Docker image for the DeepBind method (Frey lab).
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This repository contains our slightly modified version of the DeepBind code from the Frey lab. There are patches to fix a few bugs and a Dockerfile to package the code and some test data.
We have set up an automated build here. Pushes should automatically trigger builds on the Docker hub. If you want to build a local image, you can run:
docker build -t giffordlab/deepbind-docker .
You can get the (public) automated image from any machine, including EC2 ones, by running:
docker pull giffordlab/deepbind-docker
Prerequisites are Docker and having the NVIDIA 346.46 driver installed (the default for CUDA 7.0; see the upstream image documentation). The tag for the source image can be used to change the CUDA version and NVIDIA driver version.
The image is based on this CUDA image. To run an image with CUDA access, run (this is customized for our machines with three GPUs):
docker run -it --rm \
--device /dev/nvidiactl \
--device /dev/nvidia-uvm \
--device /dev/nvidia0 \
--device /dev/nvidia1 \
--device /dev/nvidia2 \
giffordlab/deepbind-docker
This will launch the ENCODE example script referred to in their documentation.
The DeepBind pipeline currently has a nest of hardcoded paths for loading data, but we will clean this up soon and add examples for analyzing custom files with the container.
You can override the default CMD and then start other commands
manually:
docker run -it --rm $NVIDIA_OPTS giffordlab/deepbind-docker /bin/bash
The original code is copyright (c) 2015, Andrew Delong and Babak Alipanahi, all rights reserved. The following license agreement and terms apply (see here for details):
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Content type
Image
Digest
sha256:da41f6c71…
Size
1.8 GB
Last updated
almost 11 years ago
docker pull giffordlab/deepbind-docker