Update README/workflow

.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

README.md

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+[![Docker Image CI](https://github.com/mattgalbraith/homer-docker-singularity/actions/workflows/docker-image.yml/badge.svg)](https://github.com/mattgalbraith/homer-docker-singularity/actions/workflows/docker-image.yml)
+
 # homer-docker-singularity
-Build Docker container for homer software and (optionally) convert to Apptainer/Singularity  
-Dockerfile modified from https://github.com/chrisamiller/docker-homer
+
+## Build Docker container for Homer and (optionally) convert to Apptainer/Singularity.  
+
+HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs for UNIX-style operating systems written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.  
+http://homer.ucsd.edu/homer/  
+
+
+### Requirements:  
+gcc
+g++
+make
+perl
+zip/unzip
+gzip/gunzip
+wget
+samtools (optional)
+R (optional)
 
 ## Build docker container:  
 
 ### 1. For homer installation instructions:  
 http://homer.ucsd.edu/homer/introduction/install.html   
+http://homer.ucsd.edu/homer/download.html  
 
-### 2. Build the Docker Image
-
-#### To build your image from the command line:
-* Can do this on [Google shell](https://shell.cloud.google.com) - docker is installed and available
 
-```bash
-WORKING_DIR=`pwd` # capture current working directory (should be the top-level homer-docker-singularity directory)
-cd homer-docker
-docker build -t homer .
+### 2. Build the Docker Image
+``` bash
+# Assumes current working directory is the top-level tophat2-docker-singularity directory
+docker build -t homer:4.11.1 . # tag should match software version (configureHomer.pl can specify version version)
 ```
-
-Due to space limitations, especially on Google Cloud Shell, need to symlink to external Homer annotation directory  
+* Can do this on [Google shell](https://shell.cloud.google.com)
 
 #### To test this tool from the command line:
 Mount and use your current directory and call the tool now encapsulated within the container
 ```bash
-docker run --rm -it -v $PWD:$PWD -w $PWD homer homer
+docker run --rm -it homer:4.11.1 homer
+docker run --rm -it homer:4.11.1 perl /opt/homer/configureHomer.pl -list | grep homer
+docker run --rm -it homer:4.11.1 perl /opt/homer/configureHomer.pl -check
 ```
 
 ### 3. Download and mount homer data
+Due to space limitations, especially on Google Cloud Shell, need to link/mount Homer annotation data from outside containers  
 ```bash
-cd $WORKING_DIR
 mkdir homer_data && cd homer_data
 wget http://homer.ucsd.edu/homer/configureHomer.pl
-perl ./configureHomer.pl install hg38 # this will download "hg38" and "human" annotation packages
+perl ./configureHomer.pl -install hg38 # this will download "hg38" and "human" annotation packages
 
 # Optional: archive and compress for transfer to eg HPC without internet access
 cd .. && tar -czvf homer_data.tar.gz homer_data
@@ -42,40 +57,33 @@ tar -xzvf homer_data.tar.gz
 #### Check if homer can see mounted reference and annotation data
 ```bash
 # first set up path to homer_data
-HOMER_DATA = path/to/homer_data
+HOMER_DATA=path/to/homer_data
 # Mount homer data in container at /opt/homerdata (see symlinks created in Dockerfile)
-docker run --rm -it -v $HOMER_DATA:/opt/homerdata -v $PWD:$PWD -w $PWD homer /usr/bin/perl /opt/homer/configureHomer.pl -list
+docker run --rm -it -v $HOMER_DATA:/opt/homerdata homer:4.11.1 /usr/bin/perl /opt/homer/configureHomer.pl -list
 # output should indicate that correct genome packages are installed
 ```
 
 ## Optional: Conversion of Docker image to Singularity
 
-### 4. Build a Docker image to run Singularity
-
-```bash
-cd $WORKING_DIR/singularity-docker
-docker build -t singularity .
-```
+### 4. Build a Docker image to run Singularity  
+(skip if this image is already on your system)  
+https://github.com/mattgalbraith/singularity-docker  
 
-#### Test singularity container
-```bash
-docker run --rm -it -v $PWD:$PWD -w $PWD singularity singularity
-```
 
-### 5. Save Docker image as tar and convert to sif (using singularity run from Docker container)
-```bash
-cd $WORKING_DIR
-docker save <Image_ID> -o homer-docker.tar # = IMAGE_ID of homer image
-docker run -v "$PWD:/out" --rm -it singularity bash -c "singularity build /out/homer.sif docker-archive:///out/homer-docker.tar"
+### 5. Save Docker image as tar and convert to sif (using singularity run from Docker container)  
+``` bash
+docker images
+docker save <Image_ID> -o homer4.11.1-docker.tar && gzip homer4.11.1-docker.tar # = IMAGE_ID of tophat image
+docker run -v "$PWD":/data --rm -it singularity:1.1.5 bash -c "singularity build /data/homer4.11.1.sif docker-archive:///data/homer4.11.1-docker.tar.gz"
 ```
-NB: may build with arm64 architecture if run on M1/M2 Macbook  
+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 homer.sif file to the system on which you want to run Homer from the Singularity container
 
 ### 6. Test singularity container with mounted homer data on (HPC) system with Singularity/Apptainer available
 ```bash
 # set up path to the homer Singularity container
-HOMER_SIF=path/to/homer.sif
+HOMER_SIF=path/to/homer4.11.1.sif
 # set up path to homer_data
 HOMER_DATA=path/to/homer_data