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galaxybot

@galaxybot

[unknown]
Files will not download completely [usegalaxy.eu support] download
Hi, I have run out of space in the usegalaxy.eu server and am trying to download files to delete them from my history to make space on my ac…

Dave B.

@davebx

@hrhotz you are correct that this is not recommended, but you are also right that this approach would technically work :D

galaxybot

@galaxybot

[unknown]
hg38 for Gemini vcf database? [Uncategorized]
Hello. Two questions

Does anyone know whether there is a gemini for hg38?

If there is not a gemini for hg38 (only hg19) what is the best …

Nate Coraor

@natefoo

@behlen07 is that on usegalaxy.org?

behlen07

@behlen07

@natefoo Yes it is.

Nate Coraor

@natefoo

Could you send in a bug report using the bug icon on one of the red datasets?

behlen07

@behlen07

@natefoo I deleted the data set but will rerun the multiQC again. If it gives the error then I will submit the report

Nate Coraor

@natefoo

Qiang Gu

@qiagu

After upgrading to latest planemo, maybe galaxy as well, planemo test fails to build conda environment for my test. I used to see the conda building command in the galaxy stdout log. Now nothing is there. Do I miss anything in planemo setting or a change has occurred in galaxy?

behlen07

@behlen07

Is it normal for Gene Body Coverage (BAM) tool to take a long time? I started one treatment group 8 hours ago and it still isn't finished...

behlen07

@behlen07

@bgruening I just ran my featureCounts tool but I received only 20% mapping. I used Gencode's genome and annotated file originally so they are from the same source. Thoughts?

So I re-ran featureCounts with strandedness in "reverse" and received 76% assigned this time. I'm good to continue on, right?

galaxybot

@galaxybot

[unknown]
Length of Quality Sequence and Length of read do not match [usegalaxy.org.au support] error
Hi there!

I am a student just starting out Galaxy for the first time.

I am trying to use the CutAdapt tool to trim some reads, but I get t…

Björn Grüning

@bgruening

@behlen07 you really need to know how the library was prepared. Is it a stranded or unstranded library etc. And this information you need to feed into the worfklow.

WilliamLyman

@WilliamLyman

Is it possible to pass credentials through galaxy while running a step, (for the purpose of hitting a protected API or to access specific files?)

WilliamLyman

@WilliamLyman

I should also ask can you disable tools by user

Estelle Ancelet

@eancelet

I should also ask can you disable tools by user

Hi @WilliamLyman, you can do it with Dynamic Job Destinations : https://training.galaxyproject.org/training-material/topics/admin/tutorials/connect-to-compute-cluster/tutorial.html#dynamic-job-destinations. Is it what you are looking for ?

WilliamLyman

@WilliamLyman

Hmm so I was a bit confused by this, does this same pattern still hold when you are just executing a single script on the server?

(and not dispatching a job to an hpc environment etc.)

galaxybot

@galaxybot

[Dave B.] as I understand it, yes. Job destinations apply to all jobs.

galaxybot

@galaxybot

[unknown]
Usegalaxy, ChIPSeq, bedtools Intersect intervals, Blacklist regions [usegalaxy.org support]
Hello,

I am trying to remove the blacklisted regions from my ChIP-Seq datasets (Mapped regions to hg19 human genome, BAM files) using bedto…

behlen07

@behlen07

@bgruening I inquired after I sent the message and it was stranded

behlen07

@behlen07

@bgruening I am receiving this error message in DESeq2 "Error in DESeqDataSet(se, design = design, ignoreRank) :
some values in assay are negative
Calls: get_deseq_dataset ... DESeqDataSetFromHTSeqCount -> DESeqDataSetFromMatrix -> DESeqDataSet" when running my control vs treatment 1 vs treatment 2

Jennifer Hillman-Jackson

@jennaj

Hi Devs/admins: Users are having trouble downloading dataset collections. They abort around 1 GB of data at both usegalaxy.org and usegalaxy.eu. This isn't new and was related to an older version of curl in the past, but that doesn't seem to be the issue now. Advice?

I wasn't able to reproduce it before but will test again now at both servers. Mac/chrome + Mac/safari just to see what happens.

Nate Coraor

@natefoo

Yeah byte ranges aren't gonna work I assume because collection archives are generated as a stream on the fly?

(the middle of the 3 links where the user tries to resume)

Jennifer Hillman-Jackson

@jennaj

Right

Nate Coraor

@natefoo

The others - let me check the body size setting.

Jennifer Hillman-Jackson

@jennaj

Thanks nate!

Nate Coraor

@natefoo

It's probably this: http://nginx.org/en/docs/http/ngx_http_proxy_module.html#proxy_max_temp_file_size

behlen07

@behlen07

GOT IT @jennaj @natefoo The issue was clicking "no" as the headers in DESeq2

Nate Coraor

@natefoo

I am not sure that we have enough local disk space to increase it by much though. And these archives are potentially enormous. Too bad it doesn't block when the buffer is filled. We could also disable buffering for that endpoint - not sure if that would be advisable though, but maybe worth trying.

siuguy

@siuguy

Hello, I am having a problem when running Hands-on: Generate count table

Count.seqs tool with the following parameters Unique.seqs tool

I'm following the tutorial (16S Microbial Analysis with mothur (extended))

Anybody have any idea how to fix it>

Jennifer Hillman-Jackson

@jennaj

@behlen07 glad you figured it out. I think I also replied to your email. Asking questions here at Gitter or Galaxy Help is better than sending direct emails to individuals :)

@natefoo -- so would the workaround be to move the data into a distinct history, generate an archive, then download that instead?

seems non-obvious if that is the case... but maybe we can make it more clear in the GUI somehow

@siuguy That particular tutorial, and the steps/tools used, often repeat with slight changes, so it is easy to mix up which input use (datasets are named in similar ways). Try tracing back through what you have done so far -- you'll probably find the mixup.

Jennifer Hillman-Jackson

@jennaj

(the first time through will be the most challenging .. but once you have used the tools a few times it will become easier. that said, even I still mix up inputs sometimes :)

Nate Coraor

@natefoo

@jennaj I'm working on a fix in nginx

Jennifer Hillman-Jackson

@jennaj

:thumbsup:

galaxybot

@galaxybot

[unknown]
no files downloaded when I used "Download and Extract Reads in FASTA/Q format from NCBI SRA" tool [Uncategorized]
Executed Download and Extract Reads in FASTA/Q and successfully added 1 job to the queue.

The tool uses this input:

350: SRR_Acc_List (…

galaxybot

@galaxybot

[unknown]
ERROR : "TERM environment variable not set" [Uncategorized]
Hello everyone, I’m a new member :) I’m wrinting you because I have some issue in Galaxy when I use the tool “Unique.seqs”. The following err…

galaxybot

@galaxybot

[unknown]
FilterSamReads error [usegalaxy.org support] error, filter-bam
I always fail to run the FilterSamReads. Even my input is BAM file neither form the HISAT2 nor the CleanSam.

Please guide me on how to deal…

galaxybot

@galaxybot

[unknown]
CANU and Flye assembler tool error for nanopore data assembly [Uncategorized]
Hi all,

I know that in the previous topics, some of user were facing issues with the CANU assembler to for nanopore data assembly. I am als…

galaxybot

@galaxybot

[unknown]
cbioportal into/with Galaxy [Uncategorized] comparative-genomics
Has any one tried the integration of cbioportal into/with the Galaxy? To check the existence of mutations or in general for any other task?

WilliamLyman

@WilliamLyman

Does galaxy have a param type for "date" or anything that creates a date picker?

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