Mercurial > repos > davidecangelosi > pipe_t
annotate docker/Dockerfile @ 16:254114751c2e draft
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit f13c9430052e43a372b0bf311a663498ff79b4fe
author | davidecangelosi |
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date | Fri, 24 May 2019 10:15:57 -0400 |
parents | 5e8bf316343d |
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ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
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1 # Galaxy - PIPE_T |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
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2 # |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
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3 # VERSION 0.2 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
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4 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
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5 FROM bgruening/galaxy-stable:latest |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
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6 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
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7 MAINTAINER D. CANGELOSI, davidecangelosi@gaslini.org |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
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8 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
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9 ENV GALAXY_CONFIG_BRAND="Galaxy PIPE-T" |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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10 ENV ENABLE_TTS_INSTALL True |
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5e8bf316343d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d5c46b42061ff823c19437d1c803119ef8b95627
davidecangelosi
parents:
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11 ENV CONDA_ENSURE_CHANNELS="r,iuc,conda-forge,bioconda,defaults" |
5e8bf316343d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d5c46b42061ff823c19437d1c803119ef8b95627
davidecangelosi
parents:
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12 ENV DEPENDENCY_RESOLVERS_CONFIG_FILE="config/dependency_resolvers_conf.xml" |
5e8bf316343d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d5c46b42061ff823c19437d1c803119ef8b95627
davidecangelosi
parents:
12
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13 |
12
11393eb1c557
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d1be332a7da0e53b3e6451f0aeda0675f190dd64
davidecangelosi
parents:
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14 |
1
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
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15 RUN apt-get -y update |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
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16 RUN apt-get install -y libxml2-dev libcurl4-openssl-dev curl libcairo2-dev |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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17 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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18 #Workaround for ubuntu |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
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19 #RUN cp /etc/ssl/private/ssl-cert-snakeoil.key /etc/ |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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20 #RUN chown root:ssl-cert /etc/ssl-cert-snakeoil.key |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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21 #RUN sed -i -e "s/\/ssl\/private//g" /etc/postgresql/9.3/main/postgresql.conf |
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5e8bf316343d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d5c46b42061ff823c19437d1c803119ef8b95627
davidecangelosi
parents:
12
diff
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22 ADD docker/dependency_resolvers_conf.xml $GALAXY_ROOT/config/dependency_resolvers_conf.xml |
1
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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23 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
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24 #install pipe_t from toolshed |
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11393eb1c557
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d1be332a7da0e53b3e6451f0aeda0675f190dd64
davidecangelosi
parents:
1
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25 ADD docker/tools.yml $GALAXY_ROOT/tools.yaml |
1
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
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26 RUN install-tools $GALAXY_ROOT/tools.yaml && \ |
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5e8bf316343d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d5c46b42061ff823c19437d1c803119ef8b95627
davidecangelosi
parents:
12
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27 /tool_deps/_conda/bin/conda clean --tarballs --yes && \ |
5e8bf316343d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d5c46b42061ff823c19437d1c803119ef8b95627
davidecangelosi
parents:
12
diff
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28 rm /export/galaxy-central/ -rf |
1
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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29 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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30 #RUN chown galaxy:galaxy /usr/local/lib/R/site-library |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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31 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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32 # Mark folders as imported from the host. |
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5e8bf316343d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d5c46b42061ff823c19437d1c803119ef8b95627
davidecangelosi
parents:
12
diff
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33 VOLUME ["/export/", "/data/", "/var/lib/docker"] |
1
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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34 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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35 # Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy) |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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36 EXPOSE :80 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
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37 EXPOSE :21 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
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38 EXPOSE :8800 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
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39 |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
changeset
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40 # Autostart script that is invoked during container start |
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
diff
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41 CMD ["/usr/bin/startup"] |