Hi Alexander,
I'm glad to hear you got the jobs running. I don't think there's an
informative message that is being delivered when a job is not able to run
but looking at Galaxy (and/or CloudMan) logs might be necessary.
FYI, the version of CloudMan you're running (i.e., the currentlt released
ver
To see the data in a Data Manager, you first need to fetch the data via a
Data Manager vs. a history. So, you'll first need to install the fetch DM (
https://toolshed.g2.bx.psu.edu/repository?repository_id=cdf172d633d603c2&changeset_revision=bca4c608408c)
and then click on 'Reference Genome - fetch
Hi list,
I’ve been trying to write functional tests for a tool that produces BAM
files as output. The tests run fine when using planemo locally,
but not on the testtoolshed or on machines that do not have samtools
installed.
Apparently galaxy automatically tries to convert BAM to SAM to compare
th
Hi All,
We have our Galaxy instance installed on local HPC with MySQL database. A user
reported a issue with the tool "Merge BAM Files". The tool generated two files:
.bam and .bai. The bam file can be downloaded with no problem. But when she was
trying to download the index file (.bai) that s
Right now for each tool I have, I have to list the xml file per tool in
tool_conf.xml. I'd like to specify a directory that Galaxy will scan for a
list of xml files and load all of them. So instead of:
I can do:
I'd add this to Trello but unfortunately my company blocks t
Hi Ryan,
have you looked at this option?
# Set to True to enable monitoring of tools and tool directories
# listed in any tool config file specified in tool_config_file option.
# If changes are found, tools are automatically reloaded. Watchdog (
# https://pypi.python.org/pypi/watchdog ) must be
Ryan,
This is possible using the relatively new tool_dir tag.
This still looks in the tool path like other the normal tool tag.
-John
On Thu, Jun 11, 2015 at 1:16 PM, Björn Grüning
wrote:
> Hi Ryan,
>
> have you looked at this option?
>
> # Set to True to enable monitoring of tools and tool
Hi,
I'd suggest you to try to run Galaxy in a virtualenv:
$ cd
galaxy/
$ virtualenv .venv
$ ./run.sh
Cheers,
Nicola
Il 11.06.2015
19:51 Medini Annavajhala ha scritto:
> Hi All,
> Trying to install
Galaxy via instructions online and having issues with fetching the eggs.
Very similar issue to
Thank you John and Bjoern. I will take a look at both.
On Thu, Jun 11, 2015 at 1:35 PM, John Chilton wrote:
> Ryan,
>
> This is possible using the relatively new tool_dir tag.
>
>
>
> This still looks in the tool path like other the normal tool tag.
>
> -John
>
>
> On Thu, Jun 11, 2015 at 1:16
Hi list,
How can I delete multiple tools from my galaxy installation?
So far I just know how to uninstall single ones through "Manage installed
tool shed repositories" - But this is quite nasty if I want to uninstall
many of them.
Thanks,
Alexander
PS: I also posted this there: https://biostar.
Hi Alexander,
> How can I delete multiple tools from my galaxy installation?
>
> So far I just know how to uninstall single ones through "Manage installed
> tool shed repositories" - But this is quite nasty if I want to uninstall
> many of them.
in general you can do all these tasks with
http://
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