rbbt-image 0.1.36 → 0.1.37
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- checksums.yaml +4 -4
- data/bin/build_rbbt_provision_sh.rb +16 -15
- data/share/provision_scripts/R_packages.sh +2 -1
- data/share/provision_scripts/R_setup.sh +1 -1
- data/share/provision_scripts/bootstrap.sh +1 -1
- data/share/provision_scripts/gem_setup.sh +7 -3
- data/share/provision_scripts/ruby_setup.sh +8 -2
- data/share/provision_scripts/ubuntu_setup.sh +16 -9
- metadata +3 -3
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 45c46d847d1522d0d774cbdad29d9ba70bb1cc42036234dc53de6d0723403e02
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4
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+
data.tar.gz: eef195a183125dbb8f9c3d3f12157a3bff0c4ed12ef1118cd88acf3878d7bba4
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: e3d2cac785c2cd0d192f2913af0f40e6a1abb65b3daa8efd8a2e4f4c97aba672c6421e2e1a8222f753694ac7e52493de3be2af7080943e3bcaf3faec16e44aa2
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7
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+
data.tar.gz: 90c007ee52794941a8c421882779d2e6a1e147e83e9c77e59a1dd4e57e248bed87e4fd20165d530a71933e783b1e929eaa652aec86b6dc1afb176cd01a3984db
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@@ -94,7 +94,7 @@ VARIABLES[:REMOTE_WORKFLOWS] = options[:remote_workflows].split(/[\s,]+/)*" " if
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94
94
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VARIABLES[:RBBT_NOCOLOR] = "true" if options[:nocolor]
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95
95
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VARIABLES[:RBBT_NO_PROGRESS] = "true" if options[:nobar]
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96
96
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|
97
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-
options[:ruby_version] ||= "2.4
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97
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+
options[:ruby_version] ||= "2.6.4"
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98
98
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99
99
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100
100
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provision_script =<<-EOF
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@@ -290,7 +290,7 @@ provision_script +=<<-EOF
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# ====
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292
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apt-get clean
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293
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-
rm -rf /var/lib/apt/lists/* /
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293
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+
rm -rf /var/lib/apt/lists/* /var/tmp/* /usr/share/doc /usr/share/man /usr/local/share/ri
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294
294
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295
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#{ "su -l -c 'rbbt system optimize /home/#{USER}/.rbbt ' #{USER}" if OPTIMIZE}
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296
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@@ -300,9 +300,9 @@ date
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300
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EOF
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302
302
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303
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-
container_dependency = options[:container_dependency] || 'ubuntu:cosmic'
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304
303
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|
305
304
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if docker_image = options[:docker]
|
305
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+
container_dependency = options[:container_dependency] || 'ubuntu:disco'
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306
306
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dockerfile = options[:dockerfile] || File.join(root_dir, 'Dockerfile')
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307
307
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dockerfile_text = Open.read(dockerfile)
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308
308
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dockerfile_text.sub!(/^FROM.*/,'FROM ' + container_dependency) if container_dependency
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@@ -339,6 +339,7 @@ end
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339
339
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|
340
340
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if singularity_image = options[:singularity]
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341
341
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|
342
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+
container_dependency = options[:container_dependency] || 'ubuntu:disco'
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342
343
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TmpFile.with_file(nil, false) do |dir|
|
343
344
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Path.setup(dir)
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344
345
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@@ -349,10 +350,10 @@ Bootstrap: docker
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From: #{container_dependency}
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350
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|
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352
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%post
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352
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-
cat > /
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353
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+
cat > /image_provision.sh <<"EOS"
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353
354
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#{provision_script}
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354
355
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EOS
|
355
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-
bash -x /
|
356
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+
bash -x /image_provision.sh 2>&1 | tee /image_provision.log
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356
357
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ln -s /etc/rbbt_environment /.singularity.d/env/99-rbbt_environment.sh
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357
358
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chmod +x /.singularity.d/env/99-rbbt_environment.sh
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358
359
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bash -c '[ -d /usr/local/share ] || mkdir -p /usr/local/share'
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@@ -368,22 +369,22 @@ EOF
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|
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369
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Open.write(dir["singularity_bootstrap"].find, bootstrap_text)
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369
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Open.write(provision_file, provision_script)
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370
371
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|
371
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-
puts "RUN"
|
372
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-
puts "==="
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373
372
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singularity_size = options[:singularity_size] || 3072
|
374
373
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cmd_create = "singularity create -s #{singularity_size} #{singularity_image}"
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375
374
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cmd_boot = "singularity build #{singularity_image} '#{dir["singularity_bootstrap"]}'"
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375
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+
|
376
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+
|
377
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+
puts "**************"
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378
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+
puts "CREATING IMAGE: #{dir["singularity_bootstrap"].find}"
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379
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+
puts "**************"
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376
380
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puts cmd_create
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377
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-
|
378
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-
while line = io.gets
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379
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-
puts line
|
380
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-
end
|
381
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+
CMD.cmd_log(cmd_create, :log => 4)
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381
382
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|
383
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+
puts "**************"
|
384
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+
puts "BUILDING IMAGE: #{dir["singularity_bootstrap"].find}"
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385
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+
puts "**************"
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382
386
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puts cmd_boot
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383
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-
|
384
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-
while line = io.gets
|
385
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-
puts line
|
386
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-
end
|
387
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+
CMD.cmd_log(cmd_boot, :log => 4)
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387
388
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end
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388
389
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|
389
390
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end
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@@ -38,7 +38,8 @@ R_install_packages 'digest' 'gtable' 'reshape2' 'scales' 'proto'
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38
38
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R_CMD_install 'https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_1.0.0.tar.gz' ggplot2
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39
39
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40
40
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R_install_packages NMF Cairo drc Rserve gridSVG ggthemes mclust randomForest viper
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41
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-
R_install_packages pheatmap VennDiagram Hmisc pls
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41
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+
R_install_packages pheatmap VennDiagram Hmisc pls gridSVG
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42
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+
R_install_packages tidyverse
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42
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R_biocLite limma viper
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44
45
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@@ -29,8 +29,6 @@ gem install --no-document --force \
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ruby-prof \
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rbbt-util rbbt-rest rbbt-dm rbbt-text rbbt-sources rbbt-phgx rbbt-GE \
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31
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rserve-client \
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32
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-
uglifier therubyracer kramdown\
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33
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puma prawn prawn-svg
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34
32
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35
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# Get good version of lockfile
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36
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#wget http://ubio.bioinfo.cnio.es/people/mvazquezg/lockfile-2.1.4.gem -O /tmp/lockfile-2.1.4.gem
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@@ -39,4 +37,10 @@ wget http://github.com/mikisvaz/lockfile/raw/master/lockfile-2.1.5.gem -O /tmp/l
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gem install --no-document /tmp/lockfile-2.1.5.gem
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40
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# Extra things for web interface
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42
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-
gem install --no-document
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40
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+
gem install --no-document --force \
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41
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+
tokyocabinet \
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42
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+
ruby-prof \
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43
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+
rbbt-util rbbt-rest rbbt-dm rbbt-text rbbt-sources rbbt-phgx rbbt-GE \
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rserve-client \
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+
uglifier therubyracer kramdown pandoc pandoc-ruby\
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46
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puma prawn prawn-svg
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@@ -4,7 +4,12 @@
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# ============
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5
5
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6
6
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_small_version=`echo $RUBY_VERSION | cut -f 1,2 -d.`
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7
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-
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7
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+
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8
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[ -d /tmp/ruby-install ] || mkdir /tmp/ruby-install
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9
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_prewd="$(pwd)"
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cd /tmp/ruby-install
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+
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8
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wget https://cache.ruby-lang.org/pub/ruby/$_small_version/ruby-${RUBY_VERSION}.tar.gz -O "ruby.tar.gz"
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9
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tar -xvzf ruby.tar.gz
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10
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cd ruby-*/
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@@ -13,7 +18,8 @@ make && make install
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unset _small_version
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15
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-
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+
cd "$_prewd"
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22
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rm -Rf /tmp/ruby-install
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#\curl -sSL https://get.rvm.io | bash -s stable
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#source /etc/profile.d/rvm.sh
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@@ -15,7 +15,7 @@ _append_with_colon(){
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current=`_var_content $var`
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18
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-
if ! echo $current | grep "\(^\|:\)$value\(:\|$\)"
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18
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+
if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" >/dev/null 2>&1; then
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19
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eval $(echo $var)="\"$current:$value\""
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fi
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}
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@@ -26,7 +26,7 @@ _append_with_space(){
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current=`_var_content $var`
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28
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-
if ! echo $current | grep "\(^\| \)$value\( \|$\)"
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+
if ! echo $current | grep "\(^\| \)$value\( \|$\)" >/dev/null 2>&1; then
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30
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eval $(echo $var)="\"$current:$value\""
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31
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fi
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}
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@@ -37,7 +37,7 @@ _prepend_with_colon(){
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current=`_var_content $var`
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-
if ! echo $current | grep "\(^\|:\)$value\(:\|$\)"
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+
if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" >/dev/null 2>&1; then
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eval $(echo $var)="\"$value:$current\""
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fi
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43
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}
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@@ -48,18 +48,18 @@ _prepend_with_space(){
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current=`_var_content $var`
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50
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-
if ! echo $current | grep "\(^\| \)$value\( \|$\)"
|
51
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+
if ! echo $current | grep "\(^\| \)$value\( \|$\)" >/dev/null 2>&1; then
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52
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eval $(echo $var)="\"$value $current\""
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53
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fi
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54
54
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}
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55
55
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|
56
56
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_add_path(){
|
57
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-
_prepend_with_colon PATH "$1"
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57
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+
_prepend_with_colon PATH "${1%/}"
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58
58
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}
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59
59
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|
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60
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_add_libpath(){
|
61
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-
_prepend_with_colon LD_LIBRARY_PATH "$1"
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62
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-
_prepend_with_colon LD_RUN_PATH "$1"
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61
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+
_prepend_with_colon LD_LIBRARY_PATH "${1%/}"
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+
_prepend_with_colon LD_RUN_PATH "${1%/}"
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63
63
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}
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64
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EOF
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@@ -72,16 +72,19 @@ apt-get -y install software-properties-common
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72
72
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apt-get -y update
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apt-get -y update
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75
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-
apt-get -y install \
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75
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+
DEBIAN_FRONTEND=noninteractive apt-get -y install \
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76
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vim \
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77
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+
wget \
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78
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+
libc6 \
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77
79
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bison autoconf g++ libxslt1-dev make \
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78
80
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zlib1g-dev libbz2-dev libreadline-dev \
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79
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-
wget curl git openssl libyaml-0-2 libyaml-dev \
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81
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+
rsync wget curl git openssl libyaml-0-2 libyaml-dev \
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80
82
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openjdk-8-jdk \
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81
83
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libcairo2 libcairo2-dev r-base-core r-base-dev r-cran-rserve liblzma5 liblzma-dev libcurl4-openssl-dev \
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82
84
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build-essential zlib1g-dev libssl-dev libyaml-dev libffi-dev \
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83
85
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python3 python \
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84
86
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tcsh gawk \
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87
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+
pandoc \
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85
88
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libtbb-dev
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86
89
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|
87
90
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#add-apt-repository ppa:george-edison55/cmake-3.x
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@@ -99,6 +102,7 @@ ln -s /usr/lib/R/site-library/Rserve/libs/Rserve /usr/lib/R/bin/Rserve
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99
102
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|
100
103
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echo "export R_HOME='/usr/lib/R' # For Ruby's RSRuby gem" >> /etc/rbbt_environment
|
101
104
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echo '_add_path "$R_HOME/bin/" # Rserver' >> /etc/rbbt_environment
|
105
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+
echo 'export R_LIBS_USER="~/container_R/lib" # Avoid collision with host system' >> /etc/rbbt_environment
|
102
106
|
|
103
107
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[ -d /opt/bin ] || mkdir -p /opt/bin
|
104
108
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echo '_add_path "/opt/bin/"' >> /etc/rbbt_environment
|
@@ -106,6 +110,9 @@ echo '_add_path "/opt/bin/"' >> /etc/rbbt_environment
|
|
106
110
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[ -d /usr/local/bin ] || mkdir -p /usr/local/bin
|
107
111
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echo '_add_path "/usr/local/bin/"' >> /etc/rbbt_environment
|
108
112
|
|
113
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+
echo 'export LC_ALL=C.UTF-8' >> /etc/rbbt_environment
|
114
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+
|
115
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+
|
109
116
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. /etc/rbbt_environment
|
110
117
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|
111
118
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apt-get clean
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: rbbt-image
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 0.1.
|
4
|
+
version: 0.1.37
|
5
5
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platform: ruby
|
6
6
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authors:
|
7
7
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- Miguel Vazquez
|
8
8
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autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2020-03-31 00:00:00.000000000 Z
|
12
12
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dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rbbt-util
|
@@ -71,7 +71,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
71
71
|
- !ruby/object:Gem::Version
|
72
72
|
version: '0'
|
73
73
|
requirements: []
|
74
|
-
rubygems_version: 3.0.
|
74
|
+
rubygems_version: 3.0.6
|
75
75
|
signing_key:
|
76
76
|
specification_version: 4
|
77
77
|
summary: Build docker and Vagrant (VM) images
|