Merge pull request #43 from agduncan94/feature/docker-support

Feature/docker support

.gitignore

@@ -1,2 +1,3 @@
 .DS_Store
 node_modules/
+docker/data/

docker/Dockerfile

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+FROM node:latest
+
+LABEL maintainer="andrew.duncan@oicr.on.ca"
+
+ENV JBROWSE_VERSION 1.16.3
+
+# Install dependencies
+RUN apt-get -qq update --fix-missing
+RUN apt-get --no-install-recommends -y install git build-essential zlib1g-dev libxml2-dev libexpat-dev postgresql-client libpq-dev ca-certificates curl
+
+# Download JBrowse
+RUN mkdir -p /jbrowse/ && \
+    git clone --recursive https://github.com/gmod/jbrowse /jbrowse/ && \
+    cd /jbrowse/ && \
+    git checkout ${JBROWSE_VERSION}-release
+
+WORKDIR /jbrowse/
+
+# Download ICGC Viewer
+RUN git clone https://github.com/agduncan94/icgc-viewer /icgc-viewer/ && \
+    cd /icgc-viewer/ && \
+    git checkout 0.1.5 && \
+    cp -r icgc-viewer /jbrowse/plugins/icgc-viewer && \
+    cat ./data/jbrowse.conf > /jbrowse/jbrowse.conf
+
+# Setup JBrowse
+RUN ./setup.sh && \
+    ./bin/cpanm --force JSON Hash::Merge PerlIO::gzip Devel::Size \
+    Heap::Simple Heap::Simple::XS List::MoreUtils Exception::Class Test::Warn Bio::Perl \
+    Bio::DB::SeqFeature::Store File::Next Bio::DB::Das::Chado && \
+    rm -rf /root/.cpan/
+
+
+# Expose port 3000
+EXPOSE 3000

docker/README.md

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+# Running JBrowse with ICGC Plugin in Docker
+This will get JBrowse with the ICGC Viewer Plugin running with Express on port 3000.
+
+Based on [enuggetry/docker-jbrowse](https://github.com/enuggetry/docker-jbrowse)
+
+## Build and Run from Dockerfile
+### Setup data
+*Important*: Place your track data in `./data`. This maps to `/jbrowse/data` in the container, which is where JBrowse stores reference data and track information.
+
+### Build the docker image
+`docker build . -t jbrowse-with-icgc`
+
+### Run the docker image
+`docker run -p 3000:3000 -v {pwd}/data:/jbrowse/data jbrowse-with-icgc utils/jb_run.js -p 3000`
+
+Note: You can run in the background using the detach mode (-d)
+
+`docker run -d -p 3000:3000 -v {pwd}/data:/jbrowse/data jbrowse-with-icgc utils/jb_run.js -p 3000`
+
+## Build and Run from Docker Compose
+You can also use Docker Compose to build the image. Ensure you are working in the same directory as the `docker-compose.yml`.
+
+### Build docker-compose
+`docker-compose build`
+
+### Run the docker-compose
+`docker-compose up`
+
+Note: You can run in the background using the detach mode (-d)
+
+`docker-compose up -d`
+
+## Load refseq and tracks
+If you already have your tracks.conf and seq/, etc., you can simply put these files into your `./data` directory.
+
+You will have to put the RefSeq data into the `./data` directory. Download the GRCH37 `.fa` and `.fa.fai` files from online (ex. http://bioinfo.hpc.cam.ac.uk/downloads/datasets/fasta/grch37/). Then put the following in `./data/tracks.conf` (note files may be named something else).
+
+```
+refSeqs=GRCh37.genome.fa.fai
+  
+[tracks.refseqs]
+urlTemplate=GRCh37.genome.fa
+```
+
+Now go to `localhost:3000` and you should see JBrowse with your refdata and tracks!
+
+### Enter the Docker Container
+
+You can enter the container by doing the following:
+
+```
+# Get container ID
+docker ps
+
+# Enter container
+docker exec -it <container-id> /bin/bash
+```

docker/docker-compose.yml

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+version: '3'
+services:
+  jbrowse:
+    build: .
+    command: utils/jb_run.js -p 3000
+    ports:
+    - "3000:3000"
+    volumes:
+    - ./data:/jbrowse/data
+