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Helena
@hexylena:matrix.org
[m]
you might need to npm -i
M Bernt
@bernt-matthias:matrix.org
[m]
Thanks for the tip .. but
npm ERR! Package x11 was not found in the pkg-config search path.
npm ERR! Perhaps you should add the directory containing `x11.pc'
npm ERR! to the PKG_CONFIG_PATH environment variable
npm ERR! No package 'x11' found
npm ERR! Package xi was not found in the pkg-config search path.
npm ERR! Perhaps you should add the directory containing `xi.pc'
npm ERR! to the PKG_CONFIG_PATH environment variable
npm ERR! No package 'xi' found
npm ERR! Package xext was not found in the pkg-config search path.
npm ERR! Perhaps you should add the directory containing `xext.pc'
npm ERR! to the PKG_CONFIG_PATH environment variable
npm ERR! No package 'xext' found
npm ERR! gyp: Call to 'pkg-config --libs-only-L --libs-only-other x11 xi xext' returned exit status 1 while in angle/src/angle.gyp. while loading dependencies of binding.gyp while trying to load binding.gyp
npm ERR! gyp ERR! configure error
Actually I just wanted to have a pdf version of the latest versions of the transcriptomics tutorials
Would be cool to have the possibility to download this somewhere, or?
1 reply
Helena
@hexylena:matrix.org
[m]
opening the URL and doing ctrl-P is more or less equivalent to what's going on in the backend for the pdf generation, I can recommend this in the interim
You can also use chromium --headless --disable-gpu --print-to-pdf=file1.pdf https://.... if you need to automate it.
If there was more demand for PDFs, absolutely we could add this! But you're the first person to try and build PDFs since years so, I have the feeling the demand is relatively low.
M Bernt
@bernt-matthias:matrix.org
[m]

Sure. .. How then about printing the webpage with all boxes unfolded :)

Maybe galaxyproject/training-material#3798

Helena
@hexylena:matrix.org
[m]
one sec we have that
?expand-all=true
should do it
but maybe I didn't update that for the New Boxes
nope
i'll make a PR, maybe you can merge it M Bernt
galaxyproject/training-material#3844 another rarely used feature, thanks for finding that bug :)
M Bernt
@bernt-matthias:matrix.org
[m]
Thanks. Technically I can merge I guess, can we break anything? .. then I would be hesitant to merge since i have no idea of this :)
Helena
@hexylena:matrix.org
[m]
please merge it
it will not break anything
the failure mode is the feature continues to not work
nothing else can go wrong since the GTN is very JS light (intentionally)
M Bernt
@bernt-matthias:matrix.org
[m]
Thanks @shiltemann :)
M Bernt
@bernt-matthias:matrix.org
[m]
Excellent. Already working.

What do you think about removing the pdf creation docs from the tutorials:

or maybe replace it by this ?expand-all=true trick?

tiagodragonetti
@tiagodragonetti_twitter
hello
I`m trying to help my wife in her job, and I need some help to make a Volcano Plot. I got 2 different DNA in GEO, with the extension fastq and upload to galaxy, but the tutorials said to convert to tubular and this option dont appear to me. Do you guys know some tutorial with the way to do this volcano plot?
bgruening
@bgruening:matrix.org
[m]
@tiagodragonetti_twitter: you can not simply convert a fastq file into a tabular for plotting. There are a lot of different ways how you need to map your sequences to a reference genome, than all peaks or count reads and all of that is dependent on your scientific question.
People spent days and weeks to that, with various parameter settings and tools.
You will find a lot tutorials in our training material how to do that, but you need to learn more about the type of data that you have. What the scientific question is and then pick a tutorial.
Michael
@mchlou
Hello, I am having problems with my assembly. after doing metaSPADES I tried to visualize the assembly graph using Bandage both bandage graph and info. However, all metrics are showing 0 value even if there are scaffolds and contigs assembled. Mapping with BWA-MEM2 and filtering unaligned reads also returns nothing. I hope someone can help me figure out what is happening. Here is my history https://usegalaxy.eu/u/mike_lou/h/de-novo-assembly-metaspades-2
Saskia Hiltemann
@shiltemann:matrix.org
[m]

Hi All!

We are happy to announce that the next edition of the GTN Smörgåsbord training event will take place on May 22-26, 2023! 🎉

It will once again be free, online, self-paced, and choose-your-own-adventure style. It will feature all the content of previous editions, plus lots more!

The preliminary program can be found on the course website. (Several modules are still in development, so check back regularly for the updated program!)

Registration is now open!

Hope to see you all in May,

Saskia & Helena
on behalf of the GTN community

@room

wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Ha, Waterman butterfly! So that's why Helena has spent her time on that subject! Very nice :-)
Helena
@hexylena:matrix.org
[m]
it's objectively the best map projection
I'm still trying to get a working choropleth of it but it's painful :|
There's a nice Cahill projection as well, that has APAC centered which I like
but that's even rarer
I ended up settling for a Goode Homolosine in the tiaas paper because it was so impossible 😭
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Waterman butterfly splits Antarctica :( otoh climate change is going to simplify this issue in the future.
Helena
@hexylena:matrix.org
[m]
hahahah
splits a bit of greenland but, also solved in the future
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
fancy!
Helena
@hexylena:matrix.org
[m]
unfortunately none in D3 currently, and the one that is, is difficult to use as a choropleth (I really do not get the mess d3 has made of their modules across versions. Half wants 3 half wants 4)
tcwarner
@tcwarner
I am pretty new to this so sorry if this is a dumb question. I am running fill peaks and the function has been stuck on "This job is waiting to run" for 20 minutes. Is there a way to make sure it runs?
bgruening
@bgruening:matrix.org
[m]
On which server are you?
tcwarner
@tcwarner
How do you tell? I am in northeast USA
tcwarner
@tcwarner
It looks like some of the ones that did run were on Ivy Bridge/Sandy Bridge
tcwarner
@tcwarner
It does seem that it's specifically fill peaks that is not running. Everything else takes less than a minute