Anduril - Gig77/wiki GitHub Wiki
Installation inside docker
Startup base image
docker run -it ubuntu /bin/bash
Following https://code.google.com/p/anduril/wiki/CloningAnduril
echo 'deb http://csbl.fimm.fi/linux/ binary/' > /etc/apt/sources.list.d/anduril.list
wget http://csbl.fimm.fi/linux/anduril_pub.gpg -O - | apt-key add -
sudo apt-get update
sudo apt-get install anduril-local-installer
anduril-source-install
anduril-source-update
anduril-local-enable
source /root/.bashrc
Exit docker and create image from container. Note container ID from command prompt exit
docker commit <containerid> cfrech/anduril:base
Test newly created image
docker run --rm -it cfrech/anduril:base /bin/bash
anduril run --help
exit
Dockerfile (Debian Wheezy)
FROM debian:7.8
# enable to set specific mirror nearby
# RUN sed -i 's/httpredir.debian.org/ftp.at.debian.org/' /etc/apt/sources.list
RUN echo 'deb http://csbl.fimm.fi/linux/ binary/' > /etc/apt/sources.list.d/anduril.list
RUN apt-get update && apt-get install -y wget
RUN wget http://csbl.fimm.fi/linux/anduril_pub.gpg -O - | apt-key add -
RUN apt-get update && apt-get install -y --force-yes --fix-missing anduril-local-installer
RUN anduril-source-install -a
RUN anduril-source-update
RUN echo y | anduril-local-enable
Installation Moksiskaan (as clone of an existing installation)
Prepare database dump on existing server
/opt/moksiskaan/dbDump.sh out /opt/moksiskaan/dumps/moksiskaan-20150327.dbdump
Clone /opt directory
scp -r modicell@modicell:/opt/* /opt/
Remove anduril-bundles if already installed elsewhere
mv /opt/anduril-bundles/anduril.sequencing /usr/local/share/anduril-bundles/sequencing
mv /opt/anduril-bundles/anima /usr/local/share/anduril-bundles/anima
rm -rf /opt/anduril-bundles
rm -rf /opt/hibernate ln -s /opt/hibernate-release-4.3.5.Final/ /opt/hibernate /opt/moksiskaan/dbDump.sh in /opt/moksiskaan/dumps/moksiskaan-20150327.dbdump chmod a+x /opt/moksiskaan/db/piispanhiippa export MOKSISKAAN_HOME=/opt/moksiskaan/db export HIBERNATE_DIR=/opt/hibernate ln -s $MOKSISKAAN_HOME/piispanhiippa /usr/bin/piispanhiippa
Misc
Clear execution folder of unused components, keeping alignments and count files
cd execute
ls | grep -vxf <(cut -f 1 _state) | grep -vP "^(gsnap|htseq|_state|output)" | xargs rm -rf