Mercurial > repos > triasteran > catdc_docker_test
comparison smalt/instructions.sh @ 9:81f36745bc9d draft
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| author | triasteran |
|---|---|
| date | Tue, 08 Mar 2022 11:43:08 +0000 |
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| 8:7e70e7a0f4bb | 9:81f36745bc9d |
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| 1 # Run docker image 'debian/wheezy' in interactive mode | |
| 2 sudo docker run -i -t debian:wheezy | |
| 3 | |
| 4 # Run the below in this image | |
| 5 | |
| 6 apt-get update | |
| 7 apt-get install python | |
| 8 apt-get install wget | |
| 9 apt-get install mercurial | |
| 10 | |
| 11 mkdir tool | |
| 12 cd tool | |
| 13 | |
| 14 wget ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-0.7.3.tgz | |
| 15 tar -xvvzf smalt-0.7.3.tgz | |
| 16 | |
| 17 # because the smalt_wrapper.py finds the binary name based on `uname -i` which is unknown in docker | |
| 18 mv smalt-0.7.3/smalt_x86_64 smalt_unknown | |
| 19 | |
| 20 hg clone https://toolshed.g2.bx.psu.edu/repos/cjav/smalt smalt_deps | |
| 21 cp smalt_deps/smalt_wrapper.py . | |
| 22 | |
| 23 # add smalt tools to PATH (probably different ways to do this) | |
| 24 ln -s /tool/smalt_unknown /usr/bin | |
| 25 ln -s /tool/smalt_wrapper.py /usr/bin | |
| 26 | |
| 27 # make smalt_wrapper executable | |
| 28 chmod a+x /tool/smalt_wrapper.py | |
| 29 | |
| 30 # 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. | |
| 31 sudo docker commit -m "make smalt_wrapper executable" -a "Aaron Petkau" 07b937918961 apetkau/smalt:v3 | |
| 32 | |
| 33 # push to dockerhub | |
| 34 # please see instructions at http://docs.docker.com/userguide/dockerimages/#push-an-image-to-docker-hub |