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elijaholux
@elijaholux:matrix.org
[m]
Does FastQC produce a chart or table when it finishes?
bgruening
@bgruening:matrix.org
[m]
Yes you get some plots in one outputs and raw numbers in the other
elijaholux
@elijaholux:matrix.org
[m]
How do I get the plots? I have the raw numbers
bgruening
@bgruening:matrix.org
[m]
It should be in your hostory
elijaholux
@elijaholux:matrix.org
[m]
Aside from the raw numbers the only other thing in my history is FastQC on Collection 9: Web Page: list of 80 html datasets
bgruening
@bgruening:matrix.org
[m]
That looks good
It's a html page with some plots
elijaholux
@elijaholux:matrix.org
[m]
okay, (1) can I open it and visualise the plots (2) is there a way to make it so that it shows the quality of all the reads in a single plot?
actually ignore the 1st part just done it
bgruening
@bgruening:matrix.org
[m]
Use multiqc ontop of the fastqc output
elijaholux
@elijaholux:matrix.org
[m]
got it
bgruening
@bgruening:matrix.org
[m]
Cool, happy research!
elijaholux
@elijaholux:matrix.org
[m]
is there anyway to convert tar files to a compatible fasta format? Im trying to use a ref genome for hisat2 but i cant use the ref genome in the format its in
bgruening
@bgruening:matrix.org
[m]
In which format is your reference genome
It needs to be in fasta. You can unpack it outside galaxy and upload it maybe
elijaholux
@elijaholux:matrix.org
[m]
its in .tar
okay ill try that
elijaholux
@elijaholux:matrix.org
[m]
nvm think i found the same ref genome in galaxy
elijaholux
@elijaholux:matrix.org
[m]
Hi, Hisat2 has stopped running halfway, ive tried to resume the job but its still grey. Some of the files have an error message saying 'file does not contain alignment data' , is there a way to resolve this?
dheeraj-04
@dheeraj-04
Hi All, I am planning to deploy Galaxy on Cloud platform (AWS), what is the best approach to do this? I'd really appreciate your thoughts/suggestions.
santiagorevale
@santiagorevale
Hi there! There's a package in conda-forge that it's not in https://depot.galaxyproject.org/singularity/. How can I make it available in there? Thank you very much in advance!
Nolan Woods
@innovate-invent
@santiagorevale just add the conda-forge package to the hash.tsv in https://github.com/BioContainers/multi-package-containers/ and it will be built
2 replies
aslangabriel
@aslangabriel
Hi，I'd like to install islandcompare workflow in my local galaxy instance. But the running process are stuck with the error of "Following tools missing: APPLY_RULES", which can't be found in toolshed resources.
dannon
@dannon:matrix.org
[m]
Galaxy Community Call: Machine Learning Toolkit in Galaxy, now: https://galaxyproject.org/events/2022-08-04-community-call/
pranhav16
@pranhav16
I just installed planemo using conda, but how do I access my local galaxy instance? I can't get into the tools directory of galaxy as I can't find it on my PC.
Nolan Woods
@innovate-invent
Does anyone know what happened to the ability to import the steps of a workflow into another workflow?
dannon
@dannon:matrix.org
[m]
Looks like a regression, let me see what happened.
image.png
@innovate-invent: That extra icon to the side there used to just plunk the steps right in, not as a subworkflow, right?
Nolan Woods
@innovate-invent
yes, I need the steps to import, not embed a subworkflow
@aslangabriel Hi, I am the IslandCompare author. I was just about to respond to your email.
APPLY_RULES is a tool that is included with Galaxy, if you have modified the tool_conf.xml you may have disabled it
Nolan Woods
@innovate-invent
@dannon:matrix.org this might be an issue with the toolbar overflowing, hiding the icon
image.png
side-scrolling is also disabled
dannon
@dannon:matrix.org
[m]
I see the icon, it just doesn't work. I'll track it down
Nolan Woods
@innovate-invent
thanks!
Jeevan Karloss
@ajkarloss
Screenshot 2022-08-09 at 09.46.51.png
I have added a tool to our local galaxy. The tool works fine individually. But when I try to add it to a workflow, it says "Loading Details" like in the picture. Any tips?
mmotoc
@mmotoc
Hello, I have added a job this morning, and it has yet to turn from grey to yellow (and there is no loading sign). How can I check if this job is in the queue? Any ideas?
20210930
@20210930
Hello, when I upload the file and click on the eye icon, there is no file shown in the central gamaxy panel. I wonder how can I view the dataset.
I do not know how to share an image here.
dannon
@dannon:matrix.org
[m]
What sort of dataset is this? The eye icon should be the standard display method. For a screenshot, you should be able to just paste it into the chat box in most clients.
1 reply
@ajkarloss: If I saw this hanging on the client I would expect a traceback somewhere -- can you check in the web browser dev console, and also on the server log at the time when this is loaded?
dannon
@dannon:matrix.org
[m]
Glad it works for you now. Importing can initially depend on upload speed of course, and then there's a brief job that runs afterward to determine metadata that may have been backed up briefly in the queue.
stonecoldhughes
@stonecoldhughes

Hi! I want a galaxy tool to accomplish this command line invocation:

docker run -it
--name container_name --rm container_image_name
conda run -n conda_env_name_in_container python script.py -c <user defined param> -o output_file.txt

where the tool needs to accept input from the user for the "-c" option above
I want to be able to run a "script.py" with the dependencies supplied by the container
however, I am not sure how to get the tool_configuration XML file to work alongside the ENTRYPOINT in the Dockerfile to accomplish this.
stonecoldhughes
@stonecoldhughes
How can I get galaxy to run a python script with a user-supplied argument in the container?