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

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

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

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"]