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Philip Kirk
@PhilPlantMan

@PhilPlantMan was it with the same dataset that you try to import?

Yeah that's right. The file is about 1.5 gb which it handled fine before. I'm not sure how galaxy handles this but it feels like there is a cache that is full that I have no idea how to clear

gmauro
@gmauro:matrix.org
[m]
@PhilPlantMan: Can you try again? I freed a bit of space on the nodes
galaxybot
@galaxybot

[unknown]
Tool error: Remote job server indicated a problem running or monitoring this job [usegalaxy.org support]
Hello,

currently I am writing my bachelors thesis and because of this I am a bioinformatics greenhorn …

I have tried to run Screen.seqs tw…

Philip Kirk
@PhilPlantMan

@PhilPlantMan: Can you try again? I freed a bit of space on the nodes

Sure, I'll check now :)

Philip Kirk
@PhilPlantMan

@PhilPlantMan: Can you try again? I freed a bit of space on the nodes

It's working! Thank you for your help and super quick response @gmauro:matrix.org . Kind regards, Phil

adeyanov
@adeyanov
Hi, I've been trying to run SPAdes, but the job hasn't even started running and I started it days ago. Does anyone have any insight?
Arpan2123
@Arpan2123
Hi there everyone!
i am trying to start a new project involving RNA-seq analysis using the Galaxy server. I uploaded the fastq.gz file on Zenodo and linked it to my galaxy server. However, the history says that the file is 'not' fastq.gz. can anyone please help?
Cristóbal Gallardo
@gallardoalba
Hi @Arpan2123, could you provide me the Zenodo link?
Arpan2123
@Arpan2123
sure
The DOI is: 10.5281/zenodo.4453230
Cristóbal Gallardo
@gallardoalba
The access to the file is restricted, not sure if it could cause the problem
Arpan2123
@Arpan2123
Yes, I have had to restrict the access to the file. do you think that could be a problem? If I upload the data as Open access, could that solve the problem in your experience? Because, I have concern regarding to upload the data as Open access
Dave Clements
@tnabtaf
Hi All, I recommend participating in the January 2021 Papercuts, which is starting in ~1 hour and continuing for the next 26 hours. There will be prizes!
It’s a great way to get involved in a global open source, open science community. We especially want new contributors.
And contributions span all aspects of Galaxy, not just code.
galaxybot
@galaxybot

[unknown]
Unable to generate report for multiQC using QualiMap RNA-Seq QC [Uncategorized]
Hello,

I am trying to generate MultiQC report from multiple QualiMap RNA-Seq QC files. I am using ‘usegalaxy.org’.

The MultiQC runs but do…

galaxybot
@galaxybot

[unknown]
Why there is no CDD in Interproscan? [usegalaxy.eu support]
Hi,

Why there is no CDD mapping for interproscan?

BY the way, there is currently two interproscan in the tools section…why?

Thanks!

galaxybot
@galaxybot
[unknown]
normalized counts table generated by DESeq2 [usegalaxy.org support]
In the counts tables made by featureCounts, the number of counts associated with each gene is always a whole number. However, in the combine…
galaxybot
@galaxybot

[unknown]
Interpreting a principle component analysis [usegalaxy.org support]
[Screen Shot 2021-01-20 at 7.38.23 PM]

I generated this principle component analysis what is this figure telling me. How do I interpret it…

[unknown]
help learning how to read a MA plot? [usegalaxy.org support]
What type of information is represented on each axis of the MA plot? also what do the dots and the colors of the dots represent?
galaxybot
@galaxybot

[unknown]
Galaxy not using the newly created environment for tool execution. [usegalaxy.org support] admin, tool-dev, galaxy-local
Hello,

I’m running a local galaxy installation, on a new computer running Ubuntu 20.04.

I have written some tools and uploaded them using …

galaxybot
@galaxybot

[unknown]
Empty collections after [usegalaxy.org support]
Hi,

Trying to upload dataset from 7 accessions in SRA using the ‘(faster) download and extract reads in fastq format from NCBI RSA’ tool. T…

galaxybot
@galaxybot
[unknown]
Could Galaxy/HicExplorer includes samtools for bam files merge? [Uncategorized]
Could Galaxy/HicExplorer includes samtools for bam files merge? Or is there a tool for merging bam files in HicExplorer? Hi-C datasets alway…
knutwa-ext
@knutwa-ext

Hi! I wonder if the following is a known problem? And what I can do about it? I tested a tool with multiple requirement tags on our 20.05 server instance.

  1. Installation worked well from the toolshed. A conda environment was created as it should.
  2. I added one more requirement tag, and updated via toolshed. Apparently Galaxy made no attempt at dependency resolution.
  3. I therefore ran the Manage dependencies GUI. A new conda env was created.
  4. When running the tool however, the original conda env was still used. Hence, the new dependency was not available to the tool.
  5. Fortunately, uninstall-then-install worked better than simple update.

I repeated the above on my local 19.05 instance. At point 4 it got messy. I can only guess, but it looked like Galaxy attempted to create a conda env in the job directory, failed, and then ran the tool anyway outside of conda.

selten
@selten
@knutwa-ext Did you update the tool version after you altered the tool requirement tags and pushed to the Tool Shed?
knutwa-ext
@knutwa-ext
No
Dave B.
@davebx
@selten is right, it's generally a good idea to also update the tool version when making changes like that
knutwa-ext
@knutwa-ext
Thanks, I will try that. I haven't been able to work out the details of dependency resolution from the documentation. Is that just the way it is, or have I overlooked something?
selten
@selten
Well the dependency resolution with conda when adding requirements works better when you bump the version :D
There's a dependency resolvers configuration file
@davebx I'd even argue that for any change you make you should update the tool version, otherwise automatic installation with ephemeris doesn't work
galaxybot
@galaxybot
[unknown]
significants of Counts table two columns [usegalaxy.org support]
In a counts table I understand Geneid column lists the gene name but what is the (BAM) column for? what does a counts table tell me about m…
knutwa-ext
@knutwa-ext
Thanks, @selten, that's useful to know about ephemeris.
Btw, it would be interesting to know what on earth was going on in my 19.05 instance.
selten
@selten
@knutwa-ext With the tool requirements not updating or what do you mean in particular?
knutwa-ext
@knutwa-ext
I meant this bit: " I can only guess, but it looked like Galaxy attempted to create a conda env in the job directory, failed, and then ran the tool anyway outside of conda." Might require more details from me, though. And the conclusion is in any case that this is something to avoid.
selten
@selten
Well yea, it would've been easy to avoid that
I think that may be because Galaxy is set up to create a conda env upon starting a tool run. Sometimes creating conda envs fails because of for instance rate limiting by anaconda.
knutwa-ext
@knutwa-ext
Sounds reasonable. I thought that option was turned off, though. The version number change did the trick as you prescribed.
galaxybot
@galaxybot

[unknown]
Unicycler job not running [usegalaxy.org support] unicycler
Hello,

I submitted a job to unicycler over 24 hours ago to the main USA galaxy server and it is still grayed out waiting to run. How long d…

galaxybot
@galaxybot
[unknown]
tophat dataset number issue [usegalaxy.org support]
Greetings, I proceed my datasets by tophat, unfortunately, there is an issue with the dataset numbers. Some of them don’t have dataset numbe…
galaxybot
@galaxybot

[unknown]
Trouble UPARSE for FASTA [usegalaxy.org support] workflow, galaxy-local, error
Hi, I am new to Galaxy. I´m trying to generate the OTU table file, by executing “UPARSE for FASTA”.

When executing the process, an error me…

galaxybot
@galaxybot

[unknown]
Error in Analysis [usegalaxy.org support]
Hello All

Well I am new to galaxy and even the first day user.

I am stuck in an analysis for quite long time and unable to move forward.

gulshadal
@gulshadal
Hello,
Is there a tool in galaxy for identifying secondary modifications, such as m6A, in RNA sequenced through nanopore?
Nolan Woods
@innovate-invent
@gulshadal look for any tool that can be used to do that and it can readily be added to Galaxy
Björn Grüning
@bgruening
@gulshadal yes we have some tools for this. We used them for DRS-COVID samples
look at nanocompore for example