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