue working 
for something tomorrow.

Let me know if you have any issues and I can help.

-Dannon


On Mon, May 6, 2013 at 1:54 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
Hi Team,

I urgently need to resize the data partition on my galaxy cloudman instance 
without loosing anything.  I notice that there a gui on the cloudman admin page 
that will allow me to increase it to 1000GB.  If I use that will it restart all 
of the processes?  I need to maintain this as a functional instance since it 
needs to be available for use tomorrow at 8:00 AM and I do not have the time to 
rebuild it.  The gui says it will create a snapshot.  The following is what it 
says:

Expand Disk Space
Through this form you may increase the disk space available to Galaxy. All of 
the cluster services (but not the cluster) WILL BE STOPPED until the new disk 
is ready, at which point they will all be restarted. This may result in Galaxy 
jobs that are currently running to fail. Note that the new disk size must be 
larger than the current disk size.

During this process, a snapshot of your data volume will be created, which can 
optionally be left in your account. If you decide to leave the snapshot for 
reference, you may also provide a brief note that will later be visible in the 
snapshot's description. New Disk Size (minimum 100GB, maximum 1000GB):

OK
Note (optional):

 or delete the created snapshot after filesystem resizing? If checked, the 
created snapshot will not be kept

What is the likelihood that this will be successful?  Has anyone utilized it?  
Is there another way to resize the /mnt/galaxyData/ and /mnt/galaxyIndices 
partitions that will allow me to do what I need to?

Thanks,

Iry Witham


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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  http://galaxyproject.org/search/mailinglists/


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by mistake, please notify the sender by return email as soon as possible.
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Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

[Iry Witham]

I was not clear how the load balancer worked in this instance, but my goal was 
to improve performance.  I am not sure this was the correct use, but it seemed 
to work.

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 4:12 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

So you have a cluster with 9 instances and you're using ec2 load balancer with 
all of them to divert traffic?


On Mon, May 6, 2013 at 3:56 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
I have setup a load balancer, but it shows that only 1 of 9 instances are 'In 
Service.  I have set the health check to:

Ping: http:80/
Timeout: 40 seconds
Interval: 60 seconds
Unhealthy threshold: 2
Healty threshold: 10

As far as autoscaling, I am not really interested since I see no real need at 
this point.

Thanks,

Iry

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 3:41 PM

To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

Great, I'm glad it's working, and I'm sorry you ran into this bug.

As far as autoscaling, etc., what are you interested in?  I should be able to 
help out with just about anything related to Cloudman.


On Mon, May 6, 2013 at 3:03 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
That seems to be working.

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 3:01 PM

To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

The first thing that comes to mind is a bug that existed in a particular 
version of cloudman regarding the max size allowable -- can you try 999GB?


On Mon, May 6, 2013 at 2:57 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
Hi Dannon,

I have attempted the resizing.  I clicked on the disk and set it for 1000GB.  
The instance restarted, but the volume remains at 100GB.  Is this due to the 
lack of disk space?  I don't see a snapshot when I look at the AWS console 
after the restart.  Any ideas?

Thanks,

IRy

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 2:06 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

Hi Iry,

This should work, I use it regularly.  Just make sure you're not ssh'ed in and 
'in' /mnt/galaxyData or anything like that.  There's not really another way to 
do this that I'd recommend trying if you need the instance to continue working 
for something tomorrow.

Let me know if you have any issues and I can help.

-Dannon


On Mon, May 6, 2013 at 1:54 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
Hi Team,

I urgently need to resize the data partition on my galaxy cloudman instance 
without loosing anything.  I notice that there a gui on the cloudman admin page 
that will allow me to increase it to 1000GB.  If I use that will it restart all 
of the processes?  I need to maintain this as a functional instance since it 
needs to be available for use tomorrow at 8:00 AM and I do not have the time to 
rebuild it.  The gui says it will create a snapshot.  The following is what it 
says:

Expand Disk Space
Through this form you may increase the disk space available to Galaxy. All of 
the cluster services (but not the cluster) WILL BE STOPPED until the new disk 
is ready, at which point they will all be restarted. This may result in Galaxy 
jobs that are currently running to fail. Note that the new disk size must be 
larger than the current disk size.

During this process, a snapshot of your data volume will be created, which can 
optionally be left in your account. If you decide to leave the snapshot for 
reference, you may also provide a brief note that will later be visible in the 
snapshot's description. New Disk Size (minimum 100GB, maximum 1000GB):

OK
Note (optional):

 or delete the created snapshot after filesystem resizing? If checked, the 
created snapshot will not be kept

What is the likelihood that this will be successful?  Has anyone utilized it?  
Is there another way to resize the /mnt/galaxyData/ and /mnt/galaxyIndices 
partitions that will allow me to do what I need

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

[Iry Witham]

I did add nodes about the same time I setup load balancing so that was likely 
the fix.  I will definitely set the head node not to run jobs.

Thanks,
Iry

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 4:19 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

Ahh, ok.  So, unfortunately Cloudman isn't designed to be used with a load 
balancer (at least at this point).  In any given cluster you have exactly one 
master node and all of the rest are workers (which do not run web processes, 
hence the 1/9 health).

What was slow that you were trying to improve the performance of?  One thing 
I'd definitely recommend for head node performance, if you do have extra worker 
nodes, would be to go to the admin panel (your_ec2_instance/cloud/admin) and 
disable job running on the head node using the Set master to not run jobs 
option.



On Mon, May 6, 2013 at 4:15 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
I was not clear how the load balancer worked in this instance, but my goal was 
to improve performance.  I am not sure this was the correct use, but it seemed 
to work.

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 4:12 PM

To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

So you have a cluster with 9 instances and you're using ec2 load balancer with 
all of them to divert traffic?


On Mon, May 6, 2013 at 3:56 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
I have setup a load balancer, but it shows that only 1 of 9 instances are 'In 
Service.  I have set the health check to:

Ping: http:80/
Timeout: 40 seconds
Interval: 60 seconds
Unhealthy threshold: 2
Healty threshold: 10

As far as autoscaling, I am not really interested since I see no real need at 
this point.

Thanks,

Iry

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 3:41 PM

To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

Great, I'm glad it's working, and I'm sorry you ran into this bug.

As far as autoscaling, etc., what are you interested in?  I should be able to 
help out with just about anything related to Cloudman.


On Mon, May 6, 2013 at 3:03 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
That seems to be working.

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 3:01 PM

To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

The first thing that comes to mind is a bug that existed in a particular 
version of cloudman regarding the max size allowable -- can you try 999GB?


On Mon, May 6, 2013 at 2:57 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
Hi Dannon,

I have attempted the resizing.  I clicked on the disk and set it for 1000GB.  
The instance restarted, but the volume remains at 100GB.  Is this due to the 
lack of disk space?  I don't see a snapshot when I look at the AWS console 
after the restart.  Any ideas?

Thanks,

IRy

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, May 6, 2013 2:06 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

Hi Iry,

This should work, I use it regularly.  Just make sure you're not ssh'ed in and 
'in' /mnt/galaxyData or anything like that.  There's not really another way to 
do this that I'd recommend trying if you need the instance to continue working 
for something tomorrow.

Let me know if you have any issues and I can help.

-Dannon


On Mon, May 6, 2013 at 1:54 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
Hi Team,

I urgently need to resize the data partition on my galaxy cloudman instance 
without loosing anything.  I notice that there a gui on the cloudman admin page 
that will allow me to increase it to 1000GB.  If I use that will it restart all 
of the processes?  I need to maintain this as a functional

[galaxy-dev] MPileup for cloudman instance

[Iry Witham]

Hi All,

I have noticed that there is no Mpileup available in either of the tool sheds.  
Is there a simple way to install it in my instance?

Thanks,

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 
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[galaxy-dev] SnpEff Ver 3.1 produces 'no peek' results

[Iry Witham]

Hi All,

I have installed snpEff 3.1 from the galaxy toolshed into my cloud man 
instance.  The tool runs to completion, but I get an empty file.  It says as 
'no peek' in the history.  When I view the details and check the stderr and get 
the following:


WARNING: Chromosome '@PG' not found. File 
'/mnt/galaxyData/files/000/dataset_58.dat', line 85
java.lang.ArrayIndexOutOfBoundsException: 5
at 
ca.mcgill.mcb.pcingola.fileIterator.SeqChangeFilePileUp.readNext(SeqChangeFilePileUp.java:69)
at 
ca.mcgill.mcb.pcingola.fileIterator.SeqChangeFilePileUp.readNext(SeqChangeFilePileUp.java:1)
at 
ca.mcgill.mcb.pcingola.fileIterator.FileIterator.hasNext(FileIterator.java:69)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.iterateSeqChange(SnpEffCmdEff.java:139)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.runAnalysis(SnpEffCmdEff.java:750)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:689)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:564)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:276)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:75)



I reinstalled the tool and reran the job.  Now I get this from the 
stderr:


java.lang.ArrayIndexOutOfBoundsException: 7
at 
ca.mcgill.mcb.pcingola.fileIterator.SeqChangeFilePileUp.readNext(SeqChangeFilePileUp.java:70)
at 
ca.mcgill.mcb.pcingola.fileIterator.SeqChangeFilePileUp.readNext(SeqChangeFilePileUp.java:1)
at 
ca.mcgill.mcb.pcingola.fileIterator.FileIterator.hasNext(FileIterator.java:69)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.iterateSeqChange(SnpEffCmdEff.java:139)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.runAnalysis(SnpEffCmdEff.java:750)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:689)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:564)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:276)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:75)



Any ideas?

Thanks,


Iry Witham

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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Re: [galaxy-dev] Installing FreeBayes via Toolshed: Tool dependency installation error

[Iry Witham]

, del, or complex.
##INFO=ID=CIGAR,Number=A,Type=String,Description=The extended CIGAR 
representation of each alternate allele, with the exception that '=' is 
replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the 
first matched base (which is provided by default, per the spec) referred to by 
the CIGAR.
##INFO=ID=NUMALT,Number=1,Type=Integer,Description=Number of unique 
non-reference alleles in called genotypes at this position.
##INFO=ID=MEANALT,Number=A,Type=Float,Description=Mean number of unique 
non-reference allele observations per sample with the corresponding alternate 
alleles.
##INFO=ID=HWE,Number=1,Type=Float,Description=Phred-scaled discrete HWE prior 
probability of the genotyping across all samples.
##INFO=ID=LEN,Number=A,Type=Integer,Description=allele length
##INFO=ID=MQM,Number=A,Type=Float,Description=Mean mapping quality of 
observed alternate alleles
##INFO=ID=MQMR,Number=1,Type=Float,Description=Mean mapping quality of 
observed reference alleles
##INFO=ID=PAIRED,Number=A,Type=Float,Description=Proportion of observed 
alternate alleles which are supported by properly paired read fragments
##INFO=ID=PAIREDR,Number=1,Type=Float,Description=Proportion of observed 
reference alleles which are supported by properly paired read fragments
##FORMAT=ID=GT,Number=1,Type=String,Description=Genotype
##FORMAT=ID=GQ,Number=1,Type=Float,Description=Genotype Quality, the 
Phred-scaled marginal (or unconditional) probability of the called genotype
##FORMAT=ID=GL,Number=G,Type=Float,Description=Genotype Likelihood, 
log10-scaled likelihoods of the data given the called genotype for each 
possible genotype generated from the reference and alternate alleles given the 
sample ploidy
##FORMAT=ID=GLE,Number=1,Type=String,Description=Genotype Likelihood 
Explicit, same as GL, but with tags to indicate the specific genotype. For 
instance, 0^-75.22|1^-223.42|0/0^-323.03|1/0^-99.29|1/1^-802.53 represents both 
haploid and diploid genotype likilehoods in a biallelic context
##FORMAT=ID=DP,Number=1,Type=Integer,Description=Read Depth
##FORMAT=ID=RO,Number=1,Type=Integer,Description=Reference allele observation 
count
##FORMAT=ID=QR,Number=1,Type=Integer,Description=Sum of quality of the 
reference observations
##FORMAT=ID=AO,Number=A,Type=Integer,Description=Alternate allele observation 
count
##FORMAT=ID=QA,Number=A,Type=Integer,Description=Sum of quality of the 
alternate observations
#CHROM  POS ID  REF ALT QUALFILTER  INFOFORMAT  unknown



Iry

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Tuesday, April 30, 2013 1:06 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Installing FreeBayes via Toolshed: Tool dependency 
installation error

Looks like you're missing cmake, a dependency for building FreeBayes.  If 
you're able to install that for your system (available in most package 
managers) you should be good to go.

-Dannon


On Tue, Apr 30, 2013 at 1:03 PM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
Hi All,

I am trying to get Freebayes installed on a cloud man instance from the galaxy 
toolshed.  I have successfully installed the Samtools 0.1.18 package, but the 
freebayes package errors.

The Error is:

Tool shed repository: freebayes
Tool shed repository changeset revision: 28e422c589ac
Tool dependency status: Error
Tool dependency installation error: /bin/sh: cmake: not found
make[1]: *** [../bamtools/lib/libbamtools.a] Error 127
make: *** [all] Error 2
Tool dependency installation directory: 
/mnt/galaxyTools/tools/freebayes/0.9.6_9608597d12e127c847ae03aa03440ab63992fedf/devteam/freebayes/28e422c589ac

I get the following message after the error occurs:

This tool dependency is not installed correctly (see the Tool dependency 
installation error below). Choose Uninstall this tool dependency from the 
Repository Actions menu, correct problems if necessary, and try installing the 
dependency again.

I have followed this procedure and still have the same error.  I have looked at 
the Installation.log file and this is what I found:

#
git clone --recursive 
git://github.com/ekg/freebayes.githttp://github.com/ekg/freebayes.git
STDOUT
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/.git/
Submodule 'bamtools' 
(git://github.com/pezmaster31/bamtools.githttp://github.com/pezmaster31/bamtools.git)
 registered for path 'bamtools'
Submodule 'intervaltree' 
(git://github.com/ekg/intervaltree.githttp://github.com/ekg/intervaltree.git) 
registered for path 'intervaltree'
Submodule 'vcflib' 
(git://github.com/ekg/vcflib.githttp://github.com/ekg/vcflib.git) registered 
for path 'vcflib'
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/bamtools/.git

Re: [galaxy-dev] Installing FreeBayes via Toolshed: Tool dependency installation error

[Iry Witham]

I uploaded the bam file to galaxy main and get the same error.  I also 
confirmed that the hg19.fa reference does exist in my cloudman instance.  Any 
other ideas?

Thanks,
Iry

From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Wednesday, May 1, 2013 12:38 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Installing FreeBayes via Toolshed: Tool dependency 
installation error

This one may be a little out of my wheelhouse, but did you verify that the 
reference it's trying to use is available?  Does this same job work if you try 
it on galaxy main (if that's an option)?

reference=/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa


On Wed, May 1, 2013 at 8:41 AM, Iry Witham 
iry.wit...@jax.orgmailto:iry.wit...@jax.org wrote:
Hi Dannon,

I was able to get cmake installed and then reinstalled Freebayes just fine.  
However, I now am getting the following error: unable to find FASTA index entry 
for '1'. The resulting files is:

Chrom   Pos ID  Ref Alt QualFilter  InfoFormat  data
##fileformat=VCFv4.1
##fileDate=20130501
##source=freeBayes version 0.9.6
##reference=/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
##phasing=none
##commandline=freebayes --bam localbam_0.bam --fasta-reference 
/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa --vcf 
/mnt/galaxyData/files/000/dataset_101.dat
##INFO=ID=NS,Number=1,Type=Integer,Description=Number of samples with data
##INFO=ID=DP,Number=1,Type=Integer,Description=Total read depth at the locus
##INFO=ID=AC,Number=A,Type=Integer,Description=Total number of alternate 
alleles in called genotypes
##INFO=ID=AN,Number=1,Type=Integer,Description=Total number of alleles in 
called genotypes
##INFO=ID=AF,Number=A,Type=Float,Description=Estimated allele frequency in 
the range (0,1]
##INFO=ID=RO,Number=1,Type=Integer,Description=Reference allele observations
##INFO=ID=AO,Number=A,Type=Integer,Description=Alternate allele observations
##INFO=ID=SRP,Number=1,Type=Float,Description=Strand balance probability for 
the reference allele: Phred-scaled upper-bounds estimate of the probability of 
observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived 
using Hoeffding's inequality
##INFO=ID=SAP,Number=A,Type=Float,Description=Strand balance probability for 
the alternate allele: Phred-scaled upper-bounds estimate of the probability of 
observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived 
using Hoeffding's inequality
##INFO=ID=AB,Number=A,Type=Float,Description=Allele balance at heterozygous 
sites: a number between 0 and 1 representing the ratio of reads showing the 
reference allele to all reads, considering only reads from individuals called 
as heterozygous
##INFO=ID=ABP,Number=A,Type=Float,Description=Allele balance probability at 
heterozygous sites: Phred-scaled upper-bounds estimate of the probability of 
observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived 
using Hoeffding's inequality
##INFO=ID=RUN,Number=A,Type=Integer,Description=Run length: the number of 
consecutive repeats of the alternate allele in the reference genome
##INFO=ID=RPP,Number=A,Type=Float,Description=Read Placement Probability: 
Phred-scaled upper-bounds estimate of the probability of observing the 
deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's 
inequality
##INFO=ID=RPPR,Number=1,Type=Float,Description=Read Placement Probability for 
reference observations: Phred-scaled upper-bounds estimate of the probability 
of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived 
using Hoeffding's inequality
##INFO=ID=EPP,Number=A,Type=Float,Description=End Placement Probability: 
Phred-scaled upper-bounds estimate of the probability of observing the 
deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's 
inequality
##INFO=ID=EPPR,Number=1,Type=Float,Description=End Placement Probability for 
reference observations: Phred-scaled upper-bounds estimate of the probability 
of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived 
using Hoeffding's inequality
##INFO=ID=DPRA,Number=A,Type=Float,Description=Alternate allele depth ratio. 
Ratio between depth in samples with each called alternate allele and those 
without.
##INFO=ID=XRM,Number=1,Type=Float,Description=Reference allele read mismatch 
rate: The rate of SNPs + MNPs + INDELs in reads supporting the reference 
allele.
##INFO=ID=XRS,Number=1,Type=Float,Description=Reference allele read SNP rate: 
The rate of per-base mismatches (SNPs + MNPs) in reads supporting the reference 
allele.
##INFO=ID=XRI,Number=1,Type=Float,Description=Reference allele read INDEL 
rate: The rate of INDELs (gaps) in reads supporting the reference allele.
##INFO=ID=XAM,Number=A,Type=Float,Description

[galaxy-dev] Installing FreeBayes via Toolshed: Tool dependency installation error

[Iry Witham]

 '3f0d5e19596252b858a7f6eff1578e4295f549c8'
Submodule path 'fastahack': checked out 
'd1bcd7a2d52ee0e2823884c8ede22ce228d3c060'
Submodule path 'smithwaterman': checked out 
'2882633a3b89f820d692a9b3316f4891dc3a1ff8'
#

#
git submodule update --recursive
STDERR
warning: unable to rmdir fsom: Directory not empty
#

#
make
STDOUT
cd src  make
make[1]: Entering directory `/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/src'
cd ../bamtools  mkdir -p build  cd build  cmake ..  make
make[1]: Leaving directory `/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/src'
#

#
make
STDERR
/bin/sh: cmake: not found
make[1]: *** [../bamtools/lib/libbamtools.a] Error 127
make: *** [all] Error 2
#

Any ideas on how to resolve this?

Thanks,

Iry Witham


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[galaxy-dev] Adding GATK tools to Galaxy Cloudman

[Iry Witham]

Hi Team,

I am trying to get GATK tools added to my cloud instance and keep getting the 
following error: [Errno 2] No such file or directory:
'/mnt/galaxyData/tmp/tmpszWRLP/GenomeAnalysisTKLite-2.3-9-gdcdccbb/GenomeAnalysisTK.jar'.
  Then when I try to install it again I get the following: All selected tool 
dependencies are already installed.  I also get the following error: 
Initializing repository installation failed.

Thanks,

Iry

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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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[galaxy-dev] Setting up Cloudman instance

[Iry Witham]

Hi Team,

I am working on setting up a Cloudman instance for a course we are preparing.  
I have used the link provided: http://usegalaxy.org/cloudlaunch and can get an 
instance running.  The issues are as follow:

1.  I need to add tools and have not found a clear method in doing so utilizing 
the galaxy toolshed.
2.  Once I have the instance setup and shut it down I cannot restart it 
cleanly.  On restart it appears that nginx fails to launch since port 80 is not 
listening.  I have not found a way to start it manually.
3.  I have followed both the above provided url to setup an instance and the 
instructions at http://wiki.galaxyproject.org/CloudMan and have had the same 
results.

I have read a few posts of similar issues, but have not found a solution.  Any 
suggestions will be helpful.

Thanks,

Iry Witham
__
Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609
Phone: 207-288-6744
email: iry.wit...@jax.org



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[galaxy-dev] GATK fails to create Java Virtual Machine

[Iry Witham]

Hi Folks,

I received an email from one of my end users that she was having an issue with 
the Realigner Target Creator under NGS:  GATK Tools.  Here's the error:  An 
error occurred running this job: Unable to access jar file 
/hpcdata/galaxy-setup/galaxy-dist/tool-data/shared/jars/gatk/GenomeAnalysisTK.jar.
  That was easy to resolve since the jar file is located at either 
/hpcdata/galaxy-setup/galaxy-dist/tool-data/shared/jars/GATK/1.4.2/ or 
/hpcdata/galaxy-setup/galaxy-dist/tool-data/shared/jars/GATK/1.6.13/.  I 
modified the xml to point to the /1.4.2 directory and now I get Could not 
create the Java virtual machine. I have looked at the wrapper for java 
settings and restarted the Galaxy server, but am at a loss. Do you have any 
ideas?

Thanks,

Iry Witham
Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609
Phone: 207-288-6744
email: iry.wit...@jax.org



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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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[galaxy-dev] Error running cuffmerge

[Iry Witham]

Hi Folks,

I have run into an issue with cuffmerge.  I am attempting to run it with mm10 
references and it fails attempting to execute gtf_to_sam.  The following is the 
actual error message I get:


Error running cuffmerge.
[Fri Oct 19 15:13:55 2012] Beginning transcriptome assembly merge
---

[Fri Oct 19 15:13:55 2012] Preparing output location cm_output/
[Fri Oct 19 15:14:15 2012] Converting GTF files to SAM
gtf_to_sam: invalid option -- F
cufflinks v0.9.1
-
Usage:   cufflinks [options] transcripts.gtf out.sam
Options:

-r/--reference-seqreference fasta file for sequence 
bias correction [ default:   NULL ]
[FAILED]
Error: could not execute gtf_to_sam



I have assured that the indexes and loc files are correct and in place.  Can 
someone point me in the right direction?

Thanks,

Iry Witham

Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609
Phone: 207-288-6744
email: iry.wit...@jax.org



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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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[galaxy-dev] Issues with database / metadata after upgrade

[Iry Witham]

Hi Team,

I had performed an upgrade of my Galaxy server and had experienced an issue 
with some of the database / metadata files have been corrupted.  I have found 
instances where the dataset exists, but cannot be detected or read by galaxy 
when attempting to analysis data from a history.  In some cases I have been 
able to locate another copy and replace the damaged file.  What might have been 
the cause and is there a way to resolve it?  Is this a possible Postgres issue 
or since the metadata is contained in the /database/files/ directory an 
artifact of the upgrade?

Thanks,

Iry

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is intended solely for the addressee(s). If you believe you received this email 
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Re: [galaxy-dev] Issue configuring reports_wsgi.ini

[Iry Witham]

Hans,

I set the actual IP address and it works.

Thanks,
Iry

On 8/24/12 8:07 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:

Hi Iry

  - try different port
  - try the actual IP address of your host


Regards, Hans


On 08/24/2012 01:52 PM, Iry Witham wrote:
 Hi Team,

 I am attempting to get the reports interface for my galaxy server to
 function.  I have my reports.wsgi.ini configured so:

 #  HTTP Server
 --

 [server:main]

 use = egg:Paste#http
 port = 9001
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 10

 #  Galaxy Webapps Report Interface
 -

 [app:main]

 # Specifies the factory for the universe WSGI application
 paste.app_factory = galaxy.webapps.reports.buildapp:app_factory
 log_level = DEBUG

 # Database connection
 # Galaxy reports are intended for production Galaxy instances, so sqlite
 is not supported.
 # You may use a SQLAlchemy connection string to specify an external
 database.
 database_connection = postgres:///galaxy_1

 # Where dataset files are saved
 file_path = database/files
 # Temporary storage for additional datasets, this should be shared
 through the cluster
 new_file_path = database/tmp

 # Session support (beaker)
 use_beaker_session = True
 session_type = memory
 session_data_dir = %(here)s/database/beaker_sessions
 session_key = galaxysessions
 session_secret = changethisinproduction

 # Configuration for debugging middleware
 # debug = true
 use_lint = false

 # NEVER enable this on a public site (even test or QA)
 # use_interactive = true

 # path to sendmail
 # sendmail_path = /usr/sbin/sendmail

 # Address to join mailing list
 # mailing_join_addr = galaxy-user-j...@bx.psu.edu
 mailto:galaxy-user-j...@bx.psu.edu

 # Write thread status periodically to 'heartbeat.log' (careful, uses
 disk space rapidly!)
 ## use_heartbeat = True

 # Profiling middleware (cProfile based)
 ## use_profile = True

 # Mail
 smtp_server = smtp.jax.org
 error_email_to = cbr-h...@jax.org mailto:cbr-h...@jax.org

 # Use the new iframe / javascript based layout
 use_new_layout = true

 # Serving static files (needed if running standalone)
 static_enabled = True
 static_cache_time = 360
 static_dir = %(here)s/static/
 static_images_dir = %(here)s/static/images
 static_favicon_dir = %(here)s/static/favicon.ico
 static_scripts_dir = %(here)s/static/scripts/
 static_style_dir = %(here)s/static/june_2007_style/blue

 The reports_webapp.log shows no errors but the process never completes
 loading.  I stop the process manually after 20 minutes or more and no
 reports interface:

 python path is:
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.5-py2.6-lin
ux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_s
tatic-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff
194725-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.eg
g,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r
6498-py2.6.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-
linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.e
gg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6
-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.eg
g,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_2005
0316-py2.6.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg
,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.eg
g,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-li
nux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.
6.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.
6.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib,
 /usr/lib/python26.zip, /usr/lib64/python2.6,
 /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk,
 /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload,
 /usr/lib64/python2.6/site-packages,
 /usr/lib64/python2.6/site-packages/Numeric,
 /usr/lib64/python2.6/site-packages/gtk-2.0,
 /usr/local/lib64/python2.6/site-packages
 galaxy.model.custom_types DEBUG 2012-08-20 13:03:04,572 psycopg2 egg
 successfully loaded for postgres dialect
 galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,297 Enabling 'users'
 controller

[galaxy-dev] Galaxy Reports no longer functions

[Iry Witham]

Hi Team,

Since I upgraded to the latest galaxy-dist I can no longer get the reports 
interface to function.  When I go to galaxy:9001 I get the following server 
error: An error occurred. See the error logs for more information. (Turn debug 
on to display exception reports here).  The reports_webapp.log is as follows:

python path is: 
/hpcdata/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, 
/hpcdata/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, 
/usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, 
/usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, 
/usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages, 
/usr/lib64/python2.6/site-packages/Numeric, 
/usr/lib64/python2.6/site-packages/gtk-2.0, 
/usr/local/lib64/python2.6/site-packages
galaxy.model.custom_types DEBUG 2012-08-07 17:13:53,219 psycopg2 egg 
successfully loaded for postgres dialect
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,792 Enabling 'users' 
controller, class: Users
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,815 Enabling 'system' 
controller, class: System
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,909 Enabling 
'sample_tracking' controller, class: SampleTracking
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,922 Enabling 'jobs' 
controller, class: Jobs
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,942 Enabling 'workflows' 
controller, class: Workflows
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,947 Enabling 'root' 
controller, class: Report
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,950 Enabling 
'httpexceptions' middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,971 Enabling 
'recursive' middleware
/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11:
 DeprecationWarning: the md5 module is deprecated; use hashlib instead
  import md5
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,708 Enabling 'error' 
middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,749 Enabling 'trans 
logger' middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,750 Enabling 'config' 
middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,888 Enabling 
'x-forwarded-host' middleware
Starting server in PID 6345.
Traceback (most recent call last):
  File ./scripts/paster.py, line 34, in module
command.run()
  File 
/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py,
 line 84, in run
invoke(command, command_name, options, args[1:])
  File 
/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py,
 line 123, in invoke
exit_code = runner.run(args)
  File 
/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py,
 line 218, in run
result = self.command()
  File 
/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py,
 line 303, in command
serve()
  File 
/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py,
 line 287, in serve
server(app)
  File 
/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
 line 151, in server_wrapper
**context.local_conf)
  File 
/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py,
 line 57, in fix_call
val = callable(*args, **kw)
  File 
/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py,
 line 1314, in server_runner

[galaxy-dev] Strange Could not moveŠ. error

[Iry Witham]

Hi Dev-Team,

I am experiencing a strange error that I cannot replicate on two identical 
instances of my Galaxy server.  I have a tool that runs fine on my test 
instance and fails on my development instance.  The servers are identically 
configured and running the same build.  The handler.log from the successful 
instance shows the following:

galaxy.jobs DEBUG 2012-08-02 11:31:07,881 (295) Working directory for job is: 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295
galaxy.jobs.handler DEBUG 2012-08-02 11:31:07,881 dispatching job 295 to pbs 
runner
galaxy.jobs.handler INFO 2012-08-02 11:31:08,083 (295) Job dispatched
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) submitting file 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/pbs/295.sh
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) command is: perl 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl 
--out-basename cnv_seq_result --test 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1504.dat
 --ref 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1503.dat
 --genome-size 2716965481 --p-value 0.001 
--bigger-window 1.5 --no-annotate --log2-threshold 0.6; 
cd /hpcdata/galaxy-test/galaxy-setup/galaxy-dist; 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295
 . /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmplTSKeF 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/galaxy.json
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_in_HistoryDatasetAssociation_689_Oh21hx,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_kwds_HistoryDatasetAssociation_689_xgxlZy,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_out_HistoryDatasetAssociation_689_H0claK,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_results_HistoryDatasetAssociation_689_rdQBs8,,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_override_HistoryDatasetAssociation_689_B0U0MV
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,395 (295) queued in default 
queue as 112605.scyld.localdomain
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,776 
(295/112605.scyld.localdomain) PBS job state changed from N to R
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,117 
(295/112605.scyld.localdomain) PBS job state changed from R to C
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,118 
(295/112605.scyld.localdomain) PBS job has completed successfully
galaxy.jobs DEBUG 2012-08-02 11:31:27,197 finish(): Moved 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/cnv_seq_result.cnv
 to 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1555.dat
 as directed by from_work_dir
galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,249 loading metadata from 
file for: HistoryDatasetAssociation 689
galaxy.jobs DEBUG 2012-08-02 11:31:27,382 job 295 ended
galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,382 Cleaning up external 
metadata files

The same log from the failing instance shows the following:

galaxy.jobs DEBUG 2012-08-02 11:54:29,234 (113) Working directory for job is: 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113
galaxy.jobs.handler DEBUG 2012-08-02 11:54:29,234 dispatching job 113 to pbs 
runner
galaxy.jobs.handler INFO 2012-08-02 11:54:29,420 (113) Job dispatched
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) submitting file 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/pbs/113.sh
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) command is: perl 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl 
--out-basename cnv_seq_result --test 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_131.dat 
--ref 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_132.dat 
--genome-size 2716965481 --p-value 0.001 
--bigger-window 1.5 --no-annotate --log2-threshold 0.6; 
cd /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist; 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113
 . /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/universe_wsgi.ini 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/tmp/tmpgTn7ey 

Re: [galaxy-dev] Strange Could not moveŠ. error

[Iry Witham]

Hi Scott,

I am running SUSE Linux Enterprise Server 11 SP1  (x86_64) - Kernel \r (\l) on 
both servers.  These are VM's with identical configurations. I know that 
shutil.move is a python function, but I am not really sure how it works.  I 
appreciate the assistance.

Iry

From: Scott McManus scottmcma...@gatech.edumailto:scottmcma...@gatech.edu
Date: Thursday, August 2, 2012 12:59 PM
To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Strange Could not moveŠ. error

Hi Iry-

A call to shutil.move is failing, and this could be because file-copying 
semantics
are different on your test instance's OS and/or filesystem than they are on your
development instance's OS and/or filesystem. What OS and file system are you
using on each? We can also try writing a small Python script to see if 
shutil.move
is failing when copying files from a similar source directory to a similar 
destination
directory. Let me know and I'll be glad to give you a hand.

-Scott


Hi Dev-Team,

I am experiencing a strange error that I cannot replicate on two identical 
instances of my Galaxy server.  I have a tool that runs fine on my test 
instance and fails on my development instance.  The servers are identically 
configured and running the same build.  The handler.log from the successful 
instance shows the following:

galaxy.jobs DEBUG 2012-08-02 11:31:07,881 (295) Working directory for job is: 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295
galaxy.jobs.handler DEBUG 2012-08-02 11:31:07,881 dispatching job 295 to pbs 
runner
galaxy.jobs.handler INFO 2012-08-02 11:31:08,083 (295) Job dispatched
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) submitting file 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/pbs/295.sh
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) command is: perl 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl 
--out-basename cnv_seq_result --test 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1504.dat
 --ref 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1503.dat
 --genome-size 2716965481 --p-value 0.001 
--bigger-window 1.5 --no-annotate --log2-threshold 0.6; 
cd /hpcdata/galaxy-test/galaxy-setup/galaxy-dist; 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295
 . /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmplTSKeF 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/galaxy.json
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_in_HistoryDatasetAssociation_689_Oh21hx,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_kwds_HistoryDatasetAssociation_689_xgxlZy,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_out_HistoryDatasetAssociation_689_H0claK,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_results_HistoryDatasetAssociation_689_rdQBs8,,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_override_HistoryDatasetAssociation_689_B0U0MV
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,395 (295) queued in default 
queue as 112605.scyld.localdomain
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,776 
(295/112605.scyld.localdomain) PBS job state changed from N to R
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,117 
(295/112605.scyld.localdomain) PBS job state changed from R to C
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,118 
(295/112605.scyld.localdomain) PBS job has completed successfully
galaxy.jobs DEBUG 2012-08-02 11:31:27,197 finish(): Moved 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/cnv_seq_result.cnv
 to 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1555.dat
 as directed by from_work_dir
galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,249 loading metadata from 
file for: HistoryDatasetAssociation 689
galaxy.jobs DEBUG 2012-08-02 11:31:27,382 job 295 ended
galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,382 Cleaning up external 
metadata files

The same log from the failing instance shows the following:

galaxy.jobs DEBUG 2012-08-02 11:54:29,234 (113) Working directory for job is: 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113
galaxy.jobs.handler DEBUG 2012-08-02 11:54:29,234 dispatching job 113 to pbs 
runner

Re: [galaxy-dev] pbs_python issues

[Iry Witham]

Hi Nate,

I have set this as shown below:


# The URL for the default runner to use when a tool doesn't explicitly
define a
# runner below.
default_cluster_job_runner = pbs:-l nodes=1:ppn=1,walltime=20:00:00


Iry

On 7/12/12 4:29 PM, Nate Coraor n...@bx.psu.edu wrote:

On Jul 6, 2012, at 12:32 PM, Iry Witham wrote:

 I am having an issue with pbs_python loading, but not submitting jobs
to the cluster.  
 
 The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/
python scripts/scramble.py ­e pbs_python' it failed to generate the
pbs_python egg in the /galaxy-dist/eggs/ directory.
 
 Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from
my production galaxy server and restarted my test server.  It appears to
start, but when I attempt to run anything it uses the local runner and
fails.  The runner0.log shows the pbsjobrunner is loaded is below:
 
 galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner:
galaxy.jobs.runners.pbs:PBSJobRunner
 galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue
started
 galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue
started
 galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue
started
 galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue
started
 
 I can't seem to get past this point since I upgraded.  Can someone
point me in the right direction?

Hi Iry,

Did you set default_cluster_job_runner in universe_wsgi.ini?

--nate

 
 Thanks,
 Iry
 
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Re: [galaxy-dev] pbs_python issues

[Iry Witham]

Will the runner0.log or web0.log be sufficient?  If not what would you
like?

Iry

On 7/13/12 2:23 PM, Nate Coraor n...@bx.psu.edu wrote:

On Jul 13, 2012, at 9:05 AM, Iry Witham wrote:

 Hi Nate,
 
  I have set this as shown below:
 
 
 # The URL for the default runner to use when a tool doesn't explicitly
 define a
 # runner below.
 default_cluster_job_runner = pbs:-l nodes=1:ppn=1,walltime=20:00:00

This should be okay.  Could you send along the server output from startup
to job completion?

--nate

 
 
 Iry
 
 On 7/12/12 4:29 PM, Nate Coraor n...@bx.psu.edu wrote:
 
 On Jul 6, 2012, at 12:32 PM, Iry Witham wrote:
 
 I am having an issue with pbs_python loading, but not submitting jobs
 to the cluster.
 
 The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/
 python scripts/scramble.py ­e pbs_python' it failed to generate the
 pbs_python egg in the /galaxy-dist/eggs/ directory.
 
 Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg
from
 my production galaxy server and restarted my test server.  It appears
to
 start, but when I attempt to run anything it uses the local runner and
 fails.  The runner0.log shows the pbsjobrunner is loaded is below:
 
 galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner:
 galaxy.jobs.runners.pbs:PBSJobRunner
 galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop
queue
 started
 galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue
 started
 galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop
queue
 started
 galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue
 started
 
 I can't seem to get past this point since I upgraded.  Can someone
 point me in the right direction?
 
 Hi Iry,
 
 Did you set default_cluster_job_runner in universe_wsgi.ini?
 
 --nate
 
 
 Thanks,
 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
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email as soon as possible.
 



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Re: [galaxy-dev] pbs_python issues

[Iry Witham]

I was successful in getting the bps_python egg to load finally.  However,
there is an issue that remains.  When I submit a job it is sent to the
local runner and not to pbs.  Where should I start looking to change this
work?  

Thanks,
Iry

On 7/10/12 12:00 PM, galaxy-dev-requ...@lists.bx.psu.edu
galaxy-dev-requ...@lists.bx.psu.edu wrote:


Message: 3
Date: Mon, 9 Jul 2012 17:24:25 +
From: Iry Witham iry.wit...@jax.org
To: Dorset, Daniel C daniel.dor...@vanderbilt.edu
Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10
Message-ID: cc207dde.8f49%iry.wit...@jax.org
Content-Type: text/plain; charset=us-ascii

Hi Daniel,

   I did use -e previously.  The ?e was a typo in my post.  I ran it again
and it tries, but fails to generate the file(s) as shown:

:galaxy@jaxgalaxydev01:/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist
LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
fetch_one(): Trying to fetch:
  http://eggs.g2.bx.psu.edu/pbs_python/pbs_python-4.1.0.tar.gz
fetch_one(): Fetched to:
  
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/archives/pbs
_
python-4.1.0.tar.gz
unpack_source(): Unpacked to:
  
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6-
l
inux-x86_64-ucs4/pbs_python
copy_build_script(): Using build script
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/scripts/pbs_
p
ython.py
run_scramble_script(): Beginning build
run_scramble_script(): Executing in
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6-
l
inux-x86_64-ucs4/pbs_python:
  /usr/bin/python scramble.py

--
-
This script requires setuptools version 0.6c11 to run (even to display
help).  I will attempt to download it for you (from
http://pypi.python.org/packages/2.6/s/setuptools/), but
you may need to enable firewall access for this script first.
I will start the download in 8 seconds.

(Note: if this machine does not have network access, please obtain the
file

   
http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.e
g
g

and place it in this directory before rerunning this script.)
--
-
Downloading 
http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.e
g
g
checking for pbs-config... /usr/local/lib//../bin/pbs-config
Found torque version: 2.5.8
checking for python... /usr/bin/python
checking for python version... 2.6
checking for python platform... linux2
checking for python script directory...
${prefix}/lib64/python2.6/site-packages
checking for python extension module directory...
${exec_prefix}/lib64/python2.6/site-packages
configure: creating ./config.status
config.status: creating Makefile
config.status: creating setup.py
scramble(): Patching setup.py
running egg_info
creating src/pbs_python.egg-info
writing src/pbs_python.egg-info/PKG-INFO
writing top-level names to src/pbs_python.egg-info/top_level.txt
writing dependency_links to src/pbs_python.egg-info/dependency_links.txt
writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
reading manifest file 'src/pbs_python.egg-info/SOURCES.txt'
writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.6
copying src/pbs.py - build/lib.linux-x86_64-2.6
copying src/PBSQuery.py - build/lib.linux-x86_64-2.6
running build_ext
building '_pbs' extension
creating build/temp.linux-x86_64-2.6
creating build/temp.linux-x86_64-2.6/src
gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall
-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
-fasynchronous-unwind-tables -g -fwrapv -fPIC -DTORQUE_2_4
-I/usr/include/python2.6 -c src/pbs_wrap.c -o
build/temp.linux-x86_64-2.6/src/pbs_wrap.o
gcc -pthread -shared build/temp.linux-x86_64-2.6/src/pbs_wrap.o
-L/usr/local/lib -L/usr/lib64 -ltorque -lpython2.6 -o
build/lib.linux-x86_64-2.6/_pbs.so
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/PBSQuery.py -
build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/pbs.py - build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/_pbs.so - build/bdist.linux-x86_64/egg
byte-compiling build/bdist.linux-x86_64/egg/PBSQuery.py to PBSQuery.pyc
byte-compiling build/bdist.linux-x86_64/egg/pbs.py to pbs.pyc
creating stub loader for _pbs.so
byte-compiling build/bdist.linux-x86_64/egg/_pbs.py to _pbs.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/PKG-INFO -
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/SOURCES.txt -
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/dependency_links.txt -
build/bdist.linux-x86_64/egg/EGG-INFO
copying src

Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10

[Iry Witham]

 path:\n  %s % (
sys._getframe().f_code.co_name, self.name, new_egg ) )
galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for pbs_python
did not appear to fail, but no egg found to copy from expected path:
  
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6-l
inux-x86_64-ucs4/pbs_python/dist/pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.e
gg

Iry

On 7/7/12 3:10 PM, Dorset, Daniel C daniel.dor...@vanderbilt.edu wrote:



From: galaxy-dev-boun...@lists.bx.psu.edu
[galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of
galaxy-dev-requ...@lists.bx.psu.edu [galaxy-dev-requ...@lists.bx.psu.edu]
Sent: Saturday, July 07, 2012 11:00 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: galaxy-dev Digest, Vol 73, Issue 10

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Today's Topics:

   1. pbs_python issues (Iry Witham)
   2. Which css file does welcome.html use? (Dorset, Daniel C)
   3. Re: Which css file does welcome.html use? (Jeremy Goecks)


Hi Ira,

I'm in charge of a Galaxy instance that's also deployed on a PBS Cluster,
and I went through this process a couple of months ago. If I remember
correctly, when you run your Python script, you're supposed to run it
with -e not ?e Assuming that you are pointing to the correct
directory, it looks like everything else about your command is correct.

Have you tried that?

--

Message: 1
Date: Fri, 6 Jul 2012 16:32:14 +
From: Iry Witham iry.wit...@jax.org
To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] pbs_python issues
Message-ID: cc1c8b4d.8ead%iry.wit...@jax.org
Content-Type: text/plain; charset=windows-1252

I am having an issue with pbs_python loading, but not submitting jobs to
the cluster.

The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/ python
scripts/scramble.py ?e pbs_python' it failed to generate the pbs_python
egg in the /galaxy-dist/eggs/ directory.

Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from
my production galaxy server and restarted my test server.  It appears to
start, but when I attempt to run anything it uses the local runner and
fails.  The runner0.log shows the pbsjobrunner is loaded is below:

galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner:
galaxy.jobs.runners.pbs:PBSJobRunner
galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue
started
galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue started
galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue
started
galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue started

I can't seem to get past this point since I upgraded.  Can someone point
me in the right direction?

Thanks,
Iry


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Message: 2
Date: Fri, 6 Jul 2012 16:28:08 -0500
From: Dorset, Daniel C daniel.dor...@vanderbilt.edu
To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Which css file does welcome.html use?
Message-ID:

9b568b41976b54469cc6e3fd758ef83105dc006...@its-drwnem10.ds.vanderbilt.edu


Content-Type: text/plain; charset=us-ascii

OK, this is ostensibly a simple question. However, I can't find the CSS
file that welcome.html is using. In the HTML file, there's this line:

link rel=stylesheet href=style/base.css type=text/css /

However, I don't see a directory named style anywhere in the galaxy
directory tree. When I search for base.css, from the root Galaxy
installation directory, I get the following results

[galaxy-dev] pbs_python issues

[Iry Witham]

I am having an issue with pbs_python loading, but not submitting jobs to the 
cluster.

The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/ python 
scripts/scramble.py –e pbs_python' it failed to generate the pbs_python egg in 
the /galaxy-dist/eggs/ directory.

Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from my 
production galaxy server and restarted my test server.  It appears to start, 
but when I attempt to run anything it uses the local runner and fails.  The 
runner0.log shows the pbsjobrunner is loaded is below:

galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner: 
galaxy.jobs.runners.pbs:PBSJobRunner
galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue started
galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue started
galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue started
galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue started

I can't seem to get past this point since I upgraded.  Can someone point me in 
the right direction?

Thanks,
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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Re: [galaxy-dev] Server Error after fresh installation of Galaxy

[Iry Witham]

I am still experiencing issues getting my galaxy server to start since the 
upgrade.  The logs are all getting this type of error:

galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist cat runner0.log
python path is: 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, 
/usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, 
/usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, 
/usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/Numeric, 
/usr/lib64/python2.6/site-packages/gtk-2.0, 
/usr/local/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages
galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg 
successfully loaded for postgres dialect
Traceback (most recent call last):
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py, 
line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
  File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py, line 
35, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( 
'__file__', None ), self.config.database_engine_options, app=self )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/check.py,
 line 103, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '101' but this code expects version '97'.  
Please backup your database and then migrate the schema by running 'sh 
manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid

I have not dropped my database and built it fresh.  However, I have attempted 
the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade' for 
both the runner and web app ini files with the following error:

galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist sh manage_db.sh 
-c ./universe_wsgi.webapp.ini upgrade
Traceback (most recent call last):
  File ./scripts/manage_db.py, line 63, in module
main( repository=repo, url=db_url )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py,
 line 150, in main
ret = command_func(**kwargs)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
 line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
 line 327, in _migrate
changeset = schema.changeset(version)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
 line 173, in changeset
changeset = 

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

[Iry Witham]

Thanks Dannon and Bjorn for the assistance.  I followed Dannon's
suggestion and that fixed my issue.

Thanks,
Iry

On 7/3/12 1:15 PM, Dannon Baker dannonba...@me.com wrote:

It looks like what happened is that you've updated the instance that was
originally connected to this database from galaxy-central at some point
recently.  The current tip of galaxy-central is at database version 103.

The first two options that come to mind are:

1)  Hook a fresh galaxy-central clone up to this database and
`manage_db.sh downgrade 97` which should set your database back to the
version appropriate for galaxy-dist.
2)  Swap to galaxy-central instead of -dist

Taking a brief look at the migrations, #1 looks fairly safe, but as
always -- back up the database first.

-Dannon



On Jul 3, 2012, at 1:03 PM, Iry Witham wrote:

 I am still experiencing issues getting my galaxy server to start since
the upgrade.  The logs are all getting this type of error:
 
 galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist cat
runner0.log 
 python path is: 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linu
x-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10
f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-
linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.eg
g, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-l
inux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_s
tatic-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff
194725-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.eg
g, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r
6498-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-
linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.e
gg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6
-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.eg
g, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_2005
0316-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg
, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.eg
g, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-li
nux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.
6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.
6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib,
/usr/lib/python26.zip, /usr/lib64/python2.6,
/usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk,
/usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload,
/usr/lib64/python2.6/site-packages/Numeric,
/usr/lib64/python2.6/site-packages/gtk-2.0,
/usr/local/lib64/python2.6/site-packages,
/usr/lib64/python2.6/site-packages
 galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg
successfully loaded for postgres dialect
 Traceback (most recent call last):
   File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py
, line 82, in app_factory
 app = UniverseApplication( global_conf = global_conf, **kwargs )
   File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py, line
35, in __init__
 create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options, app=self
)
   File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/c
heck.py, line 103, in create_or_verify_database
 % ( db_schema.version, migrate_repository.versions.latest,
config_arg ) )
 Exception: Your database has version '101' but this code expects
version '97'.  Please backup your database and then migrate the schema
by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
 Removing PID file runner0.pid
 
 I have not dropped my database and built it fresh.  However, I have
attempted the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini
upgrade' for both the runner and web app ini files with the following
error:
 
 galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist sh
manage_db.sh -c ./universe_wsgi.webapp.ini upgrade
 Traceback (most recent call last):
   File

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

[Iry Witham]

Hi Nate,

I removed to previous instillation just to be safe and performed a new
clone.  This time it appears to be less problematic.  I am no longer
getting all of the errors.  However, I am getting an error due to my
database version.  The error is:

galaxy.model.migrate.check DEBUG 2012-06-27 12:39:11,843 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py,
 line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
  File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py,
line 35, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options, app=self )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/che
ck.py, line 103, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg
) )
Exception: Your database has version '101' but this code expects version
'97'.  Please backup your database and then migrate the schema by running
'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.



I have attempted to run sh manage_db.sh -c ./universe_wsgi.runner.ini
upgrade and that fails with the following error:

galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist sh
manage_db.sh -c ./universe_wsgi.webapp.ini upgrade
Traceback (most recent call last):
  File ./scripts/manage_db.py, line 63, in module
main( repository=repo, url=db_url )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/shell.py, line 150, in main
ret = command_func(**kwargs)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/api.py, line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err,
**opts)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/api.py, line 327, in _migrate
changeset = schema.changeset(version)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/schema.py, line 173, in changeset
changeset = self.repository.changeset(database, start_ver, version)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/repository.py, line 170, in changeset
changes = [self.version(v).script(database, op) for v in versions]
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/repository.py, line 145, in version
return self.versions.version(*p, **k)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/version.py, line 125, in version
return self.versions[VerNum(vernum)]
KeyError: VerNum(101)



It is getting closer, but I am not quite there yet.

Thanks,
Iry

On 6/22/12 11:50 AM, Nate Coraor n...@bx.psu.edu wrote:

On Jun 20, 2012, at 6:46 PM, Iry Witham wrote:

 I have recently performed a fresh installation of Galaxy utilizing the
latest distribution and am getting a sizable number of errors when
attempting to start the server.  The issue started when I performed a
merge so I decided to do the clean install as a test.  The server
appears to start just fine, but with errors reported in the logs.  The
web0.log gives the following errors and warnings (I am truncating the
file for space):
 
 galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg
successfully loaded for postgres dialect
 galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database
version 97
 galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2
egg successfully loaded for postgres dialect
 galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At
migrate_tools version 2
 galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg
successfully loaded for postgres dialect
 galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
Loading references to tool sheds from tool_sheds_conf.xml
 galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
Loaded reference to tool shed: Galaxy main tool shed
 galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
Loaded reference to tool shed: Galaxy test tool shed
 galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading
datatypes from datatypes_conf.xml
 galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding
conflicting datatype with extension 'coverage', using datatype from
datatypes_conf.xml.
 galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer
for datatype 'galaxy.datatypes.binary:Bam'
 galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer
for datatype

[galaxy-dev] Galaxy-Development site error

[Iry Witham]

Good Morning,

I have been attempting to go to the the Galaxy-Dev site this morning at 
http://gmod.827538.n3.nabble.com/Galaxy-Development-f815885.html and Get a 
Content Encoding Error message.  The error says that The page you are trying 
to view cannot be shown because it uses an invalid or unsupported form of 
compression.  This happens with Firefox 3.6.27, but not with Crome or Safari.  
 By default I use Firefox 3.6.x due to performance issues with the later 
versions.

Thanks,
Iry Witham
Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609
Phone: 207-288-6744
email: iry.wit...@jax.org


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and other Galaxy lists, please use the interface at:

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[galaxy-dev] Issues importing a shared workflow

[Iry Witham]

I have a Galaxy user who has created a workflow from a history and share it 
with me.  However, when I attempt to view and import the workflow I get the 
following error:

The owner of this workflow has disabled imports via this link.
You can return to the previous 
pagehttp://galaxy/u/anuj/w/workflow-constructed-from-history-chipseqworkflowwithcontrol

How do I fix this issue?  Are there settings that need to be modified on the 
users side?

Thanks

Iry Witham
Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609
Phone: 207-288-6744
email: iry.wit...@jax.org


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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] [Newsletter] Re: Issues importing a shared workflow

[Iry Witham]

He opened the workflow in his history and clicked options, Share or
Publish and added my email address.  When I attempted the import I click
on View in the context menu to open the workflow.  I then click Import
Workflow in the upper righthand side of the window.  I can clone it just
fine.

Iry

On 2/24/12 3:45 PM, Dannon Baker dannonba...@me.com wrote:

How did the user share the workflow with you, via link or directly with
your user?  And which import option are you using?  Does Clone in the
workflow context menu work?

-Dannon

On Feb 24, 2012, at 3:25 PM, Iry Witham wrote:

 I have a Galaxy user who has created a workflow from a history and
share it with me.  However, when I attempt to view and import the
workflow I get the following error:
 
 The owner of this workflow has disabled imports via this link.
 You can return to the previous page
 
 How do I fix this issue?  Are there settings that need to be modified
on the users side?
 
 Thanks
 
 Iry Witham
 Scientific Applications Administrator
 Scientific Computing Group
 Computational Sciences Dept.
 The Jackson Laboratory
 600 Main Street
 Bar Harbor, ME  04609
 Phone: 207-288-6744
 email: iry.wit...@jax.org
 
 
 ___
 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/



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and other Galaxy lists, please use the interface at:

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[galaxy-dev] manage_db.sh upgrade fails after fresh install of Galaxy

[Iry Witham]

I have installed a new Galaxy server utilizing the November 18,2011 
distribution on a SLES 11 VM and cannot get it to launch cleanly.  I am running 
postgreSQL v. 8.3.9 to create my database.  Once the database is created and 
running I launch my Galaxy server and within moments all of the PID fail except 
for the reports_webapp.pid.  When I tail the logs I find the following:

tail reports_webapp.log -
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,179 Enabling 
'httpexceptions' middleware
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,194 Enabling 
'recursive' middleware
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11:
 DeprecationWarning: the md5 module is deprecated; use hashlib instead
  import md5
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,272 Enabling 'error' 
middleware
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,277 Enabling 'trans 
logger' middleware
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,277 Enabling 'config' 
middleware
galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,294 Enabling 
'x-forwarded-host' middleware
Starting server in PID 20411.
serving on 0.0.0.0:9001 view at http://127.0.0.1:9001

tail web0.log -
galaxy.model.migrate.check DEBUG 2011-12-21 14:20:54,793 psycopg2 egg 
successfully loaded for postgres dialect
Traceback (most recent call last):
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/web/buildapp.py, 
line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
  File /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/app.py, 
line 39, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( 
'__file__', None ), self.config.database_engine_options )
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/model/migrate/check.py,
 line 105, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '38' but this code expects version '85'.  
Please backup your database and then migrate the schema by running 'sh 
manage_db.sh -c ./universe_wsgi.webapp.ini upgrade'.
Removing PID file web0.pid

tail runner0.log -
galaxy.model.migrate.check DEBUG 2011-12-21 14:20:54,789 psycopg2 egg 
successfully loaded for postgres dialect
Traceback (most recent call last):
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/web/buildapp.py, 
line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
  File /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/app.py, 
line 39, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( 
'__file__', None ), self.config.database_engine_options )
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/model/migrate/check.py,
 line 105, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '38' but this code expects version '85'.  
Please backup your database and then migrate the schema by running 'sh 
manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid


sh manage_db.sh upgrade -

38 - 39...

Migration script to add a synopsis column to the library table.

Traceback (most recent call last):
  File ./scripts/manage_db.py, line 63, in module
main( repository=repo, url=db_url )
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py,
 line 150, in main
ret = command_func(**kwargs)
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
 line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
 line 349, in _migrate
schema.runchange(ver, change, changeset.step)
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
 line 184, in runchange
change.run(self.engine, step)
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py,
 line 101, in run
func()
  File 
lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py,
 line 20, in upgrade
c.create( Library_table )
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/changeset/schema.py,
 line 365, in create
engine._run_visitor(visitorcallable, self, *args, **kwargs)
  File 
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py,
 line 1158, in _run_visitor

Re: [galaxy-dev] jquery script error

[Iry Witham]

I have have discovered that this error is not unique to the number of files I 
am linking.  It has been reported from several of my users that there is a 
similar issue with Internet Explorer 8.

Step 1: Import shared data into history: One user tried to import data from a 
shared library into her history.  Internet Explorer puts up an ugly message 
“Stop running this script?” Complaining that continuing to run the script will 
cause her machine to stop functioning.  Sometimes the display seemed to get 
truncated, only displaying a subset of the available datasets.  The import 
seemed to work OK, though.

Step 2:  Debug the issue using IE built-in script debugger.  I was able to 
replicate the issue and ran some minor debugging from within IE.  The results 
of this are as follows:

Error Message:  Windows Internet Explorer

Stop running this script?

A script on this page is causing Internet Explorer to run slowly.
If it continues to run, your computer might become unresponsive.

Debugging results:  Line: 1
Error: jQuery, MooTools or Prototype needs to be loaded before jStorage!

(function(f){if(!f||!(f.toJSON||Object.toJSON||window.JSON)){throw new 
Error(jQuery, MooTools or Prototype needs to be loaded before jStorage!)}var 
g={},d={jStorage:{}},h=null,j=0,l=f.toJSON||Object.toJSON||(window.JSON(JSON.encode||JSON.stringify)),e=f.evalJSON||(window.JSON(JSON.decode||JSON.parse))||function(m){return
 String(m).evalJSON()},i=false;_XMLService={isXML:function(n){var 
m=(n?n.ownerDocument||n:0).documentElement;return 
m?m.nodeName!==HTML:false},encode:function(n){if(!this.isXML(n)){return 
false}try{return new XMLSerializer().serializeToString(n)}catch(m){try{return 
n.xml}catch(o){}}return false},decode:function(n){var m=(DOMParser in 
window(new 
DOMParser()).parseFromString)||(window.ActiveXObjectfunction(p){var q=new 
ActiveXObject(Microsoft.XMLDOM);q.async=false;q.loadXML(p);return 
q}),o;if(!m){return false}o=m.call(DOMParser in window(new 
DOMParser())||window,n,text/xml);return this.isXML(o)?o:false}};function 
k(){if(localStorage in 
window){try{if(window.localStorage){d=window.localStorage;i=localStorage}}catch(p){}}else{if(globalStorage
 in 
window){try{if(window.globalStorage){d=window.globalStorage[window.location.hostname];i=globalStorage}}catch(o){}}else{h=document.createElement(link);if(h.addBehavior){h.style.behavior=url(#default#userData);document.getElementsByTagName(head)[0].appendChild(h);h.load(jStorage);var
 
n={};try{n=h.getAttribute(jStorage)}catch(m){}d.jStorage=n;i=userDataBehavior}else{h=null;return}}}b()}function
 
b(){if(d.jStorage){try{g=e(String(d.jStorage))}catch(m){d.jStorage={}}}else{d.jStorage={}}j=d.jStorage?String(d.jStorage).length:0}function
 
c(){try{d.jStorage=l(g);if(h){h.setAttribute(jStorage,d.jStorage);h.save(jStorage)}j=d.jStorage?String(d.jStorage).length:0}catch(m){}}function
 a(m){if(!m||(typeof m!=stringtypeof m!=number)){throw new TypeError(Key 
name must be string or numeric)}return 
true}f.jStorage={version:0.1.5.0,set:function(m,n){a(m);if(_XMLService.isXML(n)){n={_is_xml:true,xml:_XMLService.encode(n)}}g[m]=n;c();return
 n},get:function(m,n){a(m);if(m in g){if(typeof 
g[m]==objectg[m]._is_xmlg[m]._is_xml){return 
_XMLService.decode(g[m].xml)}else{return g[m]}}return 
typeof(n)==undefined?null:n},deleteKey:function(m){a(m);if(m in g){delete 
g[m];c();return true}return 
false},flush:function(){g={};c();try{window.localStorage.clear()}catch(m){}return
 true},storageObj:function(){function m(){}m.prototype=g;return new 
m()},index:function(){var m=[],n;for(n in 
g){if(g.hasOwnProperty(n)){m.push(n)}}return m},storageSize:function(){return 
j},currentBackend:function(){return i},storageAvailable:function(){return 
!!i},reInit:function(){var 
m,o;if(hh.addBehavior){m=document.createElement(link);h.parentNode.replaceChild(m,h);h=m;h.style.behavior=url(#default#userData);document.getElementsByTagName(head)[0].appendChild(h);h.load(jStorage);o={};try{o=h.getAttribute(jStorage)}catch(n){}d.jStorage=o;i=userDataBehavior}b()}};k()})(window.jQuery||window.$);

jQuery, MooTools or Prototype needs to be loaded before jStorage!

I cannot replicate this with other browsers.  I have tried it with Google Crome 
and Firefox 3.6.20.

Thanks,

Iry Witham
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[galaxy-dev] manage_db.sh upgrade error

[Iry Witham]

When I run sh manage_db.sh upgrade I get the following error:

2 - 3...
Traceback (most recent call last):
  File ./scripts/manage_db.py, line 55, in module
main( repository=repo, url=db_url )
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py,
 line 150, in main
ret = command_func(**kwargs)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
 line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
 line 349, in _migrate
schema.runchange(ver, change, changeset.step)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
 line 184, in runchange
change.run(self.engine, step)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py,
 line 101, in run
func()
  File lib/galaxy/model/migrate/versions/0003_security_and_libraries.py, line 
423, in upgrade
metadata.create_all()
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py,
 line 1796, in create_all
bind.create(self, checkfirst=checkfirst, tables=tables)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py,
 line 1129, in create
self._run_visitor(self.dialect.schemagenerator, entity, 
connection=connection, **kwargs)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py,
 line 1158, in _run_visitor
visitorcallable(self.dialect, conn, **kwargs).traverse(element)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py,
 line 89, in traverse
return traverse(obj, self.__traverse_options__, self._visitor_dict)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py,
 line 200, in traverse
return traverse_using(iterate(obj, opts), obj, visitors)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py,
 line 194, in traverse_using
meth(target)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/compiler.py,
 line 829, in visit_metadata
collection = [t for t in sql_util.sort_tables(tables) if 
self._can_create(t)]
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/util.py,
 line 22, in sort_tables
return topological.sort(tuples, tables)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/topological.py,
 line 32, in sort
return [n.item for n in _sort(tuples, allitems, allow_cycles=False, 
ignore_self_cycles=True)]
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/topological.py,
 line 209, in _sort
raise CircularDependencyError(Circular dependency detected  + repr(edges) 
+ repr(queue))
sqlalchemy.exc.CircularDependencyError: Circular dependency detected 
[(form_definition_current, form_definition), (library_item_info, 
library_folder_info_association), (library_item_info, 
library_item_info_element), (library_item_info, library_item_info_permissions), 
(library_item_info, library_dataset_dataset_info_association), 
(library_item_info, library_info_association), (library_item_info, 
library_dataset_info_association), (visualization_revision, visualization), 
(form_definition, external_service), (form_definition, form_values), 
(form_definition, request_type), (form_definition, run), (form_definition, 
form_definition_current), (history_dataset_association, job_to_input_dataset), 
(history_dataset_association, job_to_output_dataset), 
(history_dataset_association, implicitly_converted_dataset_association), 
(history_dataset_association, history_dataset_association_tag_association), 
(history_dataset_association, validation_error), (history_dataset_association, 
history_dataset_association_rating_association), (history_dataset_association, 
job_external_output_metadata), (history_dataset_association, 
history_dataset_association_annotation_association), 
(history_dataset_association, 
history_dataset_association_display_at_authorization), 
(history_dataset_association, metadata_file), (galaxy_user, 
stored_workflow_rating_association), (galaxy_user, stored_workflow_menu_entry), 
(galaxy_user, library_item_info), (galaxy_user, 
visualization_user_share_association), (galaxy_user, default_user_permissions), 
(galaxy_user, 

[galaxy-dev] LookupError: No section 'main' (prefixed by 'server') found in config

[Iry Witham]

I have performed a new install of Galaxy for development and deployment 
purposes.  However, when I run the run.sh script I get the following error:

Traceback (most recent call last):
  File ./scripts/paster.py, line 34, in module
command.run()
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py,
 line 84, in run
invoke(command, command_name, options, args[1:])
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py,
 line 123, in invoke
exit_code = runner.run(args)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py,
 line 218, in run
result = self.command()
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py,
 line 274, in command
relative_to=base, global_conf=vars)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py,
 line 308, in loadserver
relative_to=relative_to, **kw)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
 line 210, in loadserver
return loadobj(SERVER, uri, name=name, **kw)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
 line 224, in loadobj
global_conf=global_conf)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
 line 248, in loadcontext
global_conf=global_conf)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
 line 278, in _loadconfig
return loader.get_context(object_type, name, global_conf)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
 line 363, in get_context
object_type, name=name)
  File 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py,
 line 528, in find_config_section
self.filename))
LookupError: No section 'main' (prefixed by 'server') found in config 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini

I have modified the universe_wsgi.ini to reflect the way our production server 
is configured.  The following is the server section of that file:

#
# Galaxy is configured by default to be useable in a single-user development
# environment.  To tune the application for a multi-user production
# environment, see the documentation at:
#
# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
#

# Throughout this sample configuration file, except where stated otherwise,
# uncommented values override the default if left unset, whereas commented
# values are set to the default value.
# examples of many of these options are explained in more detail in the wiki:
#
# Config hackers are encouraged to check there before asking for help.

#  HTTP Server --

# Configuration of the internal HTTP server.

[server:web0]
use = egg:Paste#http
port = 8080
host = 0.0.0.0
use_threadpool = true
threadpool_workers = 7

# Configuration of web server 2
[server:web1]
use = egg:Paste#http
port = 8081
host = 0.0.0.0
use_threadpool = true
threadpool_workers = 7

# Configuration of web server 3
[server:web2]
use = egg:Paste#http
port = 8082
host = 0.0.0.0
use_threadpool = true
threadpool_workers = 7

# The internal HTTP server to use.  Currently only Paste is provided.  This
# option is required.
#use = egg:Paste#http

# The port on which to listen.
#port = 8080

# The address on which to listen.  By default, only listen to localhost (Galaxy
# will not be accessible over the network).  Use '0.0.0.0' to listen on all
# available network interfaces.
#host = 0.0.0.0

# Use a threadpool for the web server instead of creating a thread for each
# request.
#use_threadpool = True

# Number of threads in the web server thread pool.
#threadpool_workers = 5

#  Filters --

# Filters sit between Galaxy and the HTTP server.

# These filters are disabled by default.  They can be enabled with
# 'filter-with' in the [app:main] section below.

# Define the gzip filter.
[filter:gzip]
use = egg:Paste#gzip

# Define the proxy-prefix filter.
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy

My production server works fine, but this one will not run.  What am I missing?

Thanks,
Iry
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Re: [galaxy-dev] Display BAM with IGV

[Iry Witham]

Hi Nate,

I have been able to get this to work on a Mac and Windows XP within
limited guide lines.  The following are what I had to do to make it work:

My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome
ver.13.0.782.215 and Safari 5.1 (6534.50).  In addition I have installed Max
OS 10.6.8 Supplemental Update 1.0.  My PC is running Windows XP SP3 with
Java 1.6.0_26, Firefox 3.6.20 and IE8.  Windows updates are at current
levels.  I have not tested this on Windows 7.

I am currently able to run the IGV-web tool from Galaxy via Firefox, Crome
and Safari on the Mac and IE8 only on Windows.  When I use either Firefox or
Crome on Windows I get the following error.


ERROR [2011-08-24 09:22:40,169]  [TrackLoader.java:211]
[SwingWorker-pool-20352093-thread-1]  java.lang.RuntimeException:
java.lang.RuntimeException: Error loading file:
http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length

ERROR [2011-08-24 09:22:40,169]  [TrackManager.java:245]
[SwingWorker-pool-20352093-thread-1]  Error loading tracks

org.broad.igv.exceptions.DataLoadException: htmlAn error occurred while
loading:
http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
0aa/data/galaxy_afa21414c9c9e7eb.bambrjava.lang.RuntimeException: Error
loading file: 
http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length

at org.broad.igv.track.TrackLoader.load(TrackLoader.java:212)

at org.broad.igv.track.TrackManager.load(TrackManager.java:271)

at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)

at 
org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.java
:2775)

at com.jidesoft.utils.SwingWorker$1.call(Unknown Source)

at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)

at java.util.concurrent.FutureTask.run(Unknown Source)

at com.jidesoft.utils.SwingWorker.run(Unknown Source)

at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown
Source)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)

at java.lang.Thread.run(Unknown Source)

This error appears to be different from the original, at least in
details though the results are the same.  I am also going to post this with
IGV support.

Thanks,
Iry


On 8/15/11 2:46 PM, Nate Coraor n...@bx.psu.edu wrote:

 Iry Witham wrote:
 Hi Nate,
 
 I have checked the nginx.conf file and they comply to the documentation:
 
  #  added to allow nginx to handle file downloads
 location /_x_accel_redirect/ {
 internal;
 alias /;
 
 I have also confirmed that the universe_wsgi.ini file contains the
 following:
 
 And the following to the [app:main] section of universe_wsgi.ini:
 nginx_x_accel_redirect_base = /_x_accel_redirect
 
 Iry
 
 This will need some in-depth debugging, then.
 
 If you access Galaxy directly via the port of its built-in web server
 (by default, 8080), and request to display a dataset, does it set the
 X-Accel-Redirect header in the response?
 
 If you access the same dataset via the nginx address but rename the
 underlying disk file, do you get an error message from nginx or from
 Galaxy?
 
 --nate
 
 
 On 8/15/11 10:46 AM, Nate Coraor n...@bx.psu.edu wrote:
 
 Iry Witham wrote:
 Hi Everyone,
 
 I have been tasked with getting the IGV working within our Galaxy
 instance.  I have modified our Nginx configuration based on the more
 advanced
 configuration under Sending files using nginx on the nginxProxy page in
 the
 wiki.  The IGV viewer component in Galaxy does not display the results from
 a
 BAM file in either the web or local instance of IGV.  I have tested with
 IGV1.5 and with version 2.03.  Neither produce a visual representation of
 the
 sequence. When attempting to use the web option we get the same error
 provided in the original post as noted below.  Has anyone gotten this to
 work
 with Nginx-0.8.53 or any of the newer versions?
 
 Hi Iry,
 
 Have you checked to make sure that your nginx server is serving the file
 for download, as opposed to the internal Galaxy web server?  In the
 original email, it looked like nginx was being bypassed entirely (due to
 serving on port 8080 - Galaxy's intenal server's default port).  But
 even once nginx is in use, it's necessary to set up X-Accel-Redirect to
 serve datasets.  See the instructions here:
 
 http://usegalaxy.org/production
 
 --nate
 
 
 Thanks,
 
 Iry Witham
 Applications Administrator
 Scientific Computing Group
 Computational Sciences Dept.
 The Jackson Laboratory
 600 Main Street
 Bar Harbor, ME  04609
 Phone: 207-288-6744
 email: iry.wit...@jax.org
 
 
 
 
 
 On Apr 27, 2011; 10:06am
 ³Hello all,
 I just updated our local copy of Galaxy and just wanted to try the new IGV
 display application.
 When I try to display a BAM file with the local IGV

Re: [galaxy-dev] Display BAM with IGV

[Iry Witham]

Hi Nate,

I have checked the nginx.conf file and they comply to the documentation:

 #  added to allow nginx to handle file downloads
location /_x_accel_redirect/ {
internal;
alias /;

I have also confirmed that the universe_wsgi.ini file contains the
following:

And the following to the [app:main] section of universe_wsgi.ini:
nginx_x_accel_redirect_base = /_x_accel_redirect

Iry

On 8/15/11 10:46 AM, Nate Coraor n...@bx.psu.edu wrote:

 Iry Witham wrote:
 Hi Everyone,
 
 I have been tasked with getting the IGV working within our Galaxy
 instance.  I have modified our Nginx configuration based on the more advanced
 configuration under Sending files using nginx on the nginxProxy page in the
 wiki.  The IGV viewer component in Galaxy does not display the results from a
 BAM file in either the web or local instance of IGV.  I have tested with
 IGV1.5 and with version 2.03.  Neither produce a visual representation of the
 sequence. When attempting to use the web option we get the same error
 provided in the original post as noted below.  Has anyone gotten this to work
 with Nginx-0.8.53 or any of the newer versions?
 
 Hi Iry,
 
 Have you checked to make sure that your nginx server is serving the file
 for download, as opposed to the internal Galaxy web server?  In the
 original email, it looked like nginx was being bypassed entirely (due to
 serving on port 8080 - Galaxy's intenal server's default port).  But
 even once nginx is in use, it's necessary to set up X-Accel-Redirect to
 serve datasets.  See the instructions here:
 
 http://usegalaxy.org/production
 
 --nate
 
 
 Thanks,
 
 Iry Witham
 Applications Administrator
 Scientific Computing Group
 Computational Sciences Dept.
 The Jackson Laboratory
 600 Main Street
 Bar Harbor, ME  04609
 Phone: 207-288-6744
 email: iry.wit...@jax.org
 
 
 
 
 
 On Apr 27, 2011; 10:06am
 ³Hello all,
 I just updated our local copy of Galaxy and just wanted to try the new IGV
 display application.
 When I try to display a BAM file with the local IGV or the web IGV I
 encounter following error complaining about the Null content-length.
 Has any of you encountered the same problem? Do I miss something?
 Thanks in advance
 
 Alex
 
 
 INFO [2011-04-27 16:00:14,440]  [TrackManager.java:225] [Thread-6]  Loading1
 resources.
 ERROR [2011-04-27 16:00:14,589]  [SeekableHTTPStream.java:59] [Thread-6]
 Null content-length for:
 http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454e
 df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
 ERROR [2011-04-27 16:00:14,590]  [TrackLoader.java:821] [Thread-6]  Error
 loading sam track
 java.lang.RuntimeException: Error loading file:
 http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454e
 df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length
 at 
 org.broad.igv.util.SeekableHTTPStream.init(SeekableHTTPStream.java:60)
 at 
 org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.j
 ava:42)
 at 
 org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.jav
 a:129)
 at 
 org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java
 :70)
 at 
 org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryRead
 er.java:80)
 at 
 org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryRead
 er.java:97)
 at 
 org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:7
 5)
 at 
 org.broad.igv.sam.AlignmentDataManager.init(AlignmentDataManager.java:69)
 at 
 org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.ja
 va:54)
 at 
 org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761)
 at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143)
 at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
 at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
 at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282)
 at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148)
 at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88)
 at 
 org.broad.igv.main.CommandListener.processGet(CommandListener.java:193)
 at org.broad.igv.main.CommandListener.run(CommandListener.java:93)
 at java.lang.Thread.run(Thread.java:636)
 ERROR [2011-04-27 16:00:14,592]  [TrackLoader.java:211] [Thread-6]
 java.lang.RuntimeException: java.lang.RuntimeException: Error loading file:
 http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454e
 df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length²
 
 
 On Apr 27, 2011; 12:33pm
 ³Hi Alex,
 
 Displaying BAM files at external applications usually requires an http server
 that supports partial gets. Unfortunately, the current lightweight http
 server that is built into Galaxy does not support these advanced http
 options

Re: [galaxy-dev] Display BAM with IGV

[Iry Witham]

On 8/15/11 2:46 PM, Nate Coraor n...@bx.psu.edu wrote:

 Iry Witham wrote:
 Hi Nate,
 
 I have checked the nginx.conf file and they comply to the documentation:
 
  #  added to allow nginx to handle file downloads
 location /_x_accel_redirect/ {
 internal;
 alias /;
 
 I have also confirmed that the universe_wsgi.ini file contains the
 following:
 
 And the following to the [app:main] section of universe_wsgi.ini:
 nginx_x_accel_redirect_base = /_x_accel_redirect
 
 Iry
 
 This will need some in-depth debugging, then.
 
 If you access Galaxy directly via the port of its built-in web server
 (by default, 8080), and request to display a dataset, does it set the
 X-Accel-Redirect header in the response?
 
 If you access the same dataset via the nginx address but rename the
 underlying disk file, do you get an error message from nginx or from
 Galaxy?
 
 --nate
 
When I add the port (8080, 8081 or 8082) I don't get the error and the IGV
opens.  That a great thing.  However, it is now minus any alignments.  But
that is a different issue.

Iry

 
 On 8/15/11 10:46 AM, Nate Coraor n...@bx.psu.edu wrote:
 
 Iry Witham wrote:
 Hi Everyone,
 
 I have been tasked with getting the IGV working within our Galaxy
 instance.  I have modified our Nginx configuration based on the more
 advanced
 configuration under Sending files using nginx on the nginxProxy page in
 the
 wiki.  The IGV viewer component in Galaxy does not display the results from
 a
 BAM file in either the web or local instance of IGV.  I have tested with
 IGV1.5 and with version 2.03.  Neither produce a visual representation of
 the
 sequence. When attempting to use the web option we get the same error
 provided in the original post as noted below.  Has anyone gotten this to
 work
 with Nginx-0.8.53 or any of the newer versions?
 
 Hi Iry,
 
 Have you checked to make sure that your nginx server is serving the file
 for download, as opposed to the internal Galaxy web server?  In the
 original email, it looked like nginx was being bypassed entirely (due to
 serving on port 8080 - Galaxy's intenal server's default port).  But
 even once nginx is in use, it's necessary to set up X-Accel-Redirect to
 serve datasets.  See the instructions here:
 
 http://usegalaxy.org/production
 
 --nate
 
 
 Thanks,
 
 Iry Witham
 Applications Administrator
 Scientific Computing Group
 Computational Sciences Dept.
 The Jackson Laboratory
 600 Main Street
 Bar Harbor, ME  04609
 Phone: 207-288-6744
 email: iry.wit...@jax.org
 
 
 
 
 
 On Apr 27, 2011; 10:06am
 ³Hello all,
 I just updated our local copy of Galaxy and just wanted to try the new IGV
 display application.
 When I try to display a BAM file with the local IGV or the web IGV I
 encounter following error complaining about the Null content-length.
 Has any of you encountered the same problem? Do I miss something?
 Thanks in advance
 
 Alex
 
 
 INFO [2011-04-27 16:00:14,440]  [TrackManager.java:225] [Thread-6]
 Loading1
 resources.
 ERROR [2011-04-27 16:00:14,589]  [SeekableHTTPStream.java:59] [Thread-6]
 Null content-length for:
 http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45
 4e
 df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
 ERROR [2011-04-27 16:00:14,590]  [TrackLoader.java:821] [Thread-6]  Error
 loading sam track
 java.lang.RuntimeException: Error loading file:
 http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45
 4e
 df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length
 at 
 org.broad.igv.util.SeekableHTTPStream.init(SeekableHTTPStream.java:60)
 at 
 org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory
 .j
 ava:42)
 at 
 org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.j
 av
 a:129)
 at 
 org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.ja
 va
 :70)
 at 
 org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryRe
 ad
 er.java:80)
 at 
 org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryRe
 ad
 er.java:97)
 at 
 org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java
 :7
 5)
 at 
 org.broad.igv.sam.AlignmentDataManager.init(AlignmentDataManager.java:69)
 at 
 org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.
 ja
 va:54)
 at 
 org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761)
 at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143)
 at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
 at 
 org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
 at 
 org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282)
 at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148)
 at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88)
 at 
 org.broad.igv.main.CommandListener.processGet