sh 用于在ubuntu 14.04 VM中部署planemo环境的脚本

Posted 2021-05-07

apt-get install python-pip
apt-get install git -y
export GALAXY_REPO=https://github.com/galaxyproject/galaxy
export GALAXY_RELEASE=release_17.01
export PLANEMO_CONDA_PREFIX="$HOME/conda"
pip install -U pip
source .bashrc
pip --version
echo $PLANEMO_CONDA_PREFIX
pip install  planemo
planemo conda_init
export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH"
planemo --version
conda --version
git clone https://github.com/chamaelj/tools-artbio.git --branch smallrnamap
cd tools-artbio/tools/small_rna_map/
planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive .
planemo conda_install .
planemo test --conda_dependency_resolution --galaxy_branch "$GALAXY_RELEASE" --galaxy_source "$GALAXY_REPO" .
HOST=$(hostname)
echo $HOST
planemo serve --port 9090 --host planemo-test --conda_dependency_resolution --galaxy_branch "$GALAXY_RELEASE" --galaxy_source "$GALAXY_REPO" .
planemo serve --port 80 --host $HOST --conda_dependency_resolution --galaxy_branch "$GALAXY_RELEASE" --galaxy_source "$GALAXY_REPO" .

#!/bin/bash

DIR=$0
IFB_HOST=$(curl --silent icanhazip.com)
docker stop $(docker ps -q)
docker rm $(docker ps -aq)
docker rmi $(docker images -q)
export GALAXY_REPO=https://github.com/galaxyproject/galaxy
export GALAXY_RELEASE=release_16.07
export PLANEMO_CONDA_PREFIX="$HOME/conda"
pip install flake8 planemo
planemo conda_init
export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH"
conda create -y -q -c bioconda --name iuc_conda samtools=0.1.19 bcftools
. activate iuc_conda
git clone https://github.com/ARTbio/tools-artbio.git
cd tools-artbio/tools/$DIR
planemo conda_install .
planemo serve --port 80 --host $IFB_HOST --conda_dependency_resolution --galaxy_branch "$GALAXY_RELEASE" --galaxy_source "$GALAXY_REPO" .