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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

Helena Rasche

@hexylena:matrix.org

[m]

https://github.com/hexylena/git-gat/blob/main/templates/nginx/galaxy.j2#L55

Lucille Delisle

@lldelisle

Thanks I should better read git-gat.

pvanheus

@pvanheus

in the tutorial I'm writing at the moment I have an "Advanced" section on using the Rule Base Uploader instead of setting up collections manually. Is there a way to collapse this and only have it show if the reader clicks on something?

Saskia Hiltemann

@shiltemann:matrix.org

[m]

Make it a tip type box ?

pvanheus

@pvanheus

ok I'll have a look at how that renders...

Ana Sosa

@AnaSF_gitlab

Hello, can I ask if someone has gone through the Reference-based RNA-Seq data analysis training?

Saskia Hiltemann

@shiltemann

@AnaSF_gitlab go for it!

Ana Sosa

@AnaSF_gitlab

@shiltemann heh thanks, I'm on it :) I got an error and not sure how to proceed. so I'm wondering if someone is familiar with this training

Saskia Hiltemann

@shiltemann

A lot of people here are familiar with the training (and lots even helped write the tutorial), so if you describe your error I'm sure somebody can help you figure it out :) you've come to the right place for questions!

Ana Sosa

@AnaSF_gitlab

Oh ok! So I'm at the mapping point using the RNA STAR tool. The output gives an error that goes: Fatal INPUT FILE error, no valid exon lines in the GTF file: /srv/galaxy/shared/database/files/000/133/dataset_133966.dat
Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.

So I understand that the .gtf file used for gene annotation does not contain the gene names in the same format, therefore not being able to compare

How can I change the name of one of the docs?

Lucille Delisle

@lldelisle

Indeed, probably you used a gtf from ensembl. Can you copy paste here the first lines of your GTF file?

Ana Sosa

@AnaSF_gitlab

The format gets all weird but here it goes

chr3R FlyBase gene 722370 722621 . - . gene_id "FBgn0085804"; gene_name "CR41571"; gene_source "FlyBase"; gene_biotype "pseudogene";

Lucille Delisle

@lldelisle

This is compatible with your genome. Do you have lines where the third field is "exon"?

Ana Sosa

@AnaSF_gitlab

Yes, there are gene, transcript, exon, CDS, start_codon...

I used the link listed in the training to download it

Lucille Delisle

@lldelisle

Did you choose the right genome then?

Ana Sosa

@AnaSF_gitlab

The training says to choose Fly (Drosophila Melanogaster): dm6 Full, which is no longer listed

there are 2 other options but none of them avoids this error from appearing

Lucille Delisle

@lldelisle

Which galaxy are you using?

Ana Sosa

@AnaSF_gitlab

.be (is this the question?)

Lucille Delisle

@lldelisle

Yes exactly.

Ana Sosa

@AnaSF_gitlab

I didn't know the reference genomes depended on the location of the server

Lucille Delisle

@lldelisle

Unfortunately for the moment, they do.

Ana Sosa

@AnaSF_gitlab

Okey, so I'll always get an error on this point as long as I'm in galaxy.be

Lucille Delisle

@lldelisle

For the moment yes.

Except if usegalaxy.be decide to install the new genome to support this training...

Helena Rasche

@hexylena:matrix.org

[m]

that should be in CVMFS, are they not using that?

Ana Sosa

@AnaSF_gitlab

@lldelisle thanks a lot for helping me understand the origin of the problem <3

@hexylena:matrix.org I'm not sure what that is, sorry

Lucille Delisle

@lldelisle

You are welcome.

@hexylena:matrix.org I don't know... Or they did not linked it to STAR...

There are only 4 choices in the last verison of STAR...

@AnaSF_gitlab , if you can, I would suggest to switch to usegalaxy.eu to do your training.

Meanwhile I will report that this genome is needed to make it work.

Ana Sosa

@AnaSF_gitlab

I filled the bugfix report but didn't pinpoint the exact origin of the problem

dannahjavens

@dannahjavens

For the Circos Tutorial, what is the link that we can use to create a Circos Plot through Galaxy?

2 replies

Ana Sosa

@AnaSF_gitlab

Hey @lldelisle , I got the answer from the admin team and they have just added the UCSC version of the D. melanogaster genome, which is called "Drosophila melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)" :)

Lucille Delisle

@lldelisle

:thumbsup:

vajiha12

@vajiha12

Hey I'm new here...Can anyone help me with namd please?

Cristóbal Gallardo

@gallardoalba:matrix.org

[m]

Hi @vajiha12, what's your problem?

vajiha12

@vajiha12

Hi @gallardoalba:matrix.org i am trying to run md run using Google collab but i got an error
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CG3RC1 CG2R51 NG3C51 (ATOMS 4692 4694 4698)

Can you help me with this?

Cristóbal Gallardo

@gallardoalba:matrix.org

[m]

Perhaps @chrisbarnettster or Simon Bray can help you.

vajiha12

@vajiha12

Ok thanks

Dave Clements

@tnabtaf

Hi All, just a reminder that all registration for GCC2021 closes in 2 hours. https://www.vibconferences.be/events/gcc2021-virtual-edition And Training Week starts Monday.

Rachel Rios

@rachelrios

Hey, how would I flag a spelling mistake? I don't think that calls for a whole bug fix in github.

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