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Pablo Moreno
@pcm32
thanks Marius, will check with these hints.
Pablo Moreno
@pcm32
@mvdbeek the newer data manager helped… it writes the loc file correctly and the loc file appears in the list of data tables, however, on reload, nothing shows in the UI for that data table… do I need to restart the instance?
Marius van den Beek
@mvdbeek
that depends on the version of Galaxy you’re running
it might be necessary
19.09 should work best for this, others need watch_tool_data_dir in the config
Pablo Moreno
@pcm32
ahhhh! thanks
Yi Sun
@sunyi000
I think I found the cause of my encoding issue, but not sure how to work around it. Hope someone could point me to the right direction. There's a CHARACTER_MAP in here https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/util/object_wrapper.py#L96 which escaped all special characters in values of all <param>. If I wrap all parameters in a json file, the escaped value is written into the file. This will cause a failure in my configfile script. Do i need to decode the Character_map in my configscript? My <param type="text"> and value is a regular expression.
thanks very much for any pointers
Nicola Soranzo
@nsoranzo
@sunyi000 Have a look at https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-param-sanitizer
Yi Sun
@sunyi000
Thank you very much @nsoranzo
galaxybot
@galaxybot
[unknown]
Cuff Suite Not Running [Uncategorized]
Cufflinks, Cuffcompare, and Cuffnorm stopped running. I tried resume paused jobs but still paused.
E.C.
@bwcont
Hello hello. UseGalaxy tools keep giving me an error "Remote job server indicated a problem running or monitoring this job." even on tools I used successfully earlier today!
E.C.
@bwcont
The tools in question are Bowtie2 and Stringtie
galaxybot
@galaxybot

[unknown]
DiffBind_ChIP-Seq_Error_message [usegalaxy.eu support] chip-seq
Hello,

Please, I am trying to run DiffBind and I am getting this error message!

Any suggestions, please!

Thank you in advance!

Warning m…

galaxybot
@galaxybot

[unknown]
snpeff iuc - error using different tools from package [Uncategorized]
Hi,

I installed the latest repository (2019-10-15) of snpeff from iuc. It seems as the installation worked without any problems, however wh…

galaxybot
@galaxybot

[unknown]
HISAT2 - Could not display BAM file [Uncategorized]
Hello!

I have local Galaxy installed. Also I used Data Manager for creating indexes.

Galaxy - 19.05

HISAT2 - 2.1.0+galaxy5

I have just t…

galaxybot
@galaxybot

[unknown]
multiple Rdata output [Uncategorized]
Hi,

I’m developping my own tool in a local Galaxy and I would like to dynamically output multiple Rdata… It works very well with my table i…

Nolan Woods
@innovate-invent
Has anyone seen:
...
  File "lib/galaxy/util/template.py", line 91, in fill_template
    raise first_exception or e
NotFound: cannot find 'dataset'
Galaxy is suddenly tossing this exception for certain datasets
It has broken the interface
Nolan Woods
@innovate-invent
It seems it is only for gff3 formatted files
yup, it is specifically files with the format set to gff3
or gff
Nolan Woods
@innovate-invent
galaxyproject/galaxy#8826
Jennifer Hillman-Jackson
@jennaj
Admin help for https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303 please -- Q: is this really a resource issue or something else recognizable as a specific problematic configuration?
galaxybot
@galaxybot
[unknown]
This job is waiting to run [usegalaxy.org support]
The job is waiting to run for more than 10 hours? There something that I can do?
galaxybot
@galaxybot
[unknown]
MasigPro,s data input ? [usegalaxy.eu support] admin, tool-dev
What is the input data for MASIGPRO’s tool ? I didnt understood the Experimental design input data ? what is that exactly? I used FeatureCou…
pvanheus
@pvanheus
is there any way to make a Galaxy tool output a value that can be used as a parameter in another tool in a workflow?
Björn Grüning
@bgruening
@pvanheus what is the use-case for this?
Marius van den Beek
@mvdbeek
@pvanheus yes, but only in workflows — Parse parameter value
https://galaxyproject.github.io/training-material/topics/galaxy-ui/tutorials/workflow-parameters/tutorial.html#read-a-parameter-from-a-dataset
I suppose that relates to sampling an alignment file to a given depth, you could do this by calculating the coverage with samtools idxstats, then divide that value by the genome size to get the current coverage. To get the sampling factor divide current coverage by desired coverage
diegommartinezr
@diegommartinezr
Hello there, I'm trying to install SNVPhyl but is not showing up on the list, Does anyone how to install it? thank you!
Qiang Gu
@qiagu
The workflow can not preserve dataset input. I feel being able to save the whole tool parameters should be helpful, like adding a button 'save forms' next to the execute. The job rerun carries part of the functions, but doesn't work for collection and couple of other scenarios.
@diegommartinezr check the Galaxy/uwsgi log for debugging info. A simple way is searching your tool ID as a key word.
diegommartinezr
@diegommartinezr
Thanks! checking...
pvanheus
@pvanheus
@mvdbeek actually it relates to another workflow (compute constant sites -> iqtree) but your advice is spot on :)
Peter Cock
@peterjc
Galaxy/Planemo/Testing question: Has anything significant changed recently on the Galaxy dev branch with *.loc files used in tests via planemo? RE: peterjc/galaxy_blast#120
Nicola Soranzo
@nsoranzo
Not sure about loc files, but there's been a lot of changes in how all config files are found
Marius van den Beek
@mvdbeek
@peterjc I also stumbled across this. I can take a look in the afternoon
Nicola Soranzo
@nsoranzo
If that's easy to replicate, we can git bisect it
Peter Cock
@peterjc
Probably can turn the Galaxy BLAST .travis.yml into a smaller test... but yes, lots of changes on the dev branch - these tests had been broken in other ways for months :(
@mvdbeek hopefully my example helps and alongside your own you can make good progress.
Thanks both :thumbsup:
galaxybot
@galaxybot
[unknown]
Unable to change parameters for a subset of tools [usegalaxy.org support]
For multiple tools including Trim leading or trailing characters, Trim sequences, etc, I am unable to change the default parameters. If I in…
galaxybot
@galaxybot
[unknown]
tools fail when in a workflow [Uncategorized]
I wrote five tools to process genetic data. All them were verified to work correctly out of galaxy and also as isolated tools inside galaxy.…
galaxybot
@galaxybot

[unknown]
tRNA used for a specific gene across the genome [usegalaxy.eu support]
Hello, my fellow science lovers,

I am trying to determine the occurrence of a specific tRNA anticodon in a specific gene across the genome …

John Crow
@crowja
We have Galaxy set up to authenticate users against an institutional SSO. Logging in gets the user access to the Galaxy instance. Some custom tools within it make calls to external web services which require the access token to be passed. Is there an example of how to access it?
Nolan Woods
@innovate-invent
How is the token passed?
HTTP header? url?