Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
Nate Coraor
@natefoo:matrix.org
[m]
@mmikailov: check that the tool dependencies for the tool are properly installed, you can do this from the admin UI.
That said, I believe cuffdiff is deprecated and there are other tools that should be used in its place: https://help.galaxyproject.org/t/cuffdiff-bam-sort-error/5782
Mike Mikailov
@mmikailov
Thank you very much - I will try.
Nate Coraor
@natefoo:matrix.org
[m]
If you need to make a security argument with someone in your organization, Galaxy 19.01 is no longer supported and not receiving any kind of security fixes.
Mike Mikailov
@mmikailov
Thanks again!
Mike Mikailov
@mmikailov
Where new tools such as cuffdiff are installed on Galaxy directory?
I get this: tool_script.sh: line 9: cuffdiff: command not found
If I knew the path where the tools are installed, I could export the path - may this would fix the isse.
Mike Mikailov
@mmikailov
Why does cuffdiff "Installing tool dependencies" take very long time? On Galaxy 21.09
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Yes, absolutely. Galaxy instances are independent of one another and so is their user management. Just don't create two accounts on the same server.
raphealofoe
@raphealofoe

Hi, I’m new to RNASeq data analysis using Galaxy. I have been trying for days to analyze my data files using Desq2 but it kept giving error. I got both the genome sequence (fasta) and the gene model (gff) from the same source (phytozomes). perfomed the alingment with HISAT2 and count with stringtie. Featurecount does not work for me. any help.

Deseq2 error
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 26286, 26287, 26498
Calls: get_deseq_dataset ... eval -> eval -> eval -> cbind -> cbind -> data.frame

featurecount error
//========================== featureCounts setting ===========================\
|| ||
|| Input files : 1 BAM file ||
|| o dataset_849c67a7-7b08-4e2f-b0bc-4491b7911b ... ||
|| ||
|| Output file : output ||
|| Summary : output.summary ||
|| Annotation : dataset_a5adcd4d-76e0-44de-8e60-bc950068bde6 ... ||
|| Dir for temp files : ./ ||
|| ||
|| Threads : 6 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\============================================================================//

//================================= Running ==================================\
|| ||
|| Load annotation file dataset_a5adcd4d-76e0-44de-8e60-bc950068bde6.dat ... ||

ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
The specified gene identifier attribute is 'gene_id'
An example of attributes included in your GTF annotation is 'ID=Solyc00g005280.1.1.ITAG4.0.exon.1;Parent=Solyc00g005280.1.1.ITAG4.0;pacid=51367901'
The program has to terminate.

any help

Enzyme5610
@Enzyme5610
Hello my account seems to have been deleted? Does anyone know how I could seek help regarding reinstating my account? (It says the email is does not exist, but I was logged in mere hours ago)
91425101212
@91425101212
@91425101212
Hello. I am using string tie but I get a warning my gtf file does not use.
WARNING: no reference transcripts were found for the genomic sequences where reads were mapped!
Please make sure the -G annotation file uses the same naming convention for the genome sequences.
How can I solve that?
1 reply
Melisa Magallanes
@Melisa-Magallanes
Hi there, Can the trinotate version be upgraded? at usegalaxy.org?
1 reply
Florian Wuennemann
@FloWuenne

Hi everyone, I am trying to make a multi-tool biocontainer (https://biocontainers.pro/multipackage) for a Galaxy workflow Im writing, but the version for one of my tools thats on conda doesnt exist on biocontainer... The requirement in question is :

<requirement type="package" version="1.7.1">r-optparse</requirement>
Any suggestions how to handle this?

Björn Grüning
@bgruening
You can add this here: https://github.com/BioContainers/multi-package-containers
Florian Wuennemann
@FloWuenne
Ok, how do I create a quay.io oauth token?!
Or do I just have do make a PR With the mulled environment I would like as a multi-container?
Florian Wuennemann
@FloWuenne
@bgruening: I have submitted a PR for the multi-tool:
BioContainers/multi-package-containers#1955
bgruening
@bgruening:matrix.org
[m]
Or do I just have do make a PR With the mulled environment I would like as a multi-container?
only that
And please have a look at planemo test --docker this will create you the containers locally
If you provide your tool to one of the bigger community repos, we will create those containers for you automatically
via planemo container_register
Florian Wuennemann
@FloWuenne
Ok sounds good! I hope that PR I send looks ok. I will also test out the planemo commands you shared, thanks!
Florian Wuennemann
@FloWuenne
Hm, Pull request seem to complete without issues, I guess that's good! :)
bgruening
@bgruening:matrix.org
[m]
@FloWuenne: this looks good
Are you sure you specify all those deps in the file also as part of your requirements?
It looks for me like too many dependencies.
you noramlly do not need to specify cairo in the Galaxy tool
Florian Wuennemann
@FloWuenne
Yeah, I'm fairly new to writing Galaxy tools, so I'm not 100% sure I need all of them. The reason some of them are there, is that the approach we took to write the Signac tools is very similar to the EBI Seurat tool:
https://github.com/ebi-gene-expression-group/r-seurat-scripts/blob/d539f1c54034f7b1ace6511f99e03bc81b2bf6bc/test-environment.yml
I didn't do a lot of trying to reduce packages from that list and see if it still works and just assumed they are all needed...
but besides these two (libpng=1.6.37,r-cairo=1.5_12.2), I am very sure all the others are required:
https://github.com/Single-Cell-Academy/r-signac_galaxy
Florian Wuennemann
@FloWuenne
Sorry for the dumb question, but where can I pull the container from afterward?
The list on : https://quay.io/organization/biocontainers never loads for me and gives me an error on the webpage...
Florian Wuennemann
@FloWuenne
I guess its this one, which I found in the CI GIthub action?
quay.io/biocontainers/mulled-v2-521d0ced009a310763c443d8d68165a1e08fc110:987167247bd37ebb7bb8367dea090f7d5aa0a981-0
Kamar
@amudaakindele
Hello
where can i get DNA dataset on paternity/maternity test
Rahil Choudhary
@RahilCh61217387_twitter
Sir whenever i try to login into galaxy it shows unexpected exception inapi method . I dont have knowledge about this can you please help me because i have stored so much data in it.
Your response would be very helpful for me
banjulhu
@banjulhu
Hi. Does anyone have any advice about sharing histories. I've made one for a course I'm helping teach on but when I have someone follow the link I made and import it all the files are greyed out.
3 replies
Helena Rasche
@hexylena:matrix.org
[m]
Cristóbal Gallardo: it's a current galaxy bug :(
I reported it last week
1 reply
galaxyproject/galaxy#13001 please see here for details
It's really frustrating, it made one of the courses difficult becaues we couldn't check their histories afterwords (at least not without my help/access to the database)
Helena Rasche
@hexylena:matrix.org
[m]
@banjulhu: are you on usegalaxy.eu or .org? If you're on .eu can you share the link to your history and I can manually fix it.
(feel free to direct message me or email me at helena.rasche@gmail.com if you want to keep the link private)
banjulhu
@banjulhu

Hi.

I'm on usegalaxy.eu

I made the link public as it was made up of already published data so no need for a PM.

https://usegalaxy.eu/u/ddolan/h/l3genomicsdurham

1 reply
Rahil Choudhary
@RahilCh61217387_twitter
Please help me
Anybody help me with this unexpected exception in api method
Nate Coraor
@natefoo:matrix.org
[m]
@RahilCh61217387_twitter: Which Galaxy server are you experiencing this on?