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Using environments on perun

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**''

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''**

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

''**export PATH=/scratch2/software/anaconda/bin:$PATH**''

''**source activate nameofenvironment**''

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, to run albacore or porechop or nanostat or nanoplot

''**source activate python36-generic**''

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