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  • Jan 31 2019 22:37

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    erasche on master

    Reports fix. Clear up issue in Galaxy docker… More reports fixes... and 1 more (compare)

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    martenson on martenson-patch-2

    fix typos (compare)

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Rachel Rios
@rachelrios

"Sigmoid activation function can be used both at the output layer and hidden layers of a multilayer network. They allow the network to model non-linear realtionships between input and output."

realtionships -> relationships

Helena Rasche
@hexylena:matrix.org
[m]
Hey @rachelrios ! If it's such a small fix, you can always just correct it yourself, it's really easy, every page in the GTN has an "Edit this page on GitHub" button under the Extras menu?
(Or just let us know here and we can absolutely do it.)
Rachel Rios
@rachelrios
Thanks! I will do so :)
darshanajoshi25
@darshanajoshi25
Hey
I am facing an issue in "RNA-seq genes to pathways" training session. When I performed the EGSEA it shows me an error, although all the parameters are correct. Can someone help me with this problem I am facing?
Björn Grüning
@bgruening
@darshanajoshi25 what is the error?
5 replies
bgruening
@bgruening:matrix.org
[m]
@tnabtaf: new training: galaxyproject/training-material#2689
ifubar (ross lazarus)
@ifubar:matrix.org
[m]
@darshanajoshi25: Please see https://galaxyproject.org/issues/ - look for the bug icon! thanks!
1 reply
in this tutorial, in Get.groups tool, the groups "Mock" is not getting selected. Can anybody please help me?
v888888
@v888888
I'm having a problem running "Filter, Plot and Explore Single-cell RNA-seq Data". When I get to "Markers - cluster" file and "Markers - genotype". I get empty tables, that just have the headers saying "cluster ref rank genes scores logfoldchanges pvals pvals_adj". The Scanpy PlotEmbed Tool: fail to run. I repeated all tutorial twice and always get the same error. What I am doing wrong?
fct04
@fct04
Hi, for the tutorial "From Peaks to Genes," why do we only keep 10kb downstream of the transcription start site rather than comparing the peak regions to the promoter region + the whole gene? Is the entire 12kb length considered the promoter region (I thought promoters were much shorter than that generally)? Or is it known that the protein only binds to that part of the gene? Thank you!
Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
Hi @fct04, it considers a 12kb region surrounding the transcription start site because according the original paper that region accounts for 50% of the Chip-seq peaks (it allows to simplify the analysis). This region includes the proximal region of the promoter (2kb) and a 10 kb upstream region which includes the 5' UTR (whose extension is quite variable in eukaryotes) and a fraction of the coding region.
fct04
@fct04
@gallardoalba:matrix.org thank you so much for your answer! That makes sense.
Preenon Bagchi
@PreenonBagchi_twitter
Can anybody help in providing links/database for getting fungal genome analysis (ITS analysis)?
saharalshareef
@saharalshareef:matrix.org
[m]
Hi, I try to analyze 16s Metagenomic data by following steps in 16S Microbial Analysis with mothur tutorial. i cant continue because good.fasta output from Screen.seqs is empty. and bad.accnos show table contain sample name 1 repeated 1000x time. i dont know how to continue with erorr in Unique.seqs on data 362: fasta.......what should i do?
saharalshareef
@saharalshareef:matrix.org
[m]
if the good.fasta empty and bad.fasta have 1.900.000 line created using the Screen.seqs that is mean all my seq data are bad?!!!!
1 reply
jaredbernard
@jaredbernard
Does anyone know what would cause Maker to recover far fewer buscos in the annotations (~2%) than the assembly or transcriptome have (~98% each)? I used both Augustus and SNAP predictors trained from 1st round, and then again from 2nd round. I used the Uniprot/Swissprot protein omnibus, as it worked slightly better than the proteome of a relative. I've heard that Augustus can be trained from the buscos, but I don't see how that could be done in Galaxy. Sorry for cross-posting with Galaxy Help.
Anton Nekrutenko
@nekrut
@hexylena:matrix.org @shiltemann are guys aware of a reasonably new tutorial that features group tags?
2 replies
Helena Rasche
@hexylena:matrix.org
[m]
last updated may4 2021
Helena Rasche
@hexylena:matrix.org
[m]
Yeah absolutely ok. That URL should be stable @nekrut !
pvanheus
@pvanheus
hello folks - my "make serve-gitpod" is giving me an error Liquid Exception: undefined method[]' for nil:NilClass in /workspace/training-material/_layouts/tutorial_hands_on.html` - has anyone seen this?
Saskia Hiltemann
@shiltemann:matrix.org
[m]
used to see that a lot when invalid contributors were used, but I thought helena fixed that a while ago, could it be that?
Helena Rasche
@hexylena:matrix.org
[m]
is your branch up to date?
pvanheus
@pvanheus
let me merge from upstream
Helena Rasche
@hexylena:matrix.org
[m]
took me a bit to figure out gitpod was launching from my old master branch.
rather than main
Faezeh Ghazvini
@f_ghazvini_twitter
Hi,
I am currently trying to use RNA STAR to do mapping. At first I uploaded the Homo_sapiens.GRCh38.90.gtf.gz from ensemble and the run the RNA STAR, however I get the error below:

Fatal INPUT FILE error, no valid exon lines in the GTF file: /data/dnb03/galaxy_db/files/9/f/b/dataset_9fb5c4a8-dbc8-4ebd-a0a4-13b2add7a978.dat
Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.

Jul 08 16:53:23 ...... FATAL ERROR, exiting

gzip: stdout: Broken pipe

gzip: stdout: Broken pipe

How can I solve the problem?
Helena Rasche
@hexylena:matrix.org
[m]

Hi @f_ghazvini_twitter , have you read the error message and checked your GTF and fasta files?

Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file

Faezeh Ghazvini
@f_ghazvini_twitter
yes in GTF file there isnt chromosome naming. I dont know how to fix this part
Faezeh Ghazvini
@f_ghazvini_twitter
I found the solution. The problem is that I uploaded Homo_sapiens.GRCh38.90.gtf.gz from ensemble and this file doesnt include the annotation. So I upload gencode.v38.annotation from GENECODE and it works.
pvanheus
@pvanheus
hey GTN folks: a recent update on the training-material repo caused me a bit of a hickup on Gitpod: to push to the Github Actions workflows you need to have "workflow" scope permissions. On Gitpod this was this issue: gitpod-io/gitpod#984
The solution is to go to your integrations on https://gitpod.io/integrations and make sure that your Github integration has workflow scope. The error message that you will see if this is not the case is: "refusing to allow an OAuth App to create or update workflow .github/workflows/ci-libs.yml without workflow scope" (the specific path in .github might differ)
pvanheus
@pvanheus
on Gitpod now I'm getting "/workspace/training-material/_plugins/jekyll-topic-filter.rb:171:in block in topic_filter': undefined methoddowncase' for nil:NilClass (NoMethodError)"
when trying to make serve-gitpod
oh, seems to have been caused by a typo...
Ollie White
@Ollie_W_White_twitter
Hi all, I have quite a specific question regarding using Novoplasty to assemble chloroplast genomes. I can get the program to run successfully with the example data provided here https://github.com/ndierckx/NOVOPlasty/tree/master/Test%20datasets/Chloroplast%20assembly but it looks like some of the output is missing in galaxy. Specifically, when I run it using the command line application, I get two files called 'Option_1_test_chloro.fasta' and 'Option_2_test_chloro.fasta', which are the two alternate assemblies with differing orientation of one of the contigs. When running the job I have made sure to include all output file options. I have made a workflow accessible here https://usegalaxy.eu/u/ollie_white/w/testing-chloroplast-assembly-novoplasty if anyone is interested. I am relatively new to Galaxy so apologies if I have missed something straightforward. Cheers, Ollie
1 reply
Midsummer723
@Midsummer723
HI , when I use the RStudio on Galaxy at https://usegalaxy.eu/?tool_id=interactive_tool_rstudio . I try to install the Seurat package, because I will use some more modified function. But I failed to install the "Seurat". (ERROR: dependencies ‘leiden’, ‘png’, ‘reticulate’ are not available for package ‘Seurat’). The package 'png' cannot be installed.
Faezeh Ghazvini
@f_ghazvini_twitter
Hi,
I am currently trying to use featurecounts and for some samples assigned percent are less than 50. can I use the samples which assigned percent are less than 50?
1 reply
Afif Pranaya Jati
@afifpj_twitter
Hello, I am currently practicing Reference-based RNA seq data analysis https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#visualization-of-the-expression-of-the-differentially-expressed-genes, but I could not find Read Distribution tool on the tools panel, what should I do?
3 replies
akankshabafna
@akankshabafna
@bgruening @gmauro:matrix.org @beatrizserrano My jobs have stopped due to lack of disk space. I have filled the quota request form and also emailed the same but have not received any reply. Please can you help.
Björn Grüning
@bgruening
@akankshabafna it does not help if you ask the same question in 3 channels :(
akankshabafna
@akankshabafna
@bgruening .. Apologies for the same, I was not sure which channel to post.
Ollie White
@Ollie_W_White_twitter
image.png
2 replies

Hi all, I am trying to import data into an interactive Rstudio session using gx_get(). I can open Rstudio no problem but I seem to be having an issue with the gx_get command. Below is the command

> gx_get(350)
sh: 1: /usr/local/bin/get: not found
[1] "/import/350"
Warning message:
In system(command) : error in running command

Also attached is a screen grab of the file I am trying to read into R

Should also have mentioned, I am using https://usegalaxy.eu/
Björn Grüning
@bgruening
@akankshabafna we are working on that