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TSI
docker
Commits
de7c8b61
Commit
de7c8b61
authored
Feb 20, 2019
by
C.D. Tiwari
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Updated README and gave context.
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README.md
README.md
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bioconda/Dockerfile.base
bioconda/Dockerfile.base
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bioconda/Dockerfile.py2
bioconda/Dockerfile.py2
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bioconda/Dockerfile.py3
bioconda/Dockerfile.py3
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README.md
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de7c8b61
# docker
# Docker files collection
Here you can related docker files templates for bioinformatics uses.
Incorporated best practices of docker file
Following docker images are also hosted on docker hub
[
Docker Hub
](
https://hub.docker.com/
)
## Bioconda docker images
*
ebi-biopackages.base
*
ebi-biopackages.bioconda (default with python3)
bioconda/
Dockerfile.base
Dockerfile.py2 # For python2
Dockerfile.py3 # For python3
Maintained by
[
Cloud Consultancy Team
][
1
]
, Tips and tricks with Docker
[
here
][
3
]
Documentation can be found
[
Cloud Consultancy Team docs
][
2
]
[
1
]:
https://www.ebi.ac.uk/seqdb/confluence/display/TSI/Cloud+Consultancy+Team
[
2
]:
https://tsi-ccdoc.readthedocs.io/en/master/
[
3
]:
https://tsi-ccdoc.readthedocs.io/en/master/Tech-tips/Tips-and-tricks-with-docker.html
bioconda/Dockerfile.base
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de7c8b61
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
# Author : Chandra Deep Tiwari
# Date : 10/02/2019
# Version : 0.1
...
...
@@ -7,27 +7,27 @@
# Change History
# ```````````````
# Editor Name Version Date Description
# ___________________________________________________________________________
# ___________________________________________________________________________
__
# C.D.Tiwari 0.1 19/02/18 First version, base image
#
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
# Base Image Section
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
FROM ubuntu:16.04
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
# ROOT MODE
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
# SETUP apt-fast
# Description: apt-fast is a shellscript wrapper for apt-get and
# aptitude that can drastically improve apt download
# times by downloading packages in parallel, with multiple
# connections per package.
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
RUN apt-get update && apt-get install -y aria2 git \
&& git clone https://github.com/ilikenwf/apt-fast /tmp/apt-fast \
...
...
@@ -35,19 +35,19 @@ RUN apt-get update && apt-get install -y aria2 git \
&& chmod +x /usr/bin/apt-fast \
&& cp /tmp/apt-fast/apt-fast.conf /etc
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
# Setup curl
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
RUN apt-fast update && apt-fast install -y curl
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
# Setup Fixuid
# Desc: fixuid iss a Go binary that changes a Docker container's user/group
# and file permissions that were set at build time to the UID/GID that
# the container was started with at runtime. Primary use case is in
# development Docker containers when working with host mounted volumes.
#-----------------------------------------------------------------------------
#-----------------------------------------------------------------------------
-
RUN addgroup --gid 1000 docker && \
adduser --uid 1000 --ingroup docker --home /home/docker --shell /bin/sh --disabled-password --gecos "" docker
...
...
@@ -62,9 +62,9 @@ RUN USER=docker && \
ENTRYPOINT ["fixuid"]
#--------------------------------------------------------------------------
#--------------------------------------------------------------------------
----
# Setup
#--------------------------------------------------------------------------
#--------------------------------------------------------------------------
----
RUN apt-fast update && apt-fast install -y \
build-essential \
git \
...
...
bioconda/Dockerfile.py2
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de7c8b61
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
# Author : Chandra Deep Tiwari
# Date : 19/02/2019
# Version : 0.1
...
...
@@ -7,23 +7,23 @@
# Change History
# ```````````````
# Editor Name Version Date Description
# ___________________________________________________________________________
# ___________________________________________________________________________
__
# C.D.Tiwari 0.1 19/02/18 First version,
#
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
# Base Image Section
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
FROM cdtiwari/ebi-biopackages.base:0.1
#------------------------------------------------------------------
#------------------------------------------------------------------
------------
# ROOT MODE
#------------------------------------------------------------------
#------------------------------------------------------------------
------------
#------------------------------------------------------------------
#------------------------------------------------------------------
------------
# Setup Miniconda with Python2
#-----------------------------------------------------------------
#-----------------------------------------------------------------
-------------
RUN cd /tmp \
&& curl -O https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh \
&& bash Miniconda2-latest-Linux-x86_64.sh -b -p /opt/conda
...
...
bioconda/Dockerfile.py3
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de7c8b61
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
# Author : Chandra Deep Tiwari
# Date : 19/02/2019
# Version : 0.1
...
...
@@ -7,23 +7,23 @@
# Change History
# ```````````````
# Editor Name Version Date Description
# ___________________________________________________________________________
# ___________________________________________________________________________
__
# C.D.Tiwari 0.1 19/02/18 First version,
#
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
# Base Image Section
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
--
FROM cdtiwari/ebi-biopackages.base:0.1
#------------------------------------------------------------------
#------------------------------------------------------------------
------------
# ROOT MODE
#------------------------------------------------------------------
#------------------------------------------------------------------
------------
#------------------------------------------------------------------
#------------------------------------------------------------------
------------
# Setup Miniconda with Python3
#-----------------------------------------------------------------
#-----------------------------------------------------------------
-------------
RUN cd /tmp \
&& curl -O https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda
...
...
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