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Can't download jar for eQTL analyzer #660
Description
I am trying to download the latest build (jar) for the eqtl analyzer code (https://github.com/molgenis/systemsgenetics/wiki/Discovery-of-hidden-confounders-of-QTLs). But the link to the last build does not work. Any help would be greatly appreciated.
Activity
PatrickDeelen commentedon Jun 13, 2023
Thank you for your interest. If you like I can provide a build. However, I would recommend having a look at our most recent and much more advanced effort to identify context dependent effects: https://www.biorxiv.org/content/10.1101/2022.07.28.501849v1
BennyStrobes commentedon Jun 13, 2023
Hi,
I appreciate you sharing your newer work. Very interesting.
It would be great, though, if you could share the build for the older work.
Ben
PatrickDeelen commentedon Jun 14, 2023
Sure, you can download it here: https://jenkins.harmjanwestra.nl/job/UMCG_SystemsGenetics/9/nl.systemsgenetics$eQTLInteractionAnalyser/artifact/nl.systemsgenetics/eQTLInteractionAnalyser/1.2-SNAPSHOT/eQTLInteractionAnalyser-1.2-SNAPSHOT-jar-with-dependencies.jar
BennyStrobes commentedon Jun 14, 2023
Thanks Patrick. That worked for me. I get an error when I try to run the code on my data. I'm using the following command:
'java -Xmx80g -jar ${proxy_gene_jar_file} -i ${proxy_gene_input_data_dir} -o ${proxy_gene_interaction_eqtl_results_dir} -n 1 -pc 5 -ncn -nt "1"'
I get the following error message.
The data seems to load in fine as it has the correct number of samples, genes, and covariates. Any help would be greatly appreciated? Do you have a working data set/or toy data set that you know works with this code?
BennyStrobes commentedon Jun 14, 2023
Thanks Patrick. That worked for me. I get an error when I try to run the code on my data. I'm using the following command:
'java -Xmx80g -jar ${proxy_gene_jar_file} -i ${proxy_gene_input_data_dir} -o ${proxy_gene_interaction_eqtl_results_dir} -n 1 -pc 5 -ncn -nt "1"'
I get the following error message:
The data seems to load in fine as it has the correct number of samples, genes, and covariates. Any help would be greatly appreciated? Do you have a working data set/or toy data set that you know works with this code?
PatrickDeelen commentedon Jun 19, 2023
We had a quick look but the old code proved to be a bit of challenge. We stopped using it because with Picalo we now have a much better tool to identify contexts and celltype dependent effects for eQTLs.
Regardless, I understand that you would like to us our published method instead of a preprint. We will have a closer look and hope to get back to you later this week.