tophat2-docker-singularity

Build Docker container for TopHat2 and (optionally) convert to Apptainer/Singularity.

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
https://ccb.jhu.edu/software/tophat/index.shtml

Requirements:

Bowtie2
Install within image using micromamba + env.yaml file
https://github.com/mamba-org/micromamba-docker

Build docker container:

1. For TopHat2 installation instructions:

https://ccb.jhu.edu/software/tophat/tutorial.shtml

2. Build the Docker Image

To build image from the command line:

# Assumes current working directory is the top-level tophat2-docker-singularity directory
docker build -t tophat2:2.1.1 . # tag should match software version

• Can do this on Google shell

To test this tool from the command line:

docker run --rm -it tophat2:2.1.1 tophat2 --help 

# Optional: Run with test data
wget https://ccb.jhu.edu/software/tophat/downloads/test_data.tar.gz
tar -xzvf test_data.tar.gz
cd test_data
docker run --rm -it -v "$PWD":/data -w /data tophat2:2.1.1 tophat -r 20 test_ref reads_1.fq reads_2.fq
# -v mounts current working dir as /data in container
# -w sets working dir in conatiner
# SUCCESSFUL TEST RESULT = output lines similar to this: 

# [2023-03-22 00:29:02] Beginning TopHat run (v2.1.1)
# -----------------------------------------------
# [2023-03-22 00:29:02] Checking for Bowtie
# 		  Bowtie version:	 2.2.5.0
# [2023-03-22 00:29:03] Checking for Bowtie index files (genome)..

Optional: Conversion of Docker image to Singularity

3. Build a Docker image to run Singularity

(skip if this image is already on your system)
https://github.com/mattgalbraith/singularity-docker

4. Save Docker image as tar and convert to sif (using singularity run from Docker container)

docker images
docker save <Image_ID> -o tophat2.1.1-docker.tar && gzip tophat2.1.1-docker.tar # = IMAGE_ID of tophat image
docker run -v "$PWD":/data --rm -it singularity:1.1.5 bash -c "singularity build /data/tophat2.1.1.sif docker-archive:///data/tophat2.1.1-docker.tar.gz"

NB: On Apple M1/M2 machines ensure Singularity image is built with x86_64 architecture or sif may get built with arm64

Next, transfer the tophat2.1.1.sif file to the system on which you want to run TopHat2 from the Singularity container

5. Test singularity container on (HPC) system with Singularity/Apptainer available

# set up path to the Singularity container
TOPHAT2_SIF=path/to/tophat2.1.1.sif

# Test that tophat2 can run from Singularity container
singularity run $TOPHAT2_SIF tophat2 --help # depending on system/version, singularity may be called apptainer