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BlobTools

BlobTools is a Bioinformatics application that provides a modular command-line solution for analysis of genome data sets.

BlobTools can be installed with either conda or pip. As BlobTools has not been added to the Python Package Index, we recommend installing this application using the Conda method.

Installing with conda

Versions 1.0.1 and above are available in the Bioconda channel and may be installed by following the instructions below:

module load anaconda3
conda create -n blobtools
conda activate blobtools
conda install -c bioconda blobtools

Subsequent activation as part of a job:

module load anaconda3
conda activate blobtools

Installing with pip

BlobTools may be installed using pip inside a virtualenv by following the instructions below:

module load python
virtualenv ~/blobtools_env
source ~/blobtools_env/bin/activate

git clone https://github.com/DRL/blobtools.git ~/blobtools
cd ~/blobtools

# optionally checkout a specific version
# (replace VERSION with actual version / tag)
git checkout VERSION

pip install -r requirements.txt
pip install -e .

Virtualenv usage as part of a job:

module load python
source blobtools/bin/activate

Example jobs

Conda Serial job

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load anaconda3
conda activate blobtools

blobtools create -i assembly.fna \
                 -b mapping_1.bam \
                 -t blast.out \
                 -o my_first_blobplot

Virtualenv Serial job

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load python
source ~/blobtools_env/bin/activate

~/blobtools/blobtools create \
  -i assembly.fna \
  -b mapping_1.bam \
  -t blast.out \
  -o my_first_blobplot

References