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Björn Grüning
@bgruening
there is a gitter chat box at the front-page
Marcel Kempenaar
@mkempenaar
Hi all! I'm running into some problems with FastQC. I've recently updated Galaxy (from 16.01 to 21.01, yes, long overdue) but now I'm unable to view the FastQC output webpages from within Galaxy. I've also updated to the newest FastQC tool version but whichever version I try, the page isn't rendered correctly.
None of the images/ icons are loaded for instance.
Marcel Kempenaar
@mkempenaar
It does work on https://usegalaxy.org though so it must be something on my end. If anyone has a hint what it could be, it will be much appreciated.
Marius
@mvdbeek:matrix.org
[m]
@mkempenaar: you need to add fastqc to the allowlist in the admin panel
(->Admin->Manage Allowlist->check the new fastqc tool->Submit new allowlist)
Marcel Kempenaar
@mkempenaar
Thank you Marius, that's a nice feature that I didn't yet know.
Pablo Moreno
@pcm32
Hi there, on a Jupyter interactive tool, what is the preferred method of installing required R or Python packages? I tried directly installations from R and pip and they failed, and conda takes ages (I’m trying now to install mamba first). Thanks!
Pablo Moreno
@pcm32
Or is there a mechanism by which we could add packages to the container build process for Jupyter? Maybe PR this somewhere? Thanks
bgruening
@bgruening:matrix.org
[m]
For conda always specify the r-base version
tnabtaf
@tnabtaf:matrix.org
[m]

After taking the last 3 months off, PaperCuts is back. The September Papercuts is this Thursday. PaperCuts is an online, community wide event to address relatively easy to fix friction points in any part of Galaxy.

We will be on Gitter for chat all day long, and on 3 calls spread across the day. Please take advantage of both to communicate with your collaborators around the world.

Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
Papercuts call in 5 minutes! Zoom link
Björn Grüning
@bgruening
Thanks Cris!
Carrie
@cganote
Anyone see 404 when launching jupyter notebooks from usegalaxy.org?
1 reply
David Hong
@hong7734_gitlab
When I try to log in Galaxy it says "Internal server error" from yesterday. Do you know how to solve this problem?
Nicola Soranzo
@nsoranzo:matrix.org
[m]
@hong7734_gitlab: Which Galaxy server? There are many.
David Hong
@hong7734_gitlab
@nsoranzo:matrix.org :How to find the name of Galaxy server I am using?
http://131.247.66.74:8080/ this is what I am using
dannon
@dannon:matrix.org
[m]
This looks like University of South Florida? You will probably need to contact the local folks there that run the server for this one.
Let me see if we have contact info available
David Hong
@hong7734_gitlab
@dannon:matrix.org :Yes here is University of South Florida. Thank you for helping me.
dannon
@dannon:matrix.org
[m]
Sorry, I don't know who runs this one :/
David Hong
@hong7734_gitlab
@dannon:matrix.org : No problem, I can contact our IT guy. Thanks.
dannon
@dannon:matrix.org
[m]
Good luck!
Calliope-Maria
@Calliope-Maria
Hi, I am trying to set up galaxy server on windows cents 7 for my university. Could you give me a good orientation?
1 reply
enricoperez
@enricoperez
Hi all, I am not sure if this is the right channel but I would like to point out that I was looking for the course I did back in February 15-19 2021 on "GTN Smörgåsbord: A Global Galaxy Course" and now i can see that it is starting again on September 20 - 25, 2021
1 reply
But I am not sure if this is right. please let me know because I would like to do the course again with online help. I know I can do it on my own but i thought it will be more useful for me if there was an actual interaction like last time.
Helena Rasche
@hexylena:matrix.org
[m]
why does that have my picture :|
clearly need to get nicer og: cards up for the smorgasbord-derivative events
Nicola Soranzo
@nsoranzo:matrix.org
[m]
Credit where credit is due!
enricoperez
@enricoperez
Dear shiltemann thank for your email and if you follow the following link you will see that it says September 2021 20-25 https://galaxyproject.org/events/2021-02-smorgasbord/
dannon
@dannon:matrix.org
[m]
Weird...
I'm investigating, this may be a bug in the date handling on the hub.
Dannon
@dannon
Thanks for reporting this, confirmed it's a bug that was introduced over the weekend in the date handling of these events. Fix will be deployed shortly.
Oleksandr Moskalenko
@moskalenko
Who do I nee do talk to if I want to get a full mirror of reference data from statum0. The documentation mentions reaching out to public galaxy admin.
Nate Coraor
@natefoo:matrix.org
[m]
@moskalenko: Hi, nice to meet you 😄
If you're using Ansible already, the galaxyproject.ansible role can set up a Stratum 1 for you quite easily.
If not, you just need to install CVMFS and then run cvmfs_server add-replica with the right options.
Helena Rasche
@hexylena:matrix.org
[m]
We should have a tutorial on that huh.
bgruening
@bgruening:matrix.org
[m]
Helena we had a cvmfs test role under usgegalaxy-eu
For training I think?
Helena Rasche
@hexylena:matrix.org
[m]
yeah
it wasn't a proper tuto tho, just "here's a playbook, run it and it sets up cvmfs"
I think I want that into a tuto as well, we've gotten that question a number of times, "how do I setup cvmfs" and it's so easy so we should just write something step-by-step and standalone
it'd be a decent test for the automated video generation, too.
noceto pierre-antoine
@Noceto_PA_twitter
High everyone ! just a little question because i don't understand everything on the support :/
How can I upgrade my account quota ?
10 replies
David Hong
@hong7734_gitlab
I have started to run the RNAseq QC (FASTQ Groomer) step yesterday but it is still running. It wasn't so slow like this before. Do you know why this is happened? Should I contact our server management guy?
3 replies
dilipgosar
@dilipgosar

Hi, I am having trouble running goseq . I have pasted the error. Warning message:
In pcls(G) : initial point very close to some inequality constraints
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:dplyr’:

combine, intersect, setdiff, union

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:dplyr’:

first, rename

The following object is masked from ‘package:geneLenDataBase’:

unfactor

The following objects are masked from ‘package:base’:

expand.grid, I, unname

Attaching package: ‘IRanges’

The following objects are masked from ‘package:dplyr’:

collapse, desc, slice

Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:dplyr’:

select

Using manually entered categories.
Error in [.default(summary(map), , 1) : incorrect number of dimensions
Calls: run_goseq ... goseq -> reversemapping -> [ -> [.table -> NextMethod

Ideally goseq in galaxy ask for ensembl gene id, entrez id or gene symbol. I have downloaded gtf file from UCSC it does not contain any of this. it has only refseq ids. I am getting error from gtf file downloaded ensembl since it does contain chr name for chromosome. I like to know how you can help me.