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1 # if a new ubuntu image, will need a port mapped and add some basics first
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2 # apt update ; apt install -y python3-dev python3-venv python3-wheel nano curl wget git python3-setuptools
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3 TARGDIR="/galaxy-central"
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4 PDIR="/planemo"
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5 git clone --recursive https://github.com/fubar2/planemo.git $PDIR
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6 mkdir -p $TARGDIR
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7 curl -L -s https://github.com/galaxyproject/galaxy/archive/dev.tar.gz | tar xzf - --strip-components=1 -C $TARGDIR
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8 cd $PDIR
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9 mkdir mytools
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10 python3 -m venv .venv
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11 . .venv/bin/activate
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12 python3 setup.py build
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13 python3 setup.py install
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14 planemo conda_init --conda_prefix $PDIR/con
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15 /planemo/con/bin/conda init
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16 . ~/.bashrc
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17 /planemo/con/bin/conda activate base
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18 /planemo/con/bin/conda install -y -c bioconda -c conda-forge configparser galaxyxml
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19 # without this, planemo does not work in docker... No clue why but planemo goes all pear shaped
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20 # but pip reports that it's missing - installing it explicitly seems to do some kind of magic
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21 echo "Starting first run. This takes ages and includes building the Galaxy client. Be patient. Do something else for 20 minutes"
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22 . $PDIR/.venv/bin/activate
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23 planemo tool_factory --galaxy_root $TARGDIR --port 9090 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install
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24 # planemo tool_factory --galaxy_root $TARGDIR --port 8080 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install
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25 #planemo tool_factory --galaxy_root $TARGDIR --conda_prefix $PDIR/con --port 9090 --host 0.0.0.0
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26 # planemo serve --galaxy_root /galaxy-central/ --conda_prefix /planemo/con --port 8080 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install /planemo/.venv/lib/python3.8/site-packages/planemo-0.74.1-py3.8.egg/planemo_ext/tool_factory_2
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27 # planemo serve --galaxy_root /galaxy-central/ --port 8080 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install /planemo/.venv/lib/python3.8/site-packages/planemo-0.74.1-py3.8.egg/planemo_ext/tool_factory_2
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28 # planemo serve --galaxy_root $TARGDIR --port 8080 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install /usr/local/lib/python3.6/dist-packages/planemo-0.74.1-py3.6.egg/planemo_ext/tool_factory_2/
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29
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30 # host is needed to get -p 9090:9090 to work in docker. Default 127.0.0.1 doesn't redirect :(ls -l /tmp
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