Hi Nik
Have a look at the Profile Annotations tool
(~/tools/annotation_profiler/annotation_profiler.xml)
and the file ~/tool-data/annotation_profiler_options.xml
Regards, Hans-Rudolf
On 04/19/2014 12:48 AM, Nikhil Joshi wrote:
Hi Hans,
Thanks for your response. I am trying to get just
Hi Dannon,
I'm facing the same problem now. Could you help me with the steps to delete the
migrate_tmp table manually? I'm trying to use sqlite from command line but get
the following error:
Unable to open database universe.sqlite: file is encrypted or is not a
database
Thanks and regards,
Hey Pieter, sure. The sqlite database is in sqlite3 format, so you'll need
to use 'sqlite3 database/universe.sqlite' to access it.
The following should work:
sqlite3 database/universe.sqlite '.dump migrate_tmp' temporary_backup.sql
sqlite3 database/universe.sqlite 'drop table migrate_tmp;'
Hi Dannon,
Thanks, this helped.
Just for the record: I did find a small typo in my mail and in your script :
should be migration_tmp instead of migrate_tmp;)
Best regards,
Pieter.
From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: dinsdag 22 april 2014 14:59
To: Lukasse, Pieter
Cc:
Ok, great, glad that worked for you. And, thanks for the heads up on the
actual table name :)
-Dannon
On Tue, Apr 22, 2014 at 9:14 AM, Lukasse, Pieter pieter.luka...@wur.nlwrote:
Hi Dannon,
Thanks, this helped.
Just for the record: I did find a small typo in my mail and in your
David, Tony,
I have not yet been able to reproduce the behavior you've reported here.
I will continue to investigate, but if you go to Manage installed tool
shed repositories in your Galaxy admin interface and select the Update
tool shed status option on the compute_q_values repository, your
Dear all
I am using this control to allow the user to input multiple files:
param name=input_vcfs type=data multiple=true format=vcf
label=Input VCF file(s) /
and I am using this for loop in the cheetah code to access the control:
command interpreter=bash
script.sh
...
#for $i, $input_vcf in
On Tue, Apr 22, 2014 at 3:02 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear all
I am using this control to allow the user to input multiple files:
param name=input_vcfs type=data multiple=true format=vcf
label=Input VCF file(s) /
and I am using this for loop in the cheetah code to
Does anyone have any tips about this, please :)?
Regards
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hakeem Almabrazi
Sent: Monday, April 21, 2014 3:49 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] DRMAA configuring issue
Hi,
Hi Peter
I removed the unnecessary code.
If I run the tool with just a couple of inputs I see entries in the log
files either from galaxy.jobs.runners.drmaa or from
galaxy.jobs.runners.local that the job is being dispatched as normal.
Unfortunately there is no sign of the job in the log files
Dear folks,
Could you help me double check if my understanding is correct for EMS density
mapping? For the tool CloudMap: EMS Variant Density Mapping, it does not work
for other species except C.elegans, correct?
For the workflow CloudMap EMS Variant Density Mapping workflow (takes VCF of
On Tue, Apr 22, 2014 at 4:34 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Hi Peter
I removed the unnecessary code.
If I run the tool with just a couple of inputs I see entries in the log
files either from galaxy.jobs.runners.drmaa or from
galaxy.jobs.runners.local that the job is being
Hi,
to specify -Xmx and -Xms for java based programs I set my preferred
values to $_JAVA_OPTIONS and include _JAVA_OPTIONS as
nativeSpecification with -v _JAVA_OPTIONS. That worked good so far, but
the downside is that I can not have different options for different
tools. Is there a trick I
You can create multiple variants of the 10G_memory tool with different
native specifications right? Does this work around result in too much
XML? Dynamic destinations could also be used - if you are interested I
could post a demo rule that you might be able to use.
The memory card referenced
Hi John,
Am 22.04.2014 20:45, schrieb John Chilton:
You can create multiple variants of the 10G_memory tool with different
native specifications right? Does this work around result in too much
XML? Dynamic destinations could also be used - if you are interested I
could post a demo rule that you
On Tue, Apr 22, 2014 at 1:59 PM, Björn Grüning
bjoern.gruen...@gmail.com wrote:
Hi John,
Am 22.04.2014 20:45, schrieb John Chilton:
You can create multiple variants of the 10G_memory tool with different
native specifications right? Does this work around result in too much
XML? Dynamic
:) Speechless ... I will stress test it tomorrow!
Am 22.04.2014 21:24, schrieb John Chilton:
On Tue, Apr 22, 2014 at 1:59 PM, Björn Grüning
bjoern.gruen...@gmail.com wrote:
Hi John,
Am 22.04.2014 20:45, schrieb John Chilton:
You can create multiple variants of the 10G_memory tool with
Thanks for the response. I have made some progress, but I don't seem to be
out-of-the-woods yet.
I realized that when I had invoked
sh ./scripts/migrate_tools/0010_tools.sh
I had done it as root, rather than as user galaxy. Hence I did a
chmod -R galaxy:galaxy
on both the shed_tools/ and
Hi Wesley, Carlos,
We'd very much appreciate that you both took the time to report details
about this issue. We captured this in the Trello ticket:
https://trello.com/c/FLlynVZm
This issue was closed in another thread on 2/4/2014, please see ticket
for details. May a known already, but just
Hi Tony,
It may be easiest to just uninstall / reinstall the repository from the Manage
installed tool shed repositories option in the admin menu.
Greg Von Kuster
On Apr 22, 2014, at 4:21 PM, Tony Kusalik kusa...@cs.usask.ca wrote:
Thanks for the response. I have made some progress, but I
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