Hi there!
I installed samtools according to the instructions from here: https://gatk.broadinstitute.org/hc/en-us/articles/360041320571--How-to-Install-all-software-packages-required-to-follow-the-GATK-Best-Practices
I downloaded the samtools tar file version 1.11. Unpacked it with:
tar xvjk samtools-1.11.tar.bz2
Went to the samtools directory with
cd
And then
make
Added it to my path with:
export = PATH="$path/to/folder/:$PATH"
Opened a new shell, and ran
samtools
and I get the error:
samtools command not found
Does anyone know what I am doing wrong here? Thanks.
in export = PATH="$path/to/folder/:$PATH" replace "$path/to/folder/" by your actual path to the folder where are located your samtools binaries.
Even in this case the poster may get the same error after opening the new shell, because export command do not carry over. The OP will need to put this export command into .bashrc before opening the new shell, or use samtools in the same shell where the export command was issued.
Thanks for the replies. Even when I use the same shell, I get the same error. Any other ideas? Thanks.
Thank you so much for the help! I ended up editing the .bashrc and adding samtools to the path that way, and that worked!!! Working fine now.
yes I did do that I just didn't bother to put it in the post haha thx.
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That
exportcommand was local to the shell you had open. If you open another shell then you have toexportin that shell or add this permanently to your.bashrcor relevant shell file.BTW command should be