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Nolan Woods
@innovate-invent
@mvdbeek thanks!
Abigail
@Abigail32161234_twitter
Hello,
Hello,
Is there a limit on the number of columns that can be processed?
I am joining files, and they are getting cut off after column IU.
Nolan Woods
@innovate-invent
@Abigail32161234_twitter column IU?
Has anyone experienced an issue with Galaxy not being able to locate mercurial because for some reason the venv isn't active while installing tools?
uwsgi --yaml {{ paths.config }}/galaxy.yml --uid=1000 is how I am starting it, and the virtualenv path is in the uwsgi settings
Galaxy finds its dependencies otherwise
and I have confirmed the mercurial package is installed
Abigail
@Abigail32161234_twitter
@innovate-invent IU in excel... column 255
Nolan Woods
@innovate-invent
what program are you using to join?
Brad Langhorst
@bwlang
hi all - i’m having some trouble with the join tool after a recent upgrade… i see this error: ModuleNotFoundError: No module named 'galaxy'
i think i need to install a dependency in the cluster env, but not sure which one and why it’s not already there. Anybody seen this before? I tried creating the environment by running run.sh and letting it install all the dependencies. (my setup is a bit odd in that the galaxy node does not share the same conda environment as the cluster nodes)
Brad Langhorst
@bwlang
maybe this needs to be in the base environment?? can’t tell if galaxy env is activated or not for the join tool
Nicola Soranzo
@nsoranzo
Is it the Join two Datasets tool that comes with Galaxy? i.e. id join1
In 20.05 it gained this: <requirement type="package" version="19.9.0">galaxy-util</requirement>
So you need to install this via the manage dependencies admin UI
Brad Langhorst
@bwlang
ah - thanks nicola!
Nicola Soranzo
@nsoranzo
No problem! At every release update it's good to check for new unsatisfied dependencies for the embedded tools.
There's no clean way to deal with that for embedded tools unfortunately.
Nolan Woods
@innovate-invent
@nsoranzo does galaxy-util remove the need for a tool to be able to see the galaxy root?
Nicola Soranzo
@nsoranzo
Most tools don't need to see the Galaxy root, it's the metadata setting that needs it.
Nolan Woods
@innovate-invent
tool containers still need to mount the galaxy root then?
Nolan Woods
@innovate-invent
I am having trouble with galaxies management of its venv. It doesn't activate it when running the upload tool in a container and it isn't active when trying to run mercurial during tool installation
Márcia Correa de Carvalho
@MrciaCorreadeC1_twitter
Hello everyone,
I have a life in galaxy. I am exploring the dice, using a PCA, how do I define a PC number?
Nolan Woods
@innovate-invent
Hi @MrciaCorreadeC1_twitter. I am not sure I understand what you need. Can you restate your problem with more context?
galaxybot
@galaxybot

[unknown]
transcriptsToOrfs [Uncategorized]
Hi!

I’m newbie of galaxy tool.

nice to meet you.

i have to analysis RNA-seq data using transcriptsToOrfs

so i search on google and go to…

galaxybot
@galaxybot
[unknown]
Coursera Genomic Data Science [Uncategorized]
I’m trying to use the Join tool as demonstrated in the course (they refer to previous Galaxy version). Although I’m specifying column 4 (exo…
supi
@supi31313082_twitter
Hi I need help how to get the linkage maps. I was cloupmap EMS VARIANT BUT I DON'T KNOW WHICH IS THE OUTPUT FILE. PLEASE HELP
Pablo Moreno
@pcm32
Is it advisable to add a directory that contains a many subdirectories and files, not all of them datasets, to the data library? I see that it takes very long and nothing seems to happen… no indications in logs and so on of errors neither...
Björn Grüning
@bgruening
how many entries?
if you go to sequence, you will see a few folders with many thousands of elements and its slow to load
thats why we patched in a spinner
new more ractive library is currently developed here: galaxyproject/galaxy#9905
Pablo Moreno
@pcm32
….mmm… it is a 38 TB disk with 32 TB used… so probably a lot...
does it try to assign datatypes to every file it see?
otherwise, how would you give access to admins to large disks from the UI?
Björn Grüning
@bgruening
yes, it does a "upload" with metadata detection
and if you have not specified to-symlink-data it will actually create a copy
Pablo Moreno
@pcm32
yeah, probably unfeasible then for such an amount of data...
Björn Grüning
@bgruening
link them
Pablo Moreno
@pcm32
yes I did put the symlink option...
Björn Grüning
@bgruening
and how many single files are they?
Pablo Moreno
@pcm32
probably too many to count….
in the order of 10 thousands or 100 thousands I would expect
it is also very diverse
there is also software in there, workflow files, you name it...
I guess that we will need a more granular approach and cherry pick only certain directories.
Björn Grüning
@bgruening
yeah, that sounds more reasonable :)
galaxybot
@galaxybot
[unknown]
No difference in peaks between ChIP sample and control / Bad background noise on control for ChIP-Seq / Weak enrichment for ChIP-Seq [usegalaxy.org support]
am a complete newbie to bioinformatics. Currently doing ChIP-Seq on samples looking for enrichment at sites for increased/decreased expressi…