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  • Jan 31 2019 22:37

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

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

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    fix typos (compare)

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Helena Rasche
@hexylena:matrix.org
[m]
try setting the other vars? ftp_upload_site? maybe one of those triggers it
Lucille Delisle
@lldelisle
OK
Helena Rasche
@hexylena:matrix.org
[m]
yeah I think that'll do it
Lucille Delisle
@lldelisle
Yes
It worked.
I think the doc needs to be updated because it is misleading.
1 reply
Helena Rasche
@hexylena:matrix.org
[m]
$ curl --silent https://gat-79.be.training.galaxyproject.eu/api/configuration -k | jq | grep ftp
  "ftp_upload_site": null,
the only ftp var in the configuration dict is ftp_upload_site, and I only see ftp_upload_site in the client dir
very misleading!
Lucille Delisle
@lldelisle
Yes
Helena Rasche
@hexylena:matrix.org
[m]
perfect :)
Lucille Delisle
@lldelisle
I am so happy that I managed to make it work... Thank you so much for the help
1 reply
Helena Rasche
@hexylena:matrix.org
[m]
not sure if you're familiar with how the config schema has changed in recent years, but in case anyone else isn't, now we update lib/galaxy/webapps/galaxy/config_schema.yml and run make config-rebuild to keep galaxy.yml.sample up to date.
Lucille Delisle
@lldelisle
I am absolutely not. Thanks
Helena Rasche
@hexylena:matrix.org
[m]
@lldelisle: this tutorial looks fantastic, I did not expect this!
I'll review it today then
"first version", pff, this is basically mergeable as is :)
Lucille Delisle
@lldelisle
I feel like I am filling this chat... Sorry.
Why the tools are clickable from GTN in usegalaxy.eu/org/.org.au and not .be/my local instance? Is there a variable to set?
Helena Rasche
@hexylena:matrix.org
[m]
no worries
it should be mentioned at the bottom of the frame "Click to run unavialble" or so
you need to setup some proxying for it to work
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?