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  • Jan 31 2019 22:37

    bebatut on gh-pages

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

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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.
Björn Grüning
@bgruening
@ehj000 you mean a link on the website of the training?
ehj000
@ehj000
Also, there is a glitch in the course program Day 3. Variant calling practical is listed twice, but the link to the second listing seems correct (automating workflows)
Björn Grüning
@bgruening
Ah, ok. Yes we have an updated version of that tutorial
if you have time please check again this tutorial in 15min
@ehj000 these are actually 2 different trainings
one using the Galaxy GUI
and one using the Command Line Interface to schedule Galaxy workflows
the GUI link is still in preperation, Wolfgang is recording the video as we speak
Thanks a lot for checking!
ehj000
@ehj000
Yes, I can import the files through the links. Thank you
Björn Grüning
@bgruening
Cool, thanks!!!
Setareh
@Setareh24116772_twitter
hey everyone, which mapping tool you recommend for mapping long read data from nanopore?
Setareh
@Setareh24116772_twitter
guys , I have large number of single reads from nanopore, they are not paired and I want to make a dataset collection . in the tutorial it is recommending to pair them while my data are single reads. what should I do?