Hi:
I’d be concerned about that file changing or disappearing and causing
irreproducibility.
If the URL were to a permanent location (e.g. NCBI or zenodo) maybe it’s ok.
Could it be re-computed locally if necessary (like a genome index)?
Maybe others know of examples where this is done.
Brad
Hi Galaxy folks:
We have one data set in a shared library that will not import to a history.
I am able to import it using the page for that dataset, but not from the list
of all datasets in the folder.
I’m not sure the source of the error - this particular row does not look odd to
me.=
Any Id
Flagstat might be a good choice here…
Brad
> On May 2, 2018, at 1:48 AM, Jochen Bick wrote:
>
> Hi Devon,
>
> do you mean Alignment Summary? How can I access that information and use it
> for an other tool.
>
> Cheers Jochen
>
>
> On 26.04.2018 14:14, Devon Ryan wrote:
>> There are two ali
63694 | new | handler0 |
537201 | 2016-11-30 05:40:08.343855 | new | handler0 |
537200 | 2016-11-30 05:39:20.394128 | new | handler1 |
537199 | 2016-11-30 05:38:03.913992 | new | handler0 |
So hander0 and handler1
Brad
On Wed, Nov 30, 2016 at 4:14 PM, Langhorst, Brad
ma
igured?
--nate
On Wed, Nov 30, 2016 at 1:01 AM, Langhorst, Brad
mailto:langho...@neb.com>> wrote:
Hi:
I have one user who’s jobs won’t execute on my local instance.
The user was mysteriously listed as inactive.
I reactivated and restored the handlers, still jobs are not executing.
The use
Hi:
I have one user who’s jobs won’t execute on my local instance.
The user was mysteriously listed as inactive.
I reactivated and restored the handlers, still jobs are not executing.
The user has plenty of quota (82% used)
Anybody have an idea about what might be wrong with this user?
I have
, Katherine Beaulieu
mailto:katherine.beaulieu...@gmail.com>> wrote:
Hi Brad,
So with multiple selection dropdown lists this is possible? Do you have an
example of a tool that can do this? Would it be possible to see an example of
the tools you are talking about? Thanks for the help!
K
016 at 12:05 PM, Langhorst, Brad
mailto:langho...@neb.com>> wrote:
Hi Katherine:
I’d recommend not having users type in paths if at all possible (they will make
frustrating mistakes).
If there is a selection of these maybe consider turining them into dropdown
lists.
Either way, these
Hi Katherine:
I’d recommend not having users type in paths if at all possible (they will make
frustrating mistakes).
If there is a selection of these maybe consider turining them into dropdown
lists.
Either way, these would be no different than e.g. user specified downsampling
amounts. or li
HI Katherine:
Multi-input/output should work fine…
You could have a look at the bowtie wrappers for an example.
It takes up to 2 fastq files and a reference. I can output a few files
(unmapped, mapped, etc)
Brad
—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs
On Aug 26,
tswith("package_" + name.lower()):
From: galaxy-dev
[galaxy-dev-boun...@lists.galaxyproject.org<mailto:galaxy-dev-boun...@lists.galaxyproject.org>]
on behalf of Langhorst, Brad [langho...@neb.com<mailto:langho...@neb.com>]
Sent: Friday, April
Hi Lance:
I did not hear anything about a license change for Kallisto - it still says
something like talk to our laywers for commercial use on their web site
https://pachterlab.github.io/kallisto/license
I’ve been using salmon for a few months now and find that it’s very good,
though it is alwa
Salmon works in a similar way to kallisto.
I’ve been tweaking the test toolshed wrapper of that lately, but I have not yet
figured out how to get planemo to test it properly - as soon as I do i’ll
publish it to the toolshed.
Brad
—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs
Hi Matthias:
I think it’s abandoned, I’ve tried to use it with no success.
I think it should be brought up to date or be removed to save people from
wasting time trying to get it working.
Brad
--
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs
> On Jan 20, 2016, at 3:06 AM,
Hi:
I just tried to install khmer from the toolshed.
I don’t think it’s installing correctly - but I don’t know if it’s a tool
problem or something with my setup.
the tool-dep directory has
khmer/2.0/crusoe/package_khmer_2_0/c7702a7d26e8/
but it’s empty.
This tool has a package dependency like
Hi:
When I run set_user_disk_usage.py I get that message …
Has something changed about logging?
I don’t see anything in the python script that looks like “galaxy.config”
related to a logging setup.
Brad
—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs
___
Hi:
I just installed hisat2 and the data manager from the toolshed ….
Some macros seem not to be expanded when I load the tool in the UI (even across
galaxy restarts)
e.g. I see @FTYPE@ instead of fastqsanger
the data manager produces this error:
Fatal error: Exit code 1 ()
Traceback (most rece
We run the galaxy server as a vm… for 0-30 simultaneous users on a similar size
cluster.
16 virtual cores and 8G RAM.
I use 4 web handlers and 2 job handlers behind nginx.
Brad
On Jul 14, 2015, at 1:13 PM, Benjamin Datko
mailto:bda...@carc.unm.edu>> wrote:
Hello All,
We am attempting to buil
InvalidRequestError: One or more mappers failed to initialize - can't proceed
with initialization of other mappers. Original exception was: Class
'kombu.transport.sqlalchemy.Message' is not mapped
galaxy.jobs.handler ERROR 2015-04-19 14:46:00,794 Exception in monitor_step
Traceback (most recent
;
> Planemo's building a tool documentation has a section on writing
> wrapper scripts that demonstrates the use of the new
> $__tool_directory__ variable -
> http://planemo.readthedocs.org/en/latest/writing_standalone.html#wrapping-a-script.
>
> Hope this helps,
> -John
I’m working on a very simple tool.
Rscript
samtools
R
this won’t work because Rscript is not running in the tool install directory
and can’t find simple_script.R…
I’ve just been reading
https://trello.com/c/9lQ7Sr8
Hi:
I need users to specify a project when they run a tool…
I would like this to be a select list whose set of options comes from a remote
url.
What’s the best way to achieve that UI?
Should I try to add a from_url attribute to the options tag?
Thanks,
Brad
--
Brad Langhorst, Ph.D.
Applicati
Is this a bug you want in trello?
got this back trace when attempting to get updates to the picard tool
172.17.130.111 - - [06/Feb/2015:13:45:55 -0400] "POST
/library_common/library_item_updates HTTP/1.0" 200 -
"http://galaxy.neb.com/library_common/browse_library?sort=name&f-description
_datasets.sh . Shouldn't it be the other way around, since purging
> only works on the deleted datasets? (I realise this doesn't address your
> main issue, since running it twice should have maximized free space.)
>
> Damion
>
> On 12/17/2014 01:05 PM, Langhorst, Br
My glaaxy user data area is using 40T
But the repots server only show usage of about 16T…
Im nearly out of space and I’m not sure how to resolve the disparity.
I have run the clearnup_datasets.py and other
I’m running mainenance scripts like this:
#!/bin/sh
echo 'running galaxy maintenace sc
ataManager
--
Brad Langhorst, Ph.D.
Applications and Product Development Scientist
On Nov 24, 2014, at 8:50 PM, Langhorst, Brad
mailto:langho...@neb.com>> wrote:
I recently upgraded galaxy to the 10/06 unannounced galaxy-dist.
I typically run with 2 web processes and 2 job handlers on a sing
I recently upgraded galaxy to the 10/06 unannounced galaxy-dist.
I typically run with 2 web processes and 2 job handlers on a single machine.
It seems that now the job handlers consume all RAM at startup and are killed by
the kernel.
Anybody seen something like this?
Bad job? bug?
I’m consider
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