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Falcon as a Docker container

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Jason Chin edited this page May 31, 2016 · 3 revisions

This Docker Contain is contributed by William Andreopoulos from JGI:

We have made a Docker container for Falcon, which is accessible here: https://hub.docker.com/r/billandreo/falcon_ctr3/

It can be pulled from Docker Hub with this command:

$ docker pull billandreo/falcon_ctr3

I built the image on AWS. The Dockerfile used is shown at the end of the email. To build on an AWS EC2 cluster instance I did:

    docker build -t  falcon_ctr3 .

Running on an AWS EC2 cluster instance involves mapping /mydata to the local directory /home/ubuntu/data as follows. Then the do-assemble.sh shell script with the Falcon run command will run in Docker:

    docker run -v /home/ubuntu/data:/mydata -it falcon_ctr3

I have run Falcon assemblies in a Docker image on AWS and the NERSC Cori supercomputer (using shifter). If you have questions about running Falcon with Docker, please let me know.

ubuntu@ip-172-31-50-64:~/make_falcon$ cat Dockerfile
FROM ubuntu:14.04
RUN apt-get update
RUN apt-get install -y g++ make git zlib1g-dev python
RUN apt-get install -y python-pip
RUN pip install virtualenv
RUN apt-get install -y python-dev
RUN git clone git://github.com/PacificBiosciences/FALCON-integrate.git
WORKDIR /FALCON-integrate
ENV FC fc_env
RUN virtualenv --no-site-packages  --always-copy  $FC
RUN . $FC/bin/activate
RUN git submodule update --init
RUN cd pypeFLOW && python setup.py install
RUN cd FALCON && python setup.py install
RUN cd DAZZ_DB && make
RUN cd DAZZ_DB && cp DBrm DBshow DBsplit DBstats fasta2DB ../$FC/bin/
RUN cd DALIGNER && make
RUN cd DALIGNER && cp daligner daligner_p DB2Falcon HPCdaligner LA4Falcon LAmerge LAsort  ../$FC/bin
CMD /mydata/do-assemble.sh

via Bill

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