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Nolan Woods

@innovate-invent

@aivndv_twitter https://stackoverflow.com/a/61082642

galaxybot

@galaxybot

[unknown]
DESeq2 error running htseq-count [Uncategorized]
Every time I run DESeq2 I get this fatal “undefined” error:

estimating size factors

Error in checkForExperimentalReplicates(object, modelM…

galaxybot

@galaxybot

[unknown]
edgeR error running htseq-count files [Uncategorized]
When I attempt to run edgeR under default conditions with successfully processed htseq-count files, I get fatal error: exit code 1 ():

Warn…

galaxybot

@galaxybot

[unknown]
Errors with makeblastdb & blastn on very large file sets [usegalaxy.org support] galaxy-local
I am trying to follow a procedure in the following link - detailed instructions are in supplementary. I believe I have everything working un…

Wolfgang Maier

@wm75

@aivndv_twitter hmm, this error has been reported before on the help forum here: https://help.galaxyproject.org/t/trying-to-get-local-galaxy-running-but-cant-open-localhost-8080-in-browser-err-connection-refused/4726 but for Python3.6. Can you add your report there please for further debugging?

galaxybot

@galaxybot

[unknown]
Trimmomatic Work Flow Issue [usegalaxy.eu support]
Hi All,

just new to galaxy and I am designing a workflow whenever I insert a Trimmomatic into the workflow I can not update the numbers of …

galaxybot

@galaxybot

[unknown]
To convert String tie GTF file to FASTA file [Uncategorized]
I have used tool String tie to prepare reference assembly and got output data as GTF file. For structural and functional annotation I need …

olesya749

@olesya749

please help me with SAM/BAM specification

Jennifer Hillman-Jackson

@jennaj

@olesya749 Common datatypes are listed here with help plus links to related resources/details https://galaxyproject.org/learn/datatypes/

galaxybot

@galaxybot

[unknown]
single cell barcode extraction [usegalaxy.eu support]
I have tried to run single cell pre-processing workflow.but its not available for my data. I think it has a special kind of data uploading, …

galaxybot

@galaxybot

[unknown]
Fatal error: Exit code 1 () using Shovill [usegalaxy.org support] error
Hi, When I try to Shovill I keep getting this error:

Fatal error: Exit code 1 ()

[kmc] Error: some error while reading fastq file, please …

olesya749

@olesya749

I am wondering if somebody knows a tutor who can teach me Galaxy on line face to face. I am going to pay that person. Please let me know. Thank you

I live in Chicago, IL,USA. My phone number is 773-814-5566

galaxybot

@galaxybot

[unknown]
Thiết bị nhà bếp giá rẻ [usegalaxy.be support] admin, galaxy-local, error
http://camnangnhabep.info/

MaralQ

@MaralQ

Hello!

I'm trying to map my reads to human reference genome. But I don't know which build-in genome to use.

I would use Homo_sapiens.GRCh38.dna.toplevel.fa if I was using STAR.

RNA-seq single end library.

MaralQ

@MaralQ

Never mind. I'm just using hg38, the latest release.

galaxybot

@galaxybot

[unknown]
Version update for Galaxy environment [usegalaxy.org support] error
It is written " * Download and Extract Reads in FASTA/Q* format from NCBI SRA (Galaxy Version 2.10.8+galaxy0) ". But only Galaxy Version (…

galaxybot

@galaxybot

[unknown]
cannot add tools in local Galaxy [Uncategorized]
I installed the local Galaxy in Ubuntu subsystem in my Windows 10 computer. I used “nano galaxy.yml” to enter galaxy yml file and added my e…

galaxybot

@galaxybot

[unknown]
Tool error with STAR aligner [usegalaxy.org support] error, rna-star
STAR aligner encountered following errors in all available versions.

tool error

An error occurred with this dataset:

Encountered an un…

tensionhead

@tensionhead

Hello, I am developing a galaxy tool which produces an html report to summarize the results. However when looking at this report within galaxy, all the CSS styles get ignored and hence it looks horrible. However if I download that very same html and open it via file:/// it looks as it should.

Apparently that happened before: https://biostar.galaxyproject.org/p/12025/index.html but there is no solution/answer?!

Björn Grüning

@bgruening

@tensionhead please look at this Galaxy setting https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/galaxy.yml.sample#L1194 and the following.

HTML can be portnatially harmful, so Galaxy disables the "harful" parts. If you trust the tool you can whitelist the HTML output from a particual tool

tensionhead

@tensionhead

ah, great thx @bgruening !

Björn Grüning

@bgruening

Your welcome!

tensionhead

@tensionhead

little follow up question, on my local testing galaxy instance I see: ./test/unit/config/config_manage/embedded/config/galaxy.yml and
./test/unit/config/config_manage/simple/config/galaxy.yml I could whitelist my tool in one of these?

Björn Grüning

@bgruening

Please look into ./config/galaxy.yml

it might be called ./config/galaxy.yml.sample. In this case copy the file so that you have a galaxy.yml file.

tensionhead

@tensionhead

Got it and it works.. phew, that makes for a good start of the week thanks again!

Björn Grüning

@bgruening

hehe :)

galaxybot

@galaxybot

[fubar] @bgruening: does this kind of "papercut" make a galaxy configuration gui worthwhile? Plenty of help text in the yml - could be a Galaxy tool :)

tensionhead

@tensionhead

Hi, I uploaded a tool to https://testtoolshed.g2.bx.psu.edu/repository?repository_id=0a3480fb2f5eb710&changeset_revision=5e07fe722e0e However in my local galaxy instance, it apparently doesn't get listed/found

Ha, actually nevermind sorry.. it just took like 30min, now it's there :)

Hugo Jiménez Hernández

@HugoJH

Hello folks. I just got slurm backend runner working with two worker nodes (tested with very simple sbatch file ) on my local galaxy. The thing is once I tried to execute a tool from galaxy interface it crashed with the following message: "This job failed for reasons that could not be determined."
Took a peek into the logs and nothing really helpful (at least for me): https://pastebin.com/DQi01C2G
Any suggestions?

Nicola Soranzo

@nsoranzo

@HugoJH You may want to ask this on https://gitter.im/galaxyproject/admins

Hugo Jiménez Hernández

@HugoJH

Thank you @nsoranzo. :D

Dave Clements

@tnabtaf

@olesya749 Just saw your post from 3 days ago. (With apologies). I don't know of anyone who does one on one training. However, there is a wealth of training material here, and there is a dedicated Gitter Channel for the Galaxy Training Network. Those are good places to start.

We also list any trainings we know about here. The next intro training is see is this one, which is free. It will be in your evening (9pm-midnight).

galaxybot

@galaxybot

[unknown]
Data Usage and Job Processing Issues [usegalaxy.org support]
I’m having an issue that I think is related to my disk usage.

I accidentally permanently deleted a huge number of files from the history I’…

galaxybot

@galaxybot

[unknown]
Abundance of OTU's [usegalaxy.org support]
Is Mothur the only metagenomic toolset that provides the number of sequences/OTU? I would love to use map with BWA-MEM/Bowtie2 and get abund…

galaxybot

@galaxybot

[unknown]
Determining the haplotype [usegalaxy.eu support] vcf
Hello everyone,

we just started sequencing bloodgroups by using ngs. We are using the MiSeq from Illumina and our reads are 150 bp long.

I…

galaxybot

@galaxybot

[unknown]
Trinity de novo assembly of RNA-Seq data [usegalaxy.org support] error
Dear Galaxy Admins,

First of all, I would like to thank a lot for this Great Galaxy server. I was used this to perform my RNA-seq analysis …

Violetatil

@Violetatil

Hi everybody! I am trying to create a galaxy workflow for a Genome Data Science course. I have mapped 3 end pair RNA seq using a reference genome, I have run Hisat2 and now Im trying to run cufflinks but, it's an hour ago I have 3 jobs queued and it doesn't work.

What 's the problem?

Nolan Woods

@innovate-invent

@Violetatil assuming you are using usegalaxy.org, the queue can be quite long

galaxybot

@galaxybot

[unknown]
How to restrict VCF variants using a gene list with the set function in SnpSift? [Uncategorized] admin, vcf
Hello,

I am trying to restrict VCF variants using a gene list (text file) with the set function in SnpSift.

After annotating with ANOVAR a…

Andrés Culasso

@DrACulasso_twitter

Hello. I've downloaded galaxy from github and followed the scarce indications to get it running, but when I run the sh run.sh command to start galaxy, the process terminate with error building the client "Install prebuilt node (12.16.3)" and looks like it tries to download something and get a 404 (not found) error. I'm SMP Debian 4.19.152-1 (2020-10-18) i686 GNU/Linux. ¿Any idea on how to solve this? thanks in advance

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