Skip to content

Create Docker file #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
nselem wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Create Docker file #1

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
51 changes: 51 additions & 0 deletions Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
##########################################################
# Dockerfile to build a Genomic-fluidity-scripts container image
# Based on Ubuntu
############################################################

# Set the base image to the BioPerl prebuilt prerequisites image

FROM bioperl/bioperl-deps

# File Author / Maintainer
MAINTAINER Nelly Selem <nselem84@gmail.com>

# First Bioperl Modules copied from Hilmar Lapp <hlapp@drycafe.net> bioperl
# Install modules recommended by BioPerl.
# We can't include Bio::ASN1::EntrezGene here yet, because it declares
# a dependency on BioPerl, thus pulling in BioPerl first.
RUN cpanm \
Bio::Phylo

# -------------------------------------------------------------
# Install BioPerl from GitHub current master branch.
#
# This is the actual installation step of BioPerl itself :-)
# -------------------------------------------------------------
RUN cpanm -v \
https://github.com/bioperl/bioperl-live/archive/master.tar.gz

# Install modules recommended by BioPerl that depend on BioPerl.
# (Don't ask. See above.)
RUN cpanm \
Bio::ASN1::EntrezGene


## Cloning fluidity scripts Weitz Group
RUN apt-get update && apt-get install -y git
RUN git clone https://github.com/WeitzGroup/Genomic-fluidity-scripts

## Bioperl module
RUN cpanm \
Bio::Tools::Run::StandAloneBlast

# Installing blast legacy
RUN apt-get install -y blast2

RUN mkdir /usr/src/fluidity
COPY . /usr/src/fluidity
ENV PATH $PATH:/Genomic-fluidity-scripts:
WORKDIR /Genomic-fluidity-scripts
RUN chmod +x *
WORKDIR /usr/src/fluidity