rtd_upgrade.sh 1.64 KB
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#!/bin/bash
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# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
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# Copyright [2016-2021] EMBL-European Bioinformatics Institute
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# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#      http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

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# Bail out if anything goes wrong
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set -e

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# Restart from a clean state
rm -rf "$1"
mkdir -p "$1"
cd "$1"
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echo ISSUE
cat /etc/issue
echo PERLVERSION
perl --version
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mkdir packages
cd packages
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# List of extra packages we need
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apt-get download \
     libdbi-perl \
     libdbd-sqlite3-perl \
     libjson-xs-perl \
     libjson-perl \
     libcommon-sense-perl \
     libtypes-serialiser-perl \
     libxml-xpath-perl \
     libparse-recdescent-perl \
     libipc-run-perl \
     libio-pty-perl \
     libgraphviz-perl \
     doxypy \
     libproc-daemon-perl \

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mkdir ../root
for i in *.deb; do dpkg -x "$i" ../root/; done
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git clone --branch master --depth 1 https://github.com/Ensembl/ensembl.git ../ensembl
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git clone --branch version/2.5 --depth 1 https://github.com/Ensembl/ensembl-hive-docker-swarm.git ../ensembl-hive-docker-swarm
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rm -f ../../../contrib/docker-swarm
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ln -s "$1/ensembl-hive-docker-swarm/docs" ../../../contrib/docker-swarm