galantelab/tipseqhunter repository overview

⁠TIPseqHunter

⁠Getting Started

⁠Motivation

Here we present the docker⁠ version of TIPseqHunter pipeline. This approach has the ability to encapsulate all java dependencies, read aligners, genome indexes and biological annotation files needed by both steps of the pipeline: TIPseqHunterPipelinejar.sh⁠ and [TipseqHunterPipelineJarSomatic.sh], once manipulating all these dependencies ends up being a little tricky depending on user expertise.

⁠Prerequisities

In order to run this container you'll need docker installed.

• Windows⁠
• OS X⁠
• Linux⁠

⁠Acquiring TIPseqHunter Image

⁠Manual Installation

Clone this repository:

$ git clone https://github.com/galantelab/tipseq_hunter.git

Inside the tipseq_hunter folder, build the image:

$ docker build --build-arg tarball_url=https://bioinfohsl-webusers.s3.amazonaws.com/tmiller/tipseq_hunter_data.tar.gz -t tipseqhunter .

Another and better option is using the Makefile⁠ inside tipseq_hunter folder:

$ make build

⁠Pulling Image

Pull tipseqhunter image from dockerhub⁠ registry:

$ docker pull galantelab/tipseqhunter

Or using Makefile:

$ make pull

⁠Usage

Once installed the docker image, the user may apply the Makefile⁠, in order to automate the process of creating the container and running the pipeline, as well as using the ordinary docker run command.

⁠Examples with docker run

By default the TIPseqHunterPipelinejar/TipseqHunterPipelineJarSomatic runs in a container-private folder. You need to change this using flags, like user (-u), current directory, and volumes (-w and -v). It is important to mount the fastq directory and output directory, that way docker can find the required files:

$ docker run \
	--rm \
	-u $(id -u):$(id -g) \
	-v path_to_fastq_folder:path_to_fastq_folder \
	-v path_to_output_folder:path_to_output_folder \
	-w path_to_output_folder \
	tipseqhunter \
		TIPseqHunterPipelineJar.sh path_to_fastq_folder path_to_output_folder fastq_r1 key_r1 key_r2 number_of_reads

That command sets the user UID:GID, mounts the input/ouput directories, sets the current working directory as the output folder and, finally, runs TIPseqHunterPipelinejar.sh script. In the end, the container is automatically removed.

The TIPseqHunterPipelinejar/TIPseqHunterPipelineJarSomatic runs based on some cutoffs. There is a default value to each one, but you might change it through environment variables. The best way to do it is by a configuration file to the docker run command. You can find an example in config.env⁠ file, which is already set to the default values. To use it with docker run:

$ docker run \
	--rm \
	--env-file=config.env \
	-u $(id -u):$(id -g) \
	-v path_to_fastq_folder:path_to_fastq_folder \
	-v path_to_output_folder:path_to_output_folder \
	-w path_to_output_folder \
	tipseqhunter \
		TIPseqHunterPipelineJar.sh path_to_fastq_folder path_to_output_folder fastq_r1 key_r1 key_r2 number_of_reads

⁠Examples with Makefile

The Makefile can be used to build, pull and run the TIPseqHunter scripts inside docker:

$ make

help                           This help
build                          Build the image
build-nc                       Build the image without caching
pull                           Pull the latest tagged image from the dockerhub registry
remove                         Remove the lattest tagged image
run                            Run TIPseqHunter pipeline completely
run-pipeline                   Run TIPseqHunterPipelineJar.sh
run-pipeline-somatic           Run TIPseqHunterPipelineJarSomatic.sh
up                             Pull and run TIPseqHunter pipeline completely
stop                           Stop and remove a running container
version                        Output the current version

When running the pipeline, the Makefile automatically searches for a file named config.env in the current directory, so if it exists, you can just call:

$ make run

Or use another file with a different name:

$ make run CONFIG=another_config.txt

The arguments to TIPseqHunterPipelinejar/TIPseqHunterPipelineJarSomatic can be passed into the config.env or through the command line:

$ make run \
	CONFIG=another_config.txt \
	INPUT_DIR=fastq_folder \
	OUTPUT_DIR=ouput_folder \
	FASTQ_R1=example_R1.fa \
	KEY_R1=R1 \
	KEY_R2=R2 \
	READ_NUM=123456

That is it! :smile: