Bianca_Singularity

Singularity container for running basic Bioinformatic analysis on the Bianca cluster.

The environment contains

Abyss

ARCS

bedtools

BESST

BCFtools

biobambam

bwa

Canvas

CD-hit

Cite-seq-count

ClustalO

cyvcf2

Delly

Emerald

ExpansionHunter

Fermi2

Freebayes

GATK 4

IchorCNA

Lumpy

Manta

minimap2

mummer

picard tools

pysam

pytabix

sambamba

samtools

sniffles	

Star

Star-fusion

SVDB

Tabix

TIDDIT

VT

WisecondorX

References are found in the /reference folder These references include:

Gencode GRCh38    : GRCh38.primary_assembly.genome.fa.gz
Gencode GRCh37    : GRCh37.primary_assembly.genome.fa.gz
ENSMBL Bonobo 1.1 : Pan_paniscus.panpan1.1.dna.toplevel.fa.gz
ENSMBL Pantro3    : Pan_troglodytes.Pan_tro_3.0.dna.toplevel.fa.gz
ENSMBL Gorilla4   : Gorilla_gorilla.gorGor4.dna.toplevel.fa.gz

reference fai and dict are available for all these references; transcript fasta and gene annotation gtf are available for the human reference genomes (Gencode). ENSMBL gtf files are available in the /reference/ENSMBL

Create the environment

The singularity environment is built using the following command

	sudo singularity build Bianca.simg Singularity

Or downloaded through the following command:

	singularity pull --name Bianca.simg shub://J35P312/Bianca_Singularity:0.0.2

Use the environment

In an interactive session, instead of loading modules, you run the  following:

	singularity shell Bianca.simg

now you have access to the conda packages within the Bianca.simg environment.

you may leave  the environemnt by typing exit.

in an sbatch script you may do the following:

    singularity exec Bianca.simg <command>

for instance, you may run nucmer using the following command:
    singularity exec Bianca.simg nucmer ref.fa contigs.fa

Edit the environment

Add more packages by editing Bianca_standard_env.conf. open the file using any text editor, and add your conda commands after line 26. you may need to create multiple conda environments within the singularity environment.