This container runs a script which, when attached to any volume exporting a /home/bwa_user/bwa_indexed directory, allows you to add a publicly available fasta formatted reference genome to be used in a dmlond/bwa_aligner alignment. It then uses the bwa command to index the genome, and creates a samtools faidx index to be used to add the sequences for hits to a bam file when it is created.
The container can be run without an attached volume, and without arguments to get a list of requirements. Reference genomes are organized in the /home/bwa_user/bwa_indexed directory by build.
Small genomes should be indexed with the -i argument, while larger genomes should be indexed with the -b argument. Unzipped reference genomes should be zipped using the -z argument to save space. The bwa and samtools indices are created on the zipped genome.
example: this will create a dmlond/bwa_reference_volume named 'bwa_references', and add a Plasmodium falciparum reference genome to it, to be used in an alignment
sudo docker run --name bwa_references dmlond/bwa_reference_volume
sudo docker run dmlond/bwa_reference -i pf3D7_v2.1.5 ftp://ftp.sanger.ac.uk/pub/pathogens/Plasmodium/falciparum/3D7/3D7.version2.1.5/Pf3D7_v2.1.5.fasta -z