Hi,
General:
Is there a quantifiable difference in data uploads, speed of processing,
general availability after the connection was/is established to Pittsburgh?
Specific:
If we loaded data to a common directory on an XSEDE resource, would our
students be able to fetch this data in a more
can I have galaxy NOT to delete these SGE
error and out files?
best,
joe
From: Edward Kirton [eskir...@lbl.gov]
Sent: Monday, November 28, 2011 4:15 PM
To: Nate Coraor
Cc: Joseph Hargitai; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Job output
AM
To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Job output not returned from cluster
Joseph Hargitai wrote:
Hi,
i was browsing through the list and found many entries for this issue but not
a definite answer.
We are actually running into this error
Hi,
just noticed that in our current setup the baseurl to post data back from ucsc
tablebrowser is not picking up the port designation.
I looked at two files:
ucsc_display_sites
inputs action=http://genome-test.cse.ucsc.edu/cgi-bin/hgTables;
check_values=false method=get
, October 13, 2011 11:19 PM
To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] moving the galaxy-dist folder structure
Hi, Joe - not sure this will help but here goes: As you know, most
tools expect to find normal executables (like bwa and samtools) on the
execution host
Hi,
trying to bring up a new instance.
1, remove old cm from S3 bucket
2, bring up new
3, get console
4, SGE and fs running
5,Database and galaxy are not running
6, on /mnt i see /mnt and galaxyData
East 1c
xy Cloudman
Admin | Report bugs | Wiki | Screencast
Only up to the most
Hi,
i was browsing through the list and found many entries for this issue but not a
definite answer.
We are actually running into this error for simple file uploads from the
internal filesystem.
thanks,
joe
___
Please keep all replies
Hi,
we moved the /home/galaxy/galaxy-dist structure to another fs. Some tools, like
fastqc, stopped working. Are there internal links that we possibly ignored?
Is there a way to adjust the installation via a download or update?
joe
___
0 0
/dev/sdb/mntautodefaults,nobootwait,comment=cloudconfig0
0
From: Enis Afgan [eaf...@emory.edu]
Sent: Thursday, September 22, 2011 8:48 AM
To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] cloud instance
for production.
I'll check your recommendation shortly.
j
From: Enis Afgan [eaf...@emory.edu]
Sent: Thursday, September 22, 2011 8:48 AM
To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] cloud instance missing /opt/sge/default/common
: Enis Afgan [afg...@gmail.com]
Sent: Tuesday, September 13, 2011 4:20 AM
To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] cloud instance missing /opt/sge/default/common
directory
Hi Joe,
If you look in /mnt/cm/paster.log on the instance, are there any indications
Hi,
Upon restarting a saved cloud instance I am missing:
-bash: /opt/sge/default/common/settings.sh: No such file or directory
-bash: /opt/sge/default/common/settings.sh: No such file or directory
all the other mounts are there and well preserved. Is this pulled from a
special place i may have
[n...@bx.psu.edu]
Sent: Friday, September 02, 2011 1:40 PM
To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] rpy - No module named rpy CentoOs install
Joseph Hargitai wrote:
additional info:
it is possible on the same node to run manually
./gsummary.py
Hi,
On our Ubuntu install stat packages and all that require rpy work fine.
On our CentOs install seeing this stubborn error that I did see from previous
post to be difficult to fix.
At first suspected the SGE issue - environment not transferring to compute
nodes. After changing the app to
to prevent this app not finding the mod
from within galaxy?
j
From: Joseph Hargitai
Sent: Thursday, September 01, 2011 12:28 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: rpy - No module named rpy CentoOs install
Hi,
On our Ubuntu install stat packages and all
R - not the correct download url,
Which URL are you talking about? The wiki page on dependencies
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
correctly links to the R project as http://www.r-project.org/
you are correct, however the tools_fabfile.py has
version = 2.11.1
Hi,
so for local install i can uncomment the R and rpy from your script as far as
at the _install_R.. part?
j
From: Enis Afgan [eaf...@emory.edu]
Sent: Monday, August 01, 2011 12:37 PM
To: Joseph Hargitai
Cc: Galaxy Dev
Subject: Re: [galaxy-user] mi-tools
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