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1 # Galaxy - SMALT
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2 # From https://toolshed.g2.bx.psu.edu/repository/view_repository?sort=Repository.name&operation=view_or_manage_repository&changeset_revision=54855bd8d107&id=ec70d959cc6d865d
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3
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4 FROM debian:wheezy
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5
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6 MAINTAINER Aaron Petkau, aaron.petkau@gmail.com
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7
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8 # make sure the package repository is up to date
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9 RUN DEBIAN_FRONTEND=noninteractive apt-get -qq update
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10
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11 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y python
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12 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y wget
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13 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y mercurial
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14
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15 RUN mkdir /tmp/smalt
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16 WORKDIR /tmp/smalt
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17
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18 RUN wget ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-0.7.3.tgz
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19 RUN tar -xvvzf smalt-0.7.3.tgz
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20 RUN cp smalt-0.7.3/smalt_x86_64 /usr/bin/smalt_unknown
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21
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22 RUN hg clone https://toolshed.g2.bx.psu.edu/repos/cjav/smalt smalt_deps
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23 RUN cp smalt_deps/smalt_wrapper.py /usr/bin/smalt_wrapper.py
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24 RUN chmod a+x /usr/bin/smalt_wrapper.py
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25
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26 RUN apt-get clean && rm -rf /tmp/smalt && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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