Mercurial > repos > triasteran > catdc_docker_test
diff smalt/instructions.sh @ 9:81f36745bc9d draft
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author | triasteran |
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date | Tue, 08 Mar 2022 11:43:08 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smalt/instructions.sh Tue Mar 08 11:43:08 2022 +0000 @@ -0,0 +1,34 @@ +# Run docker image 'debian/wheezy' in interactive mode +sudo docker run -i -t debian:wheezy + +# Run the below in this image + +apt-get update +apt-get install python +apt-get install wget +apt-get install mercurial + +mkdir tool +cd tool + +wget ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-0.7.3.tgz +tar -xvvzf smalt-0.7.3.tgz + +# because the smalt_wrapper.py finds the binary name based on `uname -i` which is unknown in docker +mv smalt-0.7.3/smalt_x86_64 smalt_unknown + +hg clone https://toolshed.g2.bx.psu.edu/repos/cjav/smalt smalt_deps +cp smalt_deps/smalt_wrapper.py . + +# add smalt tools to PATH (probably different ways to do this) +ln -s /tool/smalt_unknown /usr/bin +ln -s /tool/smalt_wrapper.py /usr/bin + +# make smalt_wrapper executable +chmod a+x /tool/smalt_wrapper.py + +# exit out of docker image and run the below to commit to new container. replace the number '07b...' with container id for the above docker container. +sudo docker commit -m "make smalt_wrapper executable" -a "Aaron Petkau" 07b937918961 apetkau/smalt:v3 + +# push to dockerhub +# please see instructions at http://docs.docker.com/userguide/dockerimages/#push-an-image-to-docker-hub