Below you will find the instructions about how to find and run software IF it is under CONDA. You should always check if the software you need is under conda as an outdated version of it may be in the environmental variables of the cluster. Since not all software available in perun can be run under an environment there are other places where you could check other_software_locations and if your software requires databases check databases_locations.

Perun has conda installed. Conda is a package and environment management system.
Conda installs, runs, and updates packages and their dependencies.
Conda creates, saves, loads and switches between environments.

to see the version of conda on perun

conda --version or conda -V

To see the list of all the environments on perun (it is very long!)

conda info --envs

The output should look like this at the top

# conda environments:
#
base * /scratch2/software/anaconda
2pg_cartesian /scratch2/software/anaconda/envs/2pg_cartesian
Quast-python2 /scratch2/software/anaconda/envs/Quast-python2
Subread /scratch2/software/anaconda/envs/Subread
Tophat /scratch2/software/anaconda/envs/Tophat
Transdecoder /scratch2/software/anaconda/envs/Transdecoder
Trimal /scratch2/software/anaconda/envs/Trimal
Trinotate /scratch2/software/anaconda/envs/Trinotate
Unicycler-python3 /scratch2/software/anaconda/envs/Unicycler-python3

The active environment is the one with an asterisk

To search the list you can do something like this

conda info --envs |grep blast
or
conda env list |grep blast ]

This will provide you with all the environments with the string blast in them
blast * /scratch2/software/anaconda/envs/blast
blast-legacy /scratch2/software/anaconda/envs/blast-legacy
blastalign /scratch2/software/anaconda/envs/blastalign
blastbesties /scratch2/software/anaconda/envs/blastbesties
crb-blast /scratch2/software/anaconda/envs/crb-blast
genblasta /scratch2/software/anaconda/envs/genblasta
genblastg /scratch2/software/anaconda/envs/genblastg
hs-blastn /scratch2/software/anaconda/envs/hs-blastn
igblast /scratch2/software/anaconda/envs/igblast
nanoblaster /scratch2/software/anaconda/envs/nanoblaster
rmblast /scratch2/software/anaconda/envs/rmblast
samblaster /scratch2/software/anaconda/envs/samblaster
ucsc-blasttopsl /scratch2/software/anaconda/envs/ucsc-blasttopsl

To activate or enter an environment

source activate name_of_environment

So

source activate blast

will place your session in the blast environment. You will notice that the prompt has changed to include the name of the environment like so

(blast) /home/curtisba

To deactivate an environment

source deactivate

To see the packages and dependencies associated with an environment

conda list (if you are already in an environment)

conda list -n nameofenvironment (if not in that environment)

(blast) /home/curtisba@perun6> conda list -n samblaster

# packages in environment at /scratch2/software/anaconda/envs/samblaster:
#
# Name Version Build Channel
libgcc 7.2.0 h69d50b8_2
libgcc-ng 7.2.0 hdf63c60_3
libstdcxx-ng 7.2.0 hdf63c60_3
samblaster 0.1.24 h2d50403_1 bioconda

SO, to invoke an environment in a qsub shell:

#!/bin/bash
#$ -S /bin/bash
. /etc/profile
#$ -cwd
export PATH=/scratch2/software/anaconda/bin:$PATH
source activate nameofenvironment [or conda activate nameofenvironment]
your command line
source deactivate

Some of the more common environments you might be interested in

source activate python36-generic (albacore, porechop, nanostat, nanoplot)
source activate rseqc+flye-python2 (flye)
source activate python27-generic (ABruijn)
source activate Unicycler-python3 (unicycler)
source activate smartdenovo-python2 (smartdenovo)
source activate nanopolish-python3 (nanopolish)
source activate canu-python3 (canu)
source activate busco

SO, before running albacore or porechop or nanostat or nanoplot

source activate python36-generic

You are already in the environment and do not know what to do next

1- invoke the executable command (see your software manual).

2- if no manual is available and you still don't know what executable to call:

let's say you want to use trnascan:
conda env list|grep 'trnascan'
trnascan-se /scratch2/software/anaconda/envs/trnascan-se
ls /scratch2/software/anaconda/envs/trnascan-se/bin/
then select your executable and directly invoke it within the environment:
tRNAscan-SE