Use Case 1
Motivation: Laptop to server
You build a pipeline on your Macbook Air and everything works well on a minimal data set. Your full blown experiment requires multiple cores and you need to move the pipeline to a powerful server that runs Ubuntu. Your software may fail to run on Ubuntu, and getting that old shell script to run on the new server is cumbersome. The following approach avoids this problem.
Requirements
sudo docker build -t use_case_1:1.0 .
Usage
sudo docker run -v /home/ubuntu/ContainerInception/sample_data/:/data -w /data use_case_1:1.0 -h
Make sure that the input files are in your current working directory before running.
Usage: ./uc-1.1.sh -r1 <READ1.fastq.gz> -r2 <READ2.fastq.gz> -a <adapters.fa> -t <trim_file> -g <ref.fa>
Options:
-r1 --read1 a read1 gzipped FASTQ file
-r2 --read2 a read2 gzipped FASTQ file
-a --adapters an adapters FASTA file
-t --trimfile a trim file for trimmomatic
-g --genome-ref a reference genome FASTA file
Example
sudo docker run -v /home/ubuntu/ContainerInception/sample_data/:/data -w /data use_case_1:1.0 -r1 sample_1_R1.fq.gz -r2 sample_1_R2.fq.gz -a Adapters.fa -t testfile_trimmomatic.txt -g reference_genome.fa