Hi ,
We would the location of the datasets our Galaxy stores to be determined
dynamically based on a set of rules. For example: for a specific role we would
like a datasets to be stored in a folder /storage/no_backup and for another
role this should be /storage/with_backup
Is there currently a
Hi all,
At gcc2013 at the storage workshop I think I heard about a feature in
galaxy, where different users could be assigned to a specific object
store.
But I can't find any documentation on this subject. Is this possible
and how do I implement this?
Thanks,
--
Central Veterinary Institute o
Hi,
I would like specify a filter based on a role. Does someone know how to do
this? I already have an example on how to do this based on user id (found at
https://wiki.galaxyproject.org/UserDefinedToolboxFilters#For_Administrators)
but now I would like to filter out menu items in case users do
Hi,
I am going to analyze one ChIP-seq data using "Gaxlaxy", the data upload,
and format converting goes well, then I use "bowtie2" to map the reads,
there is no result come out for quite a long time, the jobs is always
"waiting to run". Could you tell me how can I fix this?
PS:my account: wan...
Ok, just answering my own question ;) I found a solution, here it goes (also
attached):
import logging
log = logging.getLogger( __name__ )
def restrict_prims_metabolomics( context, tool ):
"""
This tool filter will hide MsClust for non-metabolomics users. This can be
enabled by addi
Hi,
I've installed the latest version (using GATK2.8-1) of the GATK2 wrapper here.
I've run into the following error:
# ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does
not exist.
I see via much googling that this error is due to a user input problem. I've
tried po
Hi,
do you have access to the generated commandline from Galaxy and can
paste it her?
>
> I’ve installed the latest version (using GATK2.8-1) of the GATK2
> wrapper here. I’ve run into the following error:
>
> # ERROR MESSAGE: The fasta file you specified
> (/tmp/tmp-gatk-V7IrBw) does not
Hi Peter,
On Jan 29, 2014, at 1:18 PM, Greg Von Kuster wrote:
> Hi Peter,
>
>
>>
>> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
>> 2014-01-29 missing blast_datatypes dependency (why?)
>> 2014-01-28 showing failed tests for sambamba_filter (wrong tool)
>>
>
> I'll have t
On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> On Jan 29, 2014, at 1:18 PM, Greg Von Kuster wrote:
>
>> Hi Peter,
>>
>>
>>>
>>> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
>>> 2014-01-29 missing blast_datatypes dependency (why?)
>>> 2014-01-28 showing
Hi Pieter,
glad to see that features is actually used :)
Do you mind to add your example to the wiki? Otherwise I can also add it
if you like.
Thanks,
Bjoern
> Ok, just answering my own question ;) I found a solution, here it goes
> (also attached):
>
>
>
> import logging
>
> log = logging.
Hi Bjoern,
The loc file is tabular. I put the 2bit file in the directory and had no
success. Here is the rather lengthy commandline:
#!/bin/sh
export GALAXY_SLOTS_CONFIGURED="1"
if [ -n "$SLURM_JOB_NUM_NODES" ]; then
GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
elif [ -n "$NSLOTS" ]; then
GALA
Hi Sheldon,
> The loc file is tabular. I put the 2bit file in the directory and had no
> success. Here is the rather lengthy commandline:
>
> #!/bin/sh
>
> export GALAXY_SLOTS_CONFIGURED="1"
> if [ -n "$SLURM_JOB_NUM_NODES" ]; then
> GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
> elif [ -n "$NSLOT
We do see hg19 in the reference genome box. We are using revision 8bcc13094767
of the GATK2 wrapper. The only line in the .loc file is the one listed in my
first email. I've put that line in both tool-data and
tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767 loc files. We
didn'
I have no clue what is happening. Attached is my working *.loc flile.
See select-box is also filtered by the db-key of your dataset, but I think
you habe hg19 as dbkey, otherwise you would not see the hg19 in the select
box. There must be something wrong in you *.log file.
2014-01-30 Briand, Shel
Hi,
Thanks for your help. It turns out an extra carriage return snuck into the end
of the .loc file. Once I removed that everything worked.
-Sheldon
From: bjoern.gruen...@googlemail.com [mailto:bjoern.gruen...@gmail.com]
Sent: Thursday, January 30, 2014 2:05 PM
To: Briand, Sheldon
Cc: galaxy-
Howdy,
I am having trouble uploading data on our local instance of Galaxy
here. The method is via FTP and here is the error I am seeing in the
logs:
galaxy.jobs.runners DEBUG 2014-01-30 14:29:31,987 execution of
external set_meta for job 1367 finished
galaxy.jobs DEBUG 2014-01-30 14:29:32,016 (1
Devs,
I'm having issues with a local toolshed I'm playing around with.
I turned on use_remote = True (since we have that working on our primary
galaxy instance). Web access to the tool shed, cloning, and pulling work
fine. However, I'm getting "abort: authorization failed" when trying to
"hg push
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