NetMHC Setup
=============

Using NetMHC tools in LENS
__________________________

LENS utilizes MHCflurry to estimate pMHC-specific binding affinities and
presentation scores. Nevertheless, users may wish to include other tools, such
as ``NetMHCpan`` or ``NetMHCstabpan`` to further describe pMHCs of interest. LENS
supports these tools, but users must provide their own Docker images due to
restrictive licensing. Information for creating the Docker images and modifying
LENS to use these tools is below.

Creating NetMHC Docker images
_____________________________

Users will need to create their own Docker images after obtaining their own
license for each tool. Docker images can be created using these example
Dockerfiles:

**NetMHCpan**

.. code-block:: console

  FROM ubuntu:20.04

  RUN apt-get update && apt-get upgrade -y
  RUN apt-get install -y wget vim tcsh

  COPY netMHCpan-4.1b.Linux.tar.gz /
  RUN tar xvf /netMHCpan-4.1b.Linux.tar.gz
  RUN wget https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/data.tar.gz
  RUN tar xvf data.tar.gz
  RUN mv /data /netMHCpan-4.1/data

  RUN cp -r /netMHCpan-4.1/Linux_x86_64/bin /netMHCpan-4.1/bin

  ENV NETMHCpan="/netMHCpan-4.1"

  RUN rm /data.tar.gz
  RUN rm /netMHCpan-4.1b.Linux.tar.gz

  RUN sed -i 's/\/net\/sund-nas.win.dtu.dk\/storage\/services\/www\/packages\/netMHCpan\/4.1\/netMHCpan-4.1/\/netMHCpan-4.1\/data\//g' /netMHCpan-4.1/netMHCpan

  ENV TMPDIR /tmp
  CMD ["/bin/bash"]

**NetMHCstabpan**

.. code-block:: console

  FROM ubuntu:20.04

  RUN apt-get update -y
  RUN apt-get upgrade -y
  RUN apt-get install -y wget vim tcsh gawk

  COPY netMHCstabpan-1.0a.Linux.tar.gz /
  RUN tar xvf /netMHCstabpan-1.0a.Linux.tar.gz
  RUN wget https://services.healthtech.dtu.dk/services/NetMHCstabpan-1.0/data.tar.gz
  RUN tar xvf data.tar.gz
  RUN mv /data /netMHCstabpan-1.0/data

  RUN cp -r /netMHCstabpan-1.0/Linux_x86_64/bin /netMHCstabpan-1.0/bin

  ENV NETMHCstabpan="/netMHCstabpan-1.0"

  RUN rm /data.tar.gz
  RUN rm /netMHCstabpan-1.0a.Linux.tar.gz

  RUN sed -i 's/\/net\/sund-nas.win.dtu.dk\/storage\/services\/www\/packages\/netMHCstabpan\/1.0\/netMHCstabpan-1.0/\/netMHCstabpan-1.0\/data\//g' /netMHCstabpan-1.0/netMHCstabpan

  RUN chmod -R 777 /netMHCstabpan-1.0
  ENV TMPDIR /tmp
  CMD ["/bin/bash"]

**NetCTLpan**

.. code-block:: console

  FROM ubuntu:20.04

  RUN apt-get update && apt-get upgrade -y
  RUN apt-get install -y wget vim tcsh gawk

  COPY netCTLpan-1.1b.Linux.tar.Z /
  RUN tar xvf /netCTLpan-1.1b.Linux.tar.Z

  RUN mkdir /netCTLpan-1.1/netMHCpan-2.3/Linux_x86_64/tmp
  RUN cp -r /netCTLpan-1.1/netMHCpan-2.3/Linux_x86_64/bin/* /netCTLpan-1.1/netMHCpan-2.3/Linux_x86_64/tmp
  RUN mv /netCTLpan-1.1/netMHCpan-2.3/Linux_x86_64/tmp /netCTLpan-1.1/netMHCpan-2.3/Linux_x86_64/bin/bin

  RUN wget https://services.healthtech.dtu.dk/services/NetCTLpan-1.1/data_netCTLpan-1.1.tar.Z
  RUN tar xvf data_netCTLpan-1.1.tar.Z
  RUN mv data_netCTLpan-1.1 /netCTLpan-1.1/data

  RUN wget https://services.healthtech.dtu.dk/services/NetCTLpan-1.1/data_netMHCpan-2.3.tar.Z
  RUN tar xvf data_netMHCpan-2.3.tar.Z
  RUN cp -r data_netMHCpan-2.3 /netCTLpan-1.1/netMHCpan-2.3/data
  RUN cp -r data_netMHCpan-2.3 netCTLpan-1.1/netMHCpan-2.3/Linux_x86_64/bin/data

  RUN cp -r /netCTLpan-1.1/Linux_x86_64/bin /netCTLpan-1.1/bin

  RUN sed -i 's/\/usr\/cbs\/packages\/netCTLpan\/1.1\/netCTLpan-1.1/\/netCTLpan-1.1/g' /netCTLpan-1.1/netCTLpan

  ENV NETCTLpan="/netCTLpan-1.1"
  ENV NETMHCpan="/netCTLpan-1.1/netMHCpan-2.3/Linux_x86_64/bin"

  RUN rm /netCTLpan-1.1b.Linux.tar.Z

  ENV TMPDIR /tmp
  CMD ["/bin/bash"]