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  • Jan 31 2019 22:37

    bebatut on gh-pages

    Update on: Thu Jan 31 22:36:58 … (compare)

  • Jan 31 2019 22:00

    erasche on master

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

  • Jan 31 2019 22:00
    erasche closed #1237
  • Jan 31 2019 22:00
    erasche commented #1237
  • Jan 31 2019 21:33
    jmchilton synchronize #1237
  • Jan 31 2019 21:01
    erasche labeled #1239
  • Jan 31 2019 21:01
    erasche opened #1239
  • Jan 31 2019 21:00
    natefoo opened #1238
  • Jan 31 2019 20:56
    jmchilton opened #1237
  • Jan 31 2019 20:17

    bebatut on gh-pages

    Update on: Thu Jan 31 20:17:17 … (compare)

  • Jan 31 2019 19:44

    erasche on master

    fix typos Merge pull request #1236 from g… (compare)

  • Jan 31 2019 19:44
    erasche closed #1236
  • Jan 31 2019 19:44
    martenson opened #1236
  • Jan 31 2019 19:44

    martenson on martenson-patch-2

    fix typos (compare)

  • Jan 31 2019 19:23

    bebatut on gh-pages

    Update on: Thu Jan 31 19:23:39 … (compare)

  • Jan 31 2019 19:06

    Slugger70 on master

    import some notes fix username and 1 more (compare)

  • Jan 31 2019 19:06
    Slugger70 closed #1234
  • Jan 31 2019 19:04
    erasche review_requested #1234
  • Jan 31 2019 19:03
    erasche synchronize #1234
  • Jan 31 2019 19:03
    erasche unlabeled #1234
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
sorry
Helena Rasche
@hexylena:matrix.org
[m]
It's a known bug, we're working on fixing it
Helena Rasche
@hexylena:matrix.org
[m]
We will!
Anton Nekrutenko
@nekrut
@hexylena:matrix.org can I have some guidance here:
image.png
I'm not sure where to add these tags
Anton Nekrutenko
@nekrut
Ahh ... looks like workflow annotation issues. Updated. Will see what hapend
Helena Rasche
@hexylena:matrix.org
[m]
Glad you found it @nekrut , the comments also show up directly in the "files changed" interface but they're easy to miss, I wish there was a way to have our bot post proper "review comments" with suggestions, since we have the line numbers where things need to be changed.
I'll try and have a look at it today
Anton Nekrutenko
@nekrut
yes, all good @hexylena:matrix.org , thanks!
Ollie White
@Ollie_W_White_twitter
Hi all, does anyone have any recommendations for software to create and edit videos? I want to create a video to share how galaxy works with colleagues. Cheers
1 reply
Dannon
@dannon
I liked using https://obsproject.com/ for recording and https://www.openshot.org/ for editing. Both free and cross platform. A little bit of setup to get started, but they work really well.
Ollie White
@Ollie_W_White_twitter
Thanks @dannon I will check them out!
Dave B.
@davebx
I use avidemux for editing, but openshot looks a lot easier to use
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Just noticed that building the GTN site is not only slow, but also requires a lot of memory. Since the jekyll build seems to do its entire job in memory before finally writing to _site it took a whopping 1.6 GB before completing. Is there no other way with jekyll or am I just not aware of a build flag or something?
1 reply
Helena Rasche
@hexylena:matrix.org
[m]
are you building with citations? that is the slowest part

I use a command line

jekyll serve --port 4002 --trace --config _config.yml,_config-dev.yml --incremental --destination ./_site/training-material/ --skip-initial-build --livereload -H 0.0.0.0

which has several speedups:

  • config-dev prevents the slow citations
  • incremental only rebuilds changed pages
  • skip-initial-build starts serving immediately, and only builds once things change.