?
(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
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
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
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
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
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:
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
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
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
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
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.
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):
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
: 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
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
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
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
...@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-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
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
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
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
...@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
of parent of /usr/local/nginx/sbin/nginx: 1
failed
Any help would be appreciated.
Thanks,
Iry Witham
The information in this email, including attachments, may
.
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
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
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
: 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
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
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
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
(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
FILTER 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
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
,
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
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
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
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
,
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
The information in this email, including attachments, may be confidential
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
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
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
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
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
, 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
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
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
meaningful. People will have some idea
from the subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match
search queries, but that aren't actually informative.
Today's Topics:
1. pbs_python issues (Iry Witham)
2. Which css file does welcome.html
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
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:
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
(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
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
/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
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
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
tried it with Google Crome
and Firefox 3.6.20.
Thanks,
Iry Witham
___
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
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
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
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
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
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
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