Initial commit

.github/workflows/docker-image.yml

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+name: Docker Image CI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Build the Docker image
+      run: docker build . --tag buildtest:$(date +%s)

.gitignore

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+.DS_Store

Dockerfile

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+################# BASE IMAGE ######################
+FROM --platform=linux/amd64 mambaorg/micromamba:1.3.1-focal
+# Micromamba for fast building of small conda-based containers.
+# https://github.com/mamba-org/micromamba-docker
+# The 'base' conda environment is automatically activated when the image is running.
+
+################## METADATA ######################
+LABEL base_image="mambaorg/micromamba:1.3.1-focal"
+LABEL version="1.0.0"
+LABEL software="Tophat"
+LABEL software.version="2.1.1"
+LABEL about.summary="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."
+LABEL about.home="https://ccb.jhu.edu/software/tophat/index.shtml"
+LABEL about.documentation="https://ccb.jhu.edu/software/tophat/manual.shtml"
+LABEL about.license_file=""
+LABEL about.license=""
+
+################## MAINTAINER ######################
+MAINTAINER Matthew Galbraith <matthew.galbraith@cuanschutz.edu>
+
+################## INSTALLATION ######################
+
+# Copy the yaml file to your docker image and pass it to micromamba
+COPY --chown=$MAMBA_USER:$MAMBA_USER env.yaml /tmp/env.yaml
+RUN micromamba install -y -n base -f /tmp/env.yaml && \
+    micromamba clean --all --yes

README.md

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+[![Docker Image CI](https://github.com/mattgalbraith/tophat2-docker-singularity/actions/workflows/docker-image.yml/badge.svg)](https://github.com/mattgalbraith/tophat2-docker-singularity/actions/workflows/docker-image.yml)
+
+# 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:  
+``` bash
+# 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](https://shell.cloud.google.com)
+
+#### To test this tool from the command line:
+``` bash
+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 "$PWD":/data -w /data tophat2:2.1.1 tophat -r 20 test_ref reads_1.fq reads_2.fq
+# -v mounts current working dir as /data in container
+# -w sets working dir in conatiner
+# SUCCESSFUL TEST RESULT = output lines similar to this: 
+
+# [2023-03-22 00:29:02] Beginning TopHat run (v2.1.1)
+# -----------------------------------------------
+# [2023-03-22 00:29:02] Checking for Bowtie
+# 		  Bowtie version:	 2.2.5.0
+# [2023-03-22 00:29:03] Checking for Bowtie index files (genome)..
+```
+
+## Optional: Conversion of Docker image to Singularity  
+
+### 3. Build a Docker image to run Singularity  
+(skip if this image is already on your system)  
+https://github.com/mattgalbraith/singularity-docker
+
+### 4. Save Docker image as tar and convert to sif (using singularity run from Docker container)  
+``` bash
+docker images
+docker save <Image_ID> -o tophat2.1.1-docker.tar && gzip tophat2.1.1-docker.tar # = IMAGE_ID of tophat image
+docker run -v "$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  
+``` bash
+# 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
+```

env.yaml

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+# Using an environment name other than "base" is not recommended!
+# Read https://github.com/mamba-org/micromamba-docker#multiple-environments
+# if you must use a different environment name.
+name: base
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  # - bowtie2=2.5.1 # seems to prevent mamba solving environment
+  - tophat=2.1.1