diff toolfactory/maketf.sh @ 0:f288fab71d8b draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/maketf.sh	Mon Apr 26 04:18:54 2021 +0000
@@ -0,0 +1,30 @@
+# if a new ubuntu image, will need a port mapped and add some basics first
+# apt update ; apt install -y python3-dev python3-venv python3-wheel nano curl wget git python3-setuptools
+TARGDIR="/galaxy-central"
+PDIR="/planemo"
+git clone --recursive https://github.com/fubar2/planemo.git $PDIR
+mkdir -p $TARGDIR
+curl -L -s https://github.com/galaxyproject/galaxy/archive/dev.tar.gz | tar xzf - --strip-components=1 -C $TARGDIR
+cd $PDIR
+mkdir mytools
+python3 -m venv .venv
+. .venv/bin/activate
+python3 setup.py build
+python3 setup.py install
+planemo conda_init --conda_prefix $PDIR/con
+/planemo/con/bin/conda init
+. ~/.bashrc
+/planemo/con/bin/conda activate base
+/planemo/con/bin/conda install -y -c bioconda -c conda-forge configparser galaxyxml
+# without this, planemo does not work in docker... No clue why but planemo goes all pear shaped
+# but pip reports that it's missing - installing it explicitly seems to do some kind of magic
+echo "Starting first run. This takes ages and includes building the Galaxy client. Be patient. Do something else for 20 minutes"
+. $PDIR/.venv/bin/activate
+planemo tool_factory --galaxy_root $TARGDIR --port 9090 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install 
+# planemo tool_factory --galaxy_root $TARGDIR --port 8080 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install 
+#planemo tool_factory --galaxy_root $TARGDIR --conda_prefix $PDIR/con --port 9090 --host 0.0.0.0
+# 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 
+# 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 
+# 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/
+
+# host is needed to get -p 9090:9090 to work in docker. Default 127.0.0.1 doesn't redirect :(ls -l /tmp