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Galaxy-Heatmap.make
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Galaxy-Heatmap.make
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# build a Docker Galaxy MDA Heatmap instance with visualization included
# bob brown & mike ryan 11apr2016
# assumes this script is run form the git/ top level directory and that the MDA_Heatmap repository has been pulled
#git clone https://odin.mdacc.tmc.edu/mcryan/NGCHM_Galaxy.git
#NOTE MUST RUN IN DOCKER TERMINAL WINDOW
#NOTE Script must be started while in the git/ directory
#NOTE need one parameter that is the docker virtualbox directory
echo ' MUST BE RUN IN DOCKER TERMINAL WINDOW '
echo ' Script must be started while in the git/ directory '
echo ' The one parameter that is the docker virtualbox directory '
#do not need sudo mount -t '/Users/bobbrown/VirtualBox\ VMs/boot2docker-vm/zzz' '/Users/NGCHM_Galaxy' #mount local directory to Docker
eval "$(docker-machine env default)" #https://github.com/docker/kitematic/issues/1010
docker pull bgruening/galaxy-stable #download galaxy instance
cp -r NGCHM_Galaxy '/Users/bobbrown/VirtualBox\ VMs/boot2docker-vm/zzz'
#cd ..
docker run --name="galaxy_heatmap" -v '/Users/bobbrown/VirtualBox VMs/boot2docker-vm/zzz':/tmp -d -p 8811:80 -p 7021:21 -e "[email protected],[email protected]" bgruening/galaxy-stable #name prog galaxy run on IP 8888
#fails docker run --name="galaxy_heatmap" -v git:/tmp -d -p 8811:80 -p 7021:21 -e "[email protected],[email protected]" bgruening/galaxy-stable #name prog galaxy run on IP 8888
docker-machine ip # retrieve docker IP for use with mac 192.168.99.100:8888
docker exec -it galaxy_heatmap /bin/bash #enter galaxy main directory on docker instance
cd /galaxy-central/tools
mv /tmp/NGCHM_Galaxy/mda_heatmap_gen ./MDA_Heatmaps # move file up out of NGCHM dir
mv /tmp/NGCHM_Galaxy/mda_heatmap_viz /galaxy-central/config/plugins/visualizations # move visualization to correct spot
cd /galaxy-central
#modify tool_conf.xml # add as 3 thur 5 lines of tool_conf.xml.main
sed -i '/<toolbox>/a <section id="MDAheatmap" name="TCGA_Heatmap Creation">\n <tool file="MDA_Heatmaps/mda_heatmap_gen.xml" />\n </section>' /galaxy-central/config/tool_conf.xml.main
nohup sh run.sh & #run in backgroup
rm -R /Users/NGCHM_Galaxy
docker create galaxy-heatmap
#old docker run --name="galaxy" -d -p 8888:80 -p 7021:21 -e "[email protected],[email protected]" bgruening/galaxy-stable #name prog galaxy run on IP 8888
#old docker run -v /tmp:/tmp bgruening/galaxy-stable #mount NGCHM_Galaxy as directory in image / http://stackoverflow.com/questions/15693153/mounting-directory-from-parent-system-to-container-in-docker
#docker exec -it galaxy_heatmap /galaxy-central/tools get permission denied but if two steps it is okay