forrestzhang/docker-bcbio

Docker pull

USE

Load and download reference genome

docker run   -e BCBIO_USER=$USER -e BCBIO_UID=$UID -v LOCALDIR/genomes:/home/bcbio/genomes -v LOCALDIR/data:/home/bcbio/data -v LOCALDIR/config:/home/bcbio/config  -v LOCALDIR/galaxy:/home/bcbio/galaxy bcbio-test:t1 bcbio_nextgen.py upgrade --genomes TAIR10 --aligners bowtie --aligner bwa

genome files will be saved to LOCALDIR/genomes, for example. If you set LOCALDIR as /home/forrest/Docker/bcbiodata, the genome files will be saved to your local dir /home/forrest/Docker/bcbiodata/genomes .

Build custom genomes

Build a rice TIGR7 genome.

pwd
/home/forrest/Docker/bcbiodata

Download genome fasta file.

mkdir data
cd data
wget  ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.con
wget ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.gff3

Build bwotie2 star seq index

docker run   -e BCBIO_USER=$USER -e BCBIO_UID=$UID -v /home/forrest/Docker/bcbiodata/genomes:/home/bcbio/genomes -v /home/forrest/Docker/bcbiodata/data:/home/bcbio/data -v /home/forrest/Docker/bcbiodata/config:/home/bcbio/config  -v /home/forrest/Docker/bcbiodata/galaxy:/home/bcbio/galaxy bcbio-test:t1 bcbio_setup_genome.py -f /home/bcbio/data/all.con -g /home/bcbio/data/all.gff3 --gff3 -i bowtie2 seq -n Rice -b TIGR7

Download ChIP-seq reads

mkdir /home/forrest/Docker/bcbiodata/data/cenH3/input
cd /home/forrest/Docker/bcbiodata/data/cenH3/input
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR975/SRR975442/SRR975442_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR975/SRR975442/SRR975442_2.fastq.gz

Create YAML file

fc_data: '101215'
fc_name: 'cenH3'
upload:
  dir: ../final
details:
  - analysis: chip-seq
    genome_build: TIGR7
    files: [/home/bcbio/data/cenH3/input/SRR975442_1.fastq.gz, /home/bcbio/data/cenH3/input/SRR975442_2.fastq.gz]
    description: 'Rice cenH3 ChIP-seq'
    algorithm:
      aligner: bowtie2
      trim_reads: read_through
      adapters: [truseq]