Problems installing GATK
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8 months ago

Hello everyone, I need your help with an installation. I've been trying to install GATK in a computer with Ubuntu. I've tried it with conda so it has it's own environment (using this 1) but it seems like the program only runs properly if I'm in the same directory as the GATK folder but not in others, so there's no point of having a conda environment. I also tried to install it without conda (following this 2) but I got stucked in the fifth step and couldn't stablish the path. I would appreciate any help you could gave me with this program, I've never used it. Thanks.

conda ubuntu gatk • 577 views
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What code are you running that results in the error after you install it with conda?

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Do not delete posts that have received feedback. Interact with the people that have invested effort into helping you, and work towards providing closure to your post.

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I'm sorry! It was a mistake. I didn't install it with conda but I tried installing it "normally" (following the instructions from https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4) and it worked. How I solved it was by adding the path to GATK folder and the line "export path" to the end of the file in ~/.bashrc. Then closed and opened the terminal again, and now I can call gatk in any folder without problems. Thanks for the help.

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Please add the relevant part (I tried installing ... without any problems) as an answer and accept it so anyone facing a similar problem in the future can refer to your answer.

Also, for what it's worth, installing with conda should work fine. Given that GATK is usually a jar file, unless there's a wrapper of some sort, you'll need to invoke it as something like java -jar $GATK_JAR even when installed via conda. I've not tested it though, so I'm not sure that this is how it's invoked.

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