ntation to planemo
> about developing tools for clusters and testing against them and I
> didn't encounter any problems.
>
> http://planemo.readthedocs.org/en/latest/writing_advanced.html#cluster-usage
>
>
> -John
>
> On Fri, Mar 4, 2016 at 2:39 PM, D K <danielforti...@gmail.c
from my iPhone
> >
> >> On Mar 21, 2016, at 5:32 PM, Peter Cock <p.j.a.c...@googlemail.com>
> >> wrote:
> >>
> >> Hi D. K.,
> >>
> >> We're currently trying a locally compiled Python 2.7 (from source)
> >> under the shared Galaxy mount
Hi Galaxy Devs,
This may be premature but I read that for Galaxy after 16.01 that the plan
is for python 2.6 to no longer be supported. I'm currently running CentOS
6.6 which uses python 2.6. In order to be able to use newer versions of
Galaxy is my only option to upgrade to a newer version of
Hi,
I posted this question to biostars but didn't get an answer
Is it possible to use "planemo test" functionality on an SGE cluster? I can
correctly run a custom tool on an SGE cluster when I manually run a job
through the galaxy interface. If I change the job_conf.xml so that the job
is
> Essentially, Galaxy can be configured in galaxy.ini to install it's own
> > miniconda and resolve dependencies on it's own.
> >
> > Hope this helps,
> > Bjoern
> >
> > Am 03.05.2016 um 23:05 schrieb D K:
> >> Hi Galaxy-Devs
> >>
> >> I wo
Hi Galaxy Devs,
I posted this question on biostars but didn't get an answer so I'll try
here:
I just tried upgrading my local instance of Galaxy from 15.10 to 16.01.
When I start it up I get an error. Does anyone have any suggestions?
galaxy@galaxy galaxy$ sh run.sh
Activating virtualenv at
ump it up my priority list a bit.
>
> -Dannon
>
> On Tue, Aug 16, 2016 at 6:25 PM, D K <danielforti...@gmail.com> wrote:
>
>> Hi Galaxy-devs
>>
>> I've created a workflow that processes some NGS data. Since many of the
>> intermediate files are really large
I'm trying to get a list of all the datasets in a folder using BioBlend. I
don't see a function for doing this in the API documentation. I can use
"show_folder" to get some information regarding the contents of a folder,
but not the dataset IDs themselves
This is as far as I've gotten:
s =
. under tmp with test.xml
I've also tried putting these files under galaxy-test/tool-data, test-data,
etc... and that didn't help either.
I'm not understanding what I'm doing wrong here. Any additional suggestions
would be appreciated.
Thanks!
On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo <nso
mple file - although in that case I would have
> expected a different error message:
>
> https://github.com/galaxyproject/planemo/issues/530
> https://github.com/galaxyproject/planemo/issues/530
>
> Is planemo lint happy with your tool?
>
> Peter
>
>
> On Thu, Oct
and the "twobit.loc" in
"galaxy-test/test-data" and "galaxy-test/tool-data" then I get the same
error again. I'd like to be able to put the files here instead of in their
own directory structure.
Thanks!
On Fri, Oct 7, 2016 at 10:04 AM, D K <danielforti...@gmail.
Hi galaxy-dev,
I'm having a problem running a test using planemo where I would like the
value of a parameter taken from one of the data tables. I get the following
error in planemo:
'Error creating a job for these tool inputs - Parameter
refGenomeSource_type requires a value, but has no legal
Great! that fixed the issue
On Fri, Aug 26, 2016 at 10:20 AM, Dannon Baker <dannon.ba...@gmail.com>
wrote:
> Ok, so it should be gone, I guess. Check 'git status', maybe it's just
> there as an untracked file (and if so, just rm it)?
>
> On Fri, Aug 26, 2016 at 12:55 PM
> this a custom modification you have?
>
> -Dannon
>
> On Fri, Aug 26, 2016 at 12:30 PM, D K <danielforti...@gmail.com> wrote:
>
>> Hi Galaxy-devs,
>>
>> I just tried upgrading to 16.07 from 16.01 and get this error when
>> starting up:
>>
>
> exist? If it does not, it may be a leftover .pyc file (which you can
> delete safely). If you'd like to just clean out *all* the compiled python
> (which is also safe), run something like ```find -name "*.pyc"
> -delete```.
>
> On Fri, Aug 26, 2016 at 12:35 PM, D K
Hi Galaxy-devs,
I just tried upgrading to 16.07 from 16.01 and get this error when starting
up:
> Traceback (most recent call last):
> File "./scripts/paster.py", line 26, in
> serve.run()
> File
> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
> line 1061, in
, 2016 at 8:19 PM, D K <danielforti...@gmail.com> wrote:
> Hi Galaxy-devs,
>
> On my local instance of Galaxy (v16.07) when a user imports a shared data
> library file into their history and clicks on the "Selected datasets
> imported into history. Click this to start analyzi
Hi,
I'm trying to use the "$__tool_directory__" variable in
but it's not working as shown in the documentation.
echo "$__tool_directory__"
This returns a blank in the "Tool Version" field
Any suggestions?
Thanks!
___
Please keep all
Hi Galaxy-devs,
On my local instance of Galaxy (v16.07) when a user imports a shared data
library file into their history and clicks on the "Selected datasets
imported into history. Click this to start analyzing it." popup, they get
directed back to the Galaxy log in page regardless if they are
Hi galaxy-devs,
I get an "Internal Server Error" when trying to "Export History to File". I
get the following in my paster.log file:
>
Error - : 'NoneType' object has no
> attribute 'execute'
> File '/opt/galaxy/lib/galaxy/web/framework/middleware/error.py', line 151
> in __call__
>
nctionality for what I'm
after in "History" (e.g. show_matching_datasets) but not for "Library".
Any help would be greatly appreciated!
On Fri, Feb 24, 2017 at 10:29 AM, D K <danielforti...@gmail.com> wrote:
> I'm trying to get a list of all the datasets in a folder using B
nstitute of Immunobiology and Epigenetics
>> Stübeweg 51
>> 79108 Freiburg
>> Germany
>>
>>
>> On Thu, Mar 2, 2017 at 8:30 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>> >
>> > this sounds more like a browser issue to me
>> > whic
uery.js:3232)
> at Object.add [as done] (jquery.js:3291)
> at t.fn.init.vt.fn.ready (jquery.js:3542)
> at callback (menu.js:116)
> at Object.t.success (backbone.js:1051)
> at l (jquery.js:3232)
> at Object.fireWith [as resolveWith] (jquery.js:3362)
On Thu
m or similar).
>
> thanks
>
> M.
>
>
> On Wed, Mar 8, 2017 at 1:34 PM D K <danielforti...@gmail.com> wrote:
>
>> Hi Martin,
>>
>> I've tried this on both v16.07 and v16.10
>>
>> D
>>
>>
>>
>> On Wed, Mar 8, 2017 at
this (admins load all of the instance's libraries) could you
> try loading the library list as a normal user? How many libraries do you
> have on the instance?
>
> Thanks
>
> Martin
>
> On Thu, Mar 2, 2017 at 12:38 PM D K <danielforti...@gmail.com> wrote:
>
>> Hi Martin /
Is it possible to move the file locations of Shared data libraries that
have already been added to the system? I just tried moving some of these
files to a new location (e.g. /somewhere/files to
/somewhere_else/libraries) and updating the galaxy.ini entry to point to
the new location. However,
Is it possible to use environment variables within ? I'm
trying to use git commit information as the version ID in galaxy where the
path $GITREPO can change:
e.g.
git --git-dir="$GITREPO/project.git" log -n 1
origin/master | grep -P "commit|Author|Date"
Thanks!
Hi Galaxy-devs,
I recently ran into odd behavior when jobs were submitted at the same time
to our cluster (jobs wouldn't return correctly, e.g. ). I changed
"cleanup_job" in galaxy.ini to "never" to see what was going on in my
job_working_directory (/scratch/galaxy/job_working/).
It looks like
It looks like uploading 'xlsx' data through 'Get Data' is not working. When
I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets
automatically converted to 'BLAST xml' when using Automatic Detection. If I
select 'xlsx' during uploading I get the error message ( Warning: The file
nderstand how it would be recognised as BLAST XML...
>
> It may also be useful to see your Galaxy data types configuration file.
>
> Peter
>
> On Wed, 10 Oct 2018 at 01:39, D K wrote:
>
>> It looks like uploading 'xlsx' data through 'Get Data' is not working.
>>
g/tool_conf.xml.sample#L2
> )?
> I guess the tool reload option will only work in a single process
> setup - but the monitoring with watchdog should be sufficient to not
> need this button at all when working properly.
>
> -John
> On Wed, Nov 28, 2018 at 1:34 PM D K wrote:
I'm running version 18.05 and have noticed that when updating the
tool_conf.xml that changes don't always get loaded in all processes (e.g.
if I hit reload sometimes my changes show up and sometimes they do not).
Also, if I try to run a new tool I've added sometimes this will fail
presumably
32 matches
Mail list logo
