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Last pushed: a year ago
Short Description
PathoScope image
Full Description


Provides PathoScope, PathoStat, and BatchQC. Additional components used by PathoScope are installed with conda from the bioconda channel, including biopython, samtools, bowtie2, prinseq, cutadapt, fastqc and sra-tools.

Dockerfiles are available at GitHub at gwcbi/pathosuite_docker.

Getting Started

This image provides packages for running the PathoScope pipeline and the downstream analysis tools BatchQC and PathoStat. The PathoScope tools (LIB, MAP, ID, REP, QC) are run via command line, while the downstream tools are Shiny apps run by RStudio in the browser.

PathoScope tools

PathoScope tools are accessed via command line. First, launch the docker image in the background:

docker run -d -p 8787:8787 mlbendall/pathosuite

Now attach to the running container as rstudio user (The ID of the latest container can be found with docker ps -ql):

docker exec --user rstudio -it $(docker ps -ql) bash

PathoScope tools are run using the pathoscope command. For example:

pathoscope --help
pathoscope MAP --help

BatchQC and PathoStats

BatchQC and PathoStat are launched through RStudio. Start RStudio by launching the docker image in the background (if you have not done above):

docker run -d -p 8787:8787 mlbendall/pathosuite

Now simply open a new window in your browser and go to http://localhost:8787/. Default username and password is rstudio.

Note: if localhost does not point to running server, find the IP address of the image:

docker inspect --format '{{ .NetworkSettings.Ports }}' $(docker ps -ql)

Other tips

See the following for more information on working with the image:

List local docker images

docker images

List running containers

docker ps

List all containers, including stopped

docker ps -a

Stop a running container

docker stop <container_id>

Restart stopped container

(Find the container ID with docker ps -a).

docker run -d -p 8787:8787  <container_id>

Run PathoScope directly

In running container:

docker exec --user rstudio -it $(docker ps -ql) pathoscope --help

In new container:

docker run --user rstudio mlbendall/pathosuite pathoscope --help

Mount local directory in container

This is useful if you want to start a new container with some data residing on your
local machine, or if you want to store output outside of the container.

To run the container in background:

docker run -d -p 8787:8787 -v <host-dir>:<container-dir> mlbendall/pathosuite

where host-dir is the absolute path to the local directory you wish to mount, and container-dir is the mount point within the container. For example, to mount your home directory as localdir within user rstudio's home directory:

docker run -d -p 8787:8787 -v /Users/$(whoami):/home/rstudio/localhome mlbendall/pathosuite

This pattern is useful for running PathoScope with inputs and outputs available on the local machine. The following alias creates pathosuite as an alias that mounts the current working directory and executes pathoscope in a new container:

alias pathosuite='docker run -ti -u rstudio -v $(pwd):/hostwd -w /hostwd mlbendall/pathosuite pathoscope'


pathosuite ID --help
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