Error running convert-variation

[bsaylor23]

HI I have installed rsat using conda and I am getting the following error when I try to run the convert-variations script

Use of uninitialized value $ENV{"RSAT"} in concatenation (.) or string at /home/saylorb/miniforge3/envs/RSAT_env/bin/../share/rsat/perl-scripts/convert-variations line 159.
Can't locate LWP/Simple.pm in @INC (you may need to install the LWP::Simple module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 /usr/share/perl/5.34 /usr/local/lib/site_perl /home/saylorb/miniforge3/envs/RSAT_env/bin/../share/rsat/perl-scripts/lib/ /perl-scripts/lib) at /home/saylorb/miniforge3/envs/RSAT_env/bin/../share/rsat/perl-scripts/convert-variations line 233.
BEGIN failed--compilation aborted at /home/saylorb/miniforge3/envs/RSAT_env/bin/../share/rsat/perl-scripts/convert-variations line 233.

Is RSAT an environmental variable I was supposed to setup? It doesn't currently appear in my environment. I've checked and it looks like conda did install LWP::Simple.

I would appreciate any help you may be able to provide

[eead-csic-compbio]

Hi @bsaylor23 , the conda version of RSAT is quite old, I haven't tested it for a long time. Did you follow the instructions at https://rsa-tools.github.io/installing-RSAT/conda-install-rsat/bioconda-rsat-core.html ? Perhaps @jvanheld can add something to this.

Instead, the Docker container was recently updated and can be run as explained at https://rsa-tools.github.io/installing-RSAT/RSAT-Docker/RSAT-Docker-tuto.html, let me know if this helps, Bruno