Local PEPPER installation for variant calling

[leonorpalmeira]

Dear Pepper team,

I am trying to install PEPPER locally and have used the following:

apt-get install -y cmake \
                       make \
               git \
               gcc \
               g++ \
               autoconf \
               bzip2 \
               lzma-dev \
               zlib1g-dev \
               libcurl4-openssl-dev \
               libpthread-stubs0-dev \
               libbz2-dev \
               liblzma-dev \
               libhdf5-dev \
               python3-pip \
               python3-virtualenv \
               virtualenv
git clone https://github.com/kishwarshafin/pepper.git
cd pepper
make
make build
make install

I do see pepper and pepper_variant:

$ cd venv/bin/
$ ./pepper --version
PEPPER VERSION:  0.8.0
$ ./pepper_variant --version
PEPPER VERSION:  0.8.0

But I cannot find the binary run_pepper_margin_deepvariant described in your README to run variant calling. Is there anything special that I need to do to install it?

[kishwarshafin]

Hello, the run_pepper_margin_deepvariant is a part of the docker, it is not part of PEPPER. The docker contains a wrapper that runs PEPPER-Margin-DeepVariant simultaneously. For local development you only installed PEPPER.

[leonorpalmeira]

Hello, thanks for your answer! Would it be possible to obtain the Dockerfile describing how the docker is built as well as the code of the run_pepper_margin_deepvariant wrapper?

[kishwarshafin]

hi @leonorpalmeira , I have added you to the appropriate repo. I'll close this issue.

[leonorpalmeira]

Thank you very much!