This is an old revision of the document!
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