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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
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    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
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    erasche review_requested #1234
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    erasche synchronize #1234
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    erasche unlabeled #1234
Helena Rasche
@hexylena:matrix.org
[m]
Some of this is in make serve-quick wm75 (Wolfgang Maier)
  1. Part of the problem is duplicated citations, I suspect. We have 900 citations, like 380 of these are unique (by citation key at least). We're looking at options to cut these down significantly, the original thought was making it easy to keep references associated with tutorials, but, we may switch to one big reference file.
  2. The citation module we use doesn't cache, and that doesn't help either.
Helena Rasche
@hexylena:matrix.org
[m]
the one person who improved the citation plugin (by using the jekyll cache) doesn't have an open PR, and I can't even find their fork. So, that's where we are on improving citations. The real solution is just compile without citations and your life will be better :)
Helena Rasche
@hexylena:matrix.org
[m]
and if you're that memory constrained, we can recommend building on gitpod which PvH has been using successfully when you're ready to see how your fork renders.
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Thanks Helena Rasche ! Yes, the spike in memory consumption happens only with a full build.
make build FLAGS="--config _config.yml,_config-dev.yml" is rather fast and memory-friendly.
I didn't know about --skip-initial-build before - really useful! With _site built already make serve FLAGS="--incremental --skip-initial-build" is a superfast way to get the server up and running.
Cameron Hyde
@neoformit
Hi all, I'm just beginning the journey on Interactive Tool development. Since there are no docs on this yet (aside from server administration) I thought I'd start working on a page for the dev track - if I chip away at it I should have something useful in a few months. Any thoughts on this? Is this on anyone else's radar? Just want to make sure we're not crossing swords before I put too much time into it.
4 replies
bgruening
@bgruening:matrix.org
[m]
@neoformit that's sounds great. I'm not aware of anything in that direction.
ping @yvanlebras do you know?
Ollie White
@Ollie_W_White_twitter
Hi all! Sometimes when I run a workflow I get a random error for one of the intermediate steps and it stops the rest of the workflow from running. Is it possible to resubmit the intermediate step that produced an error and allow the rest of the workflow to finish? At the moment I just delete all the files produced by workflow start again. I thought there might be a better way than this!
Dave B.
@davebx
yes, it should give you the option, when you select rerun, to replace the original job in the workflow and try again
Ollie White
@Ollie_W_White_twitter
@davebx thanks for letting me know, I have selected a job to re-run but I can't see the option to replace the job in the original workflow? Could you tell me where you look?
Simon Bray
@simonbray:matrix.org
[m]
@Ollie_W_White_twitter: when you rerun the tool, you should see an option like this above the Execute button
just make sure to select Yes
Ollie White
@Ollie_W_White_twitter
@simonbray:matrix.org this is perfect, thanks for sharing. I assume this icon will only appear if an intermediate job fails? Ironically all my jobs are running perfectly now, and I assume this is why I can't see this?
Simon Bray
@simonbray:matrix.org
[m]
yes, this option only appears either on failed jobs which are part of workflows, or which form part of a collection
Ollie White
@Ollie_W_White_twitter
@simonbray:matrix.org I'm looking forward to a job failing now... Thanks for the tip
Simon Bray
@simonbray:matrix.org
[m]
You're welcome!
Simon Bray
@simonbray:matrix.org
[m]
:point_up: Edit: yes, this option only appears on failed jobs which either are part of workflows, or which form part of a collection
Setareh
@Setareh24116772_twitter
hello everyone, I am pretty new to Galaxy and do not have enough bioinformatic information :D I want to add a history, but the + buttom is not there and when i go to gear buttom there is no option as create new :| dose anyone have a clue? Thank you in advance
2 replies
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
This should probably be a hint in the creating a new history snippet of the training material?
1 reply
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Agreed, that's a cleaner solution!
1 reply
Helena Rasche
@hexylena:matrix.org
[m]
90942958
@90942958
Hello! I am new to Galaxy. My account was created with a temporary password. I have to change the password otherwise the account will deactivate. I tried to go in User option to change but it says password change not supported. Do I need to write a script or do something to change the password?
Björn Grüning
@bgruening
Which Galaxy server are you using?
90942958
@90942958
Galaxy Australia
Björn Grüning
@bgruening
lets ping someone from Australia :) @Slugger70
Slugger70
@Slugger70
Hey there @90942958, do you remember your password or have you forgotten it? I can reset it for you if you need.
Setareh
@Setareh24116772_twitter
Hello everyone, I did an experiment with Nanopore gridion and now I have 266 FASTQ files, I want to do the mapping for it. I followed the tutorial but for uploading the data, I dont know how should I upload them? should I make all 266 files in to one Zip file and upload ? or do them seperately?
bgruening
@bgruening:matrix.org
[m]
@Setareh24116772_twitter: seperate. And then create a collection out of it.
You can also upload them via FTP
that is probably the most stable way
Setareh
@Setareh24116772_twitter
how with FTP?
Setareh
@Setareh24116772_twitter
@bgruening:matrix.org can you please tell me how to create a collection out of it? thank you so much
pvanheus
@pvanheus
is there a way to see how many times a GTN tutorial has been viewed?
is that enough?
90942958
@90942958
Hello @Slugger70
If you don't mind can show me the path on how to change the password, please? The password generated by one of my supervisor is temporary so I need to change it to keep my account active.
Slugger70
@Slugger70
Hey there @90942958, if you go to the User menu at the top of the Galaxy page, then select User Preferences, there is a link there to Change Password.
Ollie White
@Ollie_W_White_twitter
Hello, I have downloaded SRA data using "Faster Download and Extract Reads in FASTQ" which has worked but it has created a nested list that causes problems later on I think. See https://usegalaxy.eu/u/ollie_white/h/nested-list as an example history. I am able to use "flatten collection" to remove the nested list but then I have to use "apply rule to collection" to remove the concatenated names. This seems to work but I thought there might be a more eloquent solution?
roncoronimiguel
@roncoronimiguel
Hi everyone, I'm trying to run the GTN locally, following the tutorial's instructions. I can't get past the libxml2 issue, even after installing libxml2-dev. Specifically, the recipe for 'xmllint' fails because LD cannot find '-liconv'. I'm out of ideas. Any suggestions? thanks in advance. Miguel
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
It's probably this issue: galaxyproject/training-material#1655
I was expecting this to be fixed by galaxyproject/training-material#2605 though. Are you trying to build the latest version of the gtn?
roncoronimiguel
@roncoronimiguel
@wm75:matrix.org thanks! in the end, the only thing that worked was the hack suggested in galaxyproject/training-material#1655 (but had to remove the fix from galaxyproject/training-material#2605 from the Makefile). So at least in this case, the location of the libiconv is still an issue
90942958
@90942958
@Slugger70 Thank you! Its done
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
@roncoronimiguel: Hmm, not so great :(
but good to know you figured it out.
ehj000
@ehj000
Hi. I am going through the hands-on practicals for the upcoming SARS-CoV-2 Data Analysis workshop. There seems to be dead links in the practical “Using dataset collections”. The link to the datasets for the exercise gives a 404 Not found error.