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UNLOCK
docker
Commits
b9de66b0
Commit
b9de66b0
authored
May 28, 2021
by
Nijsse, Bart
Browse files
cleanup and added gtdbtk
parent
830a04a9
Changes
1
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Dockerfile
View file @
b9de66b0
...
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@@ -16,56 +16,11 @@ LABEL tags="Base"
ENV
DEBIAN_FRONTEND=noninteractive LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LANGUAGE=en_US.UTF-8
# Install the CWL runner (cwltool)
RUN
apt-get update
&&
apt-get
install
-y
wget curl pigz nodejs build-essential cpanminus git python3 python3-dev python3-distutils
&&
\
curl https://bootstrap.pypa.io/get-pip.py
-o
get-pip.py
&&
python3 get-pip.py
&&
\
pip3
install
cwltool
&&
\
cwltool
--version
&&
pip
install
html5lib
# Enable icommands
RUN
pip
install
python-irodsclient
--upgrade
&&
\
apt-get update
&&
apt-get
install
-y
gnupg
&&
\
wget
-qO
- https://packages.irods.org/irods-signing-key.asc | apt-key add -
&&
\
echo
"# /etc/apt/sources.list.d/renci-irods.list"
|
tee
-a
/etc/apt/sources.list.d/renci-irods.list
&&
\
echo
"deb [arch=amd64] https://packages.irods.org/apt/ xenial main"
|
tee
-a
/etc/apt/sources.list.d/renci-irods.list
&&
\
apt-get update
&&
apt-get
install
-y
irods-icommands
# Some default needed stuff
RUN
apt-get update
&&
apt-get
install
-y
git build-essential curl wget nano htop pigz zip unzip
# Install Java via sdkman
RUN
apt-get update
RUN
apt-get
-qq
-y
install
\
curl
\
unzip
\
zip
RUN
rm
/bin/sh
&&
ln
-s
/bin/bash /bin/sh
RUN
apt-get
-qq
-y
install
curl
RUN
curl
-s
https://get.sdkman.io | bash
RUN
chmod
a+x
"
$HOME
/.sdkman/bin/sdkman-init.sh"
RUN
source
"
$HOME
/.sdkman/bin/sdkman-init.sh"
&&
\
sdk
install
java 11.0.9.fx-zulu
&&
\
sdk
install
gradle 6.7
&&
\
sdk
install
maven 3.6.3
# Other packages
# Base Image
FROM
ubuntu:18.04
# Metadata
LABEL
base.image="docker-registry.wur.nl/unlock/docker"
LABEL
version="1"
LABEL
software="BASE 1.0"
LABEL
software.version="0.0.0"
LABEL
description="IRODS base image for UNLOCK"
LABEL
website="https://m-unlock.gitlab.io"
LABEL
documentation="NA"
LABEL
license="NA"
LABEL
tags="Base"
# ARG cwltool_version=3.0.20200720165847
ENV
DEBIAN_FRONTEND=noninteractive LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LANGUAGE=en_US.UTF-8
# Install the CWL runner (cwltool) and pip
RUN
apt-get update
&&
apt-get
install
-y
wget curl pigz nodejs build-essential cpanminus git python3 python3-dev python3-distutils
&&
\
# Install the CWL runner (cwltool) and python and pip
RUN
apt-get update
&&
apt-get
install
-y
nodejs cpanminus python3 python3-dev python3-distutils
&&
\
curl https://bootstrap.pypa.io/get-pip.py
-o
get-pip.py
&&
python3 get-pip.py
&&
\
pip3
install
cwltool
&&
\
cwltool
--version
&&
pip
install
html5lib
...
...
@@ -79,13 +34,13 @@ RUN pip install python-irodsclient --upgrade && \
apt-get update
&&
apt-get
install
-y
irods-icommands
# Install Java via sdkman
RUN
apt-get update
RUN
apt-get
-qq
-y
install
\
curl
\
unzip
\
zip
#
RUN apt-get update
#
RUN apt-get -qq -y install \
#
curl \
#
unzip \
#
zip
RUN
rm
/bin/sh
&&
ln
-s
/bin/bash /bin/sh
RUN
apt-get
-qq
-y
install
curl
#
RUN apt-get -qq -y install curl
RUN
curl
-s
https://get.sdkman.io | bash
RUN
chmod
a+x
"
$HOME
/.sdkman/bin/sdkman-init.sh"
RUN
source
"
$HOME
/.sdkman/bin/sdkman-init.sh"
&&
\
...
...
@@ -95,25 +50,39 @@ RUN source "$HOME/.sdkman/bin/sdkman-init.sh" &&\
# Other packages
# R
RUN
apt
install
-y
software-properties-common
&&
\
RUN
apt
-get update
&&
apt-get
install
-y
software-properties-common
&&
\
apt-key adv
--keyserver
keyserver.ubuntu.com
--recv-keys
E298A3A825C0D65DFD57CBB651716619E084DAB9
&&
\
add-apt-repository
'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'
&&
\
apt update
&&
\
apt
install
-y
r-base
#
FastqPuri (RNAseq pre-processing) dependencies
#
RUN R -e "install.packages(c('pheatmap', 'knitr', 'rmarkdown' ,'stringr'))"
#
#####################################
#
###### ANALYSIS TOOLS SECTION #######
# Quast
#
# Quast
RUN
pip
install
quast
# Fix locale issue with quast
RUN
apt-get clean
&&
apt-get update
&&
apt-get
install
-y
locales
nano htop
libfontconfig1
&&
locale-gen en_US.UTF-8
&&
dpkg-reconfigure locales
RUN
apt-get clean
&&
apt-get update
&&
apt-get
install
-y
locales libfontconfig1
&&
locale-gen en_US.UTF-8
&&
dpkg-reconfigure locales
# CheckM
ENV
PATH=$PATH:/unlock/infrastructure/binaries/hmmer/hmmer-3.3.2/bin/:/unlock/infrastructure/binaries/pplacer/pplacer-Linux-v1.1.alpha17/bin/:/unlock/infrastructure/binaries/prodigal/v2.6.3/
## CheckM
RUN
pip3
install
pysam numpy matplotlib checkm-genome
&&
\
checkm data setRoot /unlock/references/databases/CheckM/
## GTDB-Tk
RUN
python3
-m
pip
install
gtdbtk
ENV
GTDBTK_DATA_PATH=/unlock/references/databases/GTDBTK/release202/
## Needed for faTools
RUN
sudo ln
-s
/usr/lib/x86_64-linux-gnu/libpng16.so.16.34.0 /usr/lib/x86_64-linux-gnu/libpng12.so.0
## SET PATH ##
ENV
CHECKM=/unlock/infrastructure/binaries/hmmer/hmmer-3.3.2/bin:/unlock/infrastructure/binaries/pplacer/pplacer-Linux-v1.1.alpha17/bin:/unlock/infrastructure/binaries/prodigal/v2.6.3
# note: CheckM and GTDB-Tk overlap with hmmer,prodigal and are not added to GTDBTK
ENV
GTDBTK=/unlock/infrastructure/binaries/Mash/mash-Linux64-v2.3:/unlock/infrastructure/binaries/FastTree/FastTree_v2.1.11:/unlock/infrastructure/binaries/Mash/mash-Linux64-v2.3:/unlock/infrastructure/binaries/fastANI/fastANI_v1.33
ENV
PATH=$PATH:$CHECKM:$GTDBTK
######################################
######################################
# Add anonymous access
ADD
irods /root/.irods
...
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