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
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.
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.
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?
I see the icon, it just doesn't work. I'll track it down
Nolan Woods
@innovate-invent
thanks!
Jeevan Karloss
@ajkarloss
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.
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?
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?