Merge pull request #6 from Mangul-Lab-USC/imrep-docker

Add docker support to ImRep

Dockerfile

@@ -0,0 +1,32 @@
+FROM ubuntu:18.04
+
+RUN apt-get update --fix-missing
+RUN apt-get install -y build-essential \
+    wget \
+    bzip2 \
+    samtools \
+    libbam-dev \
+    libhts-dev \
+    python-minimal
+
+RUN apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+ENV PATH="/root/miniconda3/bin:${PATH}"
+ARG PATH="/root/miniconda3/bin:${PATH}"
+
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && mkdir /root/.conda \
+    && bash Miniconda3-latest-Linux-x86_64.sh -b \
+    && rm -f Miniconda3-latest-Linux-x86_64.sh
+
+RUN pip install --upgrade pip
+
+WORKDIR /imrep
+COPY . .
+
+RUN cd suffix_tree && python ./setup.py install --user
+
+RUN pip install -r requirements.txt
+
+ENTRYPOINT ["python", "./imrep.py"]

README.md

@@ -6,19 +6,19 @@
 ImReP is a method for rapid and accurate profiling of the adaptive immune repertoires from regular RNA-Seq data
 
 Download ImReP using 
-```
+```bash
 git clone https://github.com/mandricigor/imrep.git
 ```
 
 Install ImReP from the base directory
 
-```
+```bash
 cd imrep
 ./install.sh 
 ```
 Run ImReP analysis by a single command for the BAM file with mapped and unmapped reads (preferred). BAM file needs to be indexed (.bai file). Forgot to save unmapped reads, we got you covered. Learn more [here](https://github.com/mandricigor/imrep/wiki/Forgot-to-save-unmapped-reads%3F)
 
-```
+```bash
 python imrep.py --bam example/toyExample.bam example/toyExample.cdr3
 ```
 
@@ -27,6 +27,28 @@ Note : ImReP is written in Python2.7. So if your cluster default Python version
 Find ImReP analysis in _toyExample_ directory. Learn more [here](https://github.com/mandricigor/imrep/wiki/Quick-Start) 
 
 
+## Docker Usage
+Docker enables you to run ImRep without needing to explicitly install and manage its dependencies. You can learn more about Docker [here](https://docs.docker.com/get-started/overview/).
+
+First, build the docker container from the current working directory:
+```bash
+git clone https://github.com/Mangul-Lab-USC/imrep.git
+# Make sure you are in the correct directory...
+cd imrep
+# build the docker container and give it a <tag> `-t`
+docker build -t imrep .
+```
+Run the docker container like so, and pass in your intended ImRep `<options>`.
+```bash
+docker run --rm -v ${PWD}:/imrep -ti imrep <options>
+```
+In this case, we mount a Docker [volume](https://docs.docker.com/storage/volumes/) `-v` to recieve the output generated from within the container locally.
+
+Here is a full example with Docker:
+```bash
+docker build -t imrep .
+docker run --rm -v ${PWD}:/imrep -ti imrep --bam example/toyExample.bam example/toyExample.cdr3
+```
 # ImReP Tutorial
 
 Use the sidebar on the right to navigate ImReP tutorial. Get started with a toy example of 200 RNA-Seq reads (_example/toyExample.bam_) distributed with ImRep package

install.sh

@@ -1,9 +1,4 @@
-pip install pysam --user
-pip install biopython==1.76 --user
-pip install intervaltree --user
-pip install jellyfish==0.5.4 --user
-pip install numpy --user
-pip install networkx --user
+pip install -r requirements.txt
 cd suffix_tree
 python setup.py install --user
 cd ..

requirements.txt

@@ -0,0 +1,6 @@
+biopython==1.76.0
+intervaltree==3.1.0
+jellyfish==0.4.0
+networkx==2.5.1
+numpy==1.20.3
+pysam==0.16.0.1