A Docker image containing inStrain is available on Docker Hub with name "mattolm/instrain:latest".
The Docker image was made by running the command make in this directory. This puts all files in this directory inside of the resulting Docker image, as well as the most recent version of inStrain available on Bioconda. If you want to make sure inStrain is up to date, or use a different version, you can run pip install instrain --upgrade within the Docker image.
Before inStrain can be run in the Docker image it must be initialized with the command ./prepare.sh; conda activate work;
After inStrain is initialized it can be run as normal by moving data into the Docker image, or by using the run_instrain.py helper script to download data from AWS S3.
This helper script was designed following the example provided by aws-batch-genomics, and is most useful for use in AWS Genomic Batch Workflows. Below are the arguments that can be provided to this wrapper script, as well as an example command of how it can be run.
usage: run_instrain.py [-h] [--bam BAM] [--fasta FASTA] [--genes GENES]
[--stb STB] [--results_directory RESULTS_DIRECTORY]
[--wd_name WD_NAME] [--command COMMAND]
[--cmd_args CMD_ARGS] [--light_upload]
[--working_dir WORKING_DIR]
optional arguments:
-h, --help show this help message and exit
--working_dir WORKING_DIR
File paths:
--bam BAM s3 path to the .bam file
--fasta FASTA s3 path to the .fasta file
--genes GENES s3 path to the genes file
--stb STB s3 path to the stb file
--results_directory RESULTS_DIRECTORY
s3 path to the folder to put the results in
Run command args:
--wd_name WD_NAME Name of the output directory
--command COMMAND The command that should go after the command inStrain
--cmd_args CMD_ARGS A string (as long as you want) that will be put after
the inStrain command, .bam, fasta, and output
directory
--light_upload By default it will upload the /raw_data folder; this
will make it not
./prepare.sh; conda activate work; ./run_instrain.py --bam {0} --fasta {1} --results_directory {2} --wd_name {3} --cmd_args='--skip_plot_generation'
"./prepare.sh; conda activate work; ./run_instrain.py --IS {0} {1} --results_directory {2} --wd_name {3} --command compare --cmd_args='--store_mismatch_locations' --scaffolds {4}