How to use GCTA on the RAP
Hi all,
I am looking to run conditional analysis via GCTA on the RAP. However, I'm not sure how to best run GCTA.
At the moment I've got a setup where on the RAP I run an RStudio workbench and install GCTA there. However, I then need to access the bfiles for most of the chromosomes, which even with downsampling to 5000 people is 276GB, so I'm hesitant to download that to my RStudio instance.
Is there another way I can use GCTA? Thank you for any help!
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4 comments
I believe GCTA is available as a bash script. You could run it this way without downloading the plink files to your instance. https://yanglab.westlake.edu.cn/software/gcta/#Overview
Thank you for your reply and for your help. Do you know where can I find the bash script? I'm only able to see downloadable zip files with executables, or on their github the source files in c++. With the bash script would this be something I'd run on my local computer and submit as a job via dx and swiss army knife?
Hi, I'm interested in the same. Did you manage to find a bash script or another way of running this please?
I managed to get GCTA running by uploading the gcta64 executable to RAP and then call it using swiss-army-knife
dx upload /home/dvandenberg/storage/software/gcta64 --dest software/gcta64
dx run swiss-army-knife -iin=software/gcta64 -iin=reference/1kG_phase3.HM3.SNP_loading.log -iin=reference/1kG_phase3.HM3.SNP_loading.pcl -iin -icmd="chmod +x gcta64 && ./gcta64 --version" --instance-type mem1_ssd1_v2_x8 --name check_gcta -y
Also possible via webinterface, but if you set dx-mount-all-inputs to true make sure to copy gcta to $HOME first because otherwise it's read only.
cp gcta64 $HOME/gcta64 && chmod +x $HOME/gcta64 && $HOME/gcta64
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