rbbt-image 0.1.37 → 0.1.39
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- checksums.yaml +4 -4
- data/bin/build_rbbt_provision_sh.rb +53 -32
- data/share/provision_scripts/R_packages.sh +6 -1
- data/share/provision_scripts/R_setup.sh +1 -1
- data/share/provision_scripts/bootstrap.sh +14 -2
- data/share/provision_scripts/gem_setup.sh +5 -5
- data/share/provision_scripts/hacks.sh +1 -1
- data/share/provision_scripts/python_setup.sh +10 -1
- data/share/provision_scripts/ruby_setup.sh +1 -1
- data/share/provision_scripts/slurm_loopback.sh +45 -0
- data/share/provision_scripts/ubuntu_setup.sh +3 -1
- metadata +4 -3
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: a15ae2d4c2941a4e142275466e4fbc6ec65391d778bc658fed5530b722d11b95
|
4
|
+
data.tar.gz: f2fbcb0d6e3c5e70b1f25665879b7a24be34bebc69592a04964630bf29ca5c82
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 745c051c7406d23f7997952e664582aceea31ee7ec6a58574fa50af4143ab3e937f7880ed07701405387c5ce9b2daf69eb3c60a04b6120c7ac36a20822d53181
|
7
|
+
data.tar.gz: e2bf862a7c9c8a76342768100d7e8ef50bf3cd6d44b4ebd21c27b16bc6a9cb0714c49c934a5bebcb56347c660991331f056dc26c1e15a68f0e69499d439d75db
|
@@ -30,6 +30,7 @@ $ #{$0} [options]
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|
30
30
|
-sr--skip_ruby Skip ruby setup installation
|
31
31
|
-sp--skip_perl Skip perl setup installation
|
32
32
|
-spy--skip_python Skip python setup installation
|
33
|
+
-spsl--skip_slurm_loopback Skip setting the slurm loopback
|
33
34
|
-sg--skip_gem Skip ruby gem installation
|
34
35
|
-sR--skip_R Skip R setup
|
35
36
|
-su--skip_user_setup Skip user setup
|
@@ -72,6 +73,7 @@ SKIP_TOKYOCABINET= options[:skip_tokyocabinet]
|
|
72
73
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SKIP_RUBY = options[:skip_ruby]
|
73
74
|
SKIP_PERL = options[:skip_perl]
|
74
75
|
SKIP_PYTHON = options[:skip_python]
|
76
|
+
SKIP_SLURM_LOOPBACK = options[:skip_slurm_loopback]
|
75
77
|
R_CUSTOM = options[:R_custom]
|
76
78
|
SKIP_R = options[:skip_R]
|
77
79
|
SKIP_BOOT = options[:skip_bootstrap]
|
@@ -123,6 +125,8 @@ end
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|
123
125
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if not SKIP_BASE_SYSTEM and R_CUSTOM
|
124
126
|
"echo 1.1 Setting custom R"
|
125
127
|
File.read(script_dir + 'R_setup.sh')
|
128
|
+
else
|
129
|
+
"echo SKIPPED Custom R\necho"
|
126
130
|
end
|
127
131
|
}
|
128
132
|
|
@@ -130,6 +134,8 @@ end
|
|
130
134
|
if not SKIP_R
|
131
135
|
"echo 1.2 Install R packages"
|
132
136
|
File.read(script_dir + 'R_packages.sh')
|
137
|
+
else
|
138
|
+
"echo SKIPPED installing R packages\necho"
|
133
139
|
end
|
134
140
|
}
|
135
141
|
|
@@ -138,7 +144,7 @@ echo "2. Setting up tokyocabinet"
|
|
138
144
|
if not SKIP_TOKYOCABINET
|
139
145
|
File.read(script_dir + 'tokyocabinet_setup.sh')
|
140
146
|
else
|
141
|
-
"echo SKIPPED\necho"
|
147
|
+
"echo SKIPPED TokyoCabinet\necho"
|
142
148
|
end
|
143
149
|
}
|
144
150
|
|
@@ -147,7 +153,7 @@ echo "3. Setting up ruby"
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|
147
153
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if not SKIP_RUBY
|
148
154
|
"export RUBY_VERSION='#{options[:ruby_version]}'\n" << File.read(script_dir + 'ruby_setup.sh')
|
149
155
|
else
|
150
|
-
"echo SKIPPED\necho"
|
156
|
+
"echo SKIPPED Ruby\necho"
|
151
157
|
end
|
152
158
|
}
|
153
159
|
|
@@ -157,7 +163,7 @@ echo "3.1. Setting up gems"
|
|
157
163
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if not SKIP_GEM
|
158
164
|
File.read(script_dir + 'gem_setup.sh')
|
159
165
|
else
|
160
|
-
"echo SKIPPED\necho"
|
166
|
+
"echo SKIPPED Ruby gems\necho"
|
161
167
|
end
|
162
168
|
}
|
163
169
|
|
@@ -167,7 +173,7 @@ echo "4.1 Setting up perl"
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|
167
173
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if not SKIP_PERL
|
168
174
|
File.read(script_dir + 'perl_setup.sh')
|
169
175
|
else
|
170
|
-
"echo SKIPPED\necho"
|
176
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+
"echo SKIPPED Perl\necho"
|
171
177
|
end
|
172
178
|
}
|
173
179
|
|
@@ -176,7 +182,16 @@ echo "4.2 Setting up python"
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|
176
182
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if not SKIP_PYTHON
|
177
183
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File.read(script_dir + 'python_setup.sh')
|
178
184
|
else
|
179
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-
"echo SKIPPED\necho"
|
185
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+
"echo SKIPPED Python\necho"
|
186
|
+
end
|
187
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+
}
|
188
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+
|
189
|
+
echo "4.3 Setting up SLURM loopback"
|
190
|
+
#{
|
191
|
+
if not SKIP_SLURM_LOOPBACK
|
192
|
+
File.read(script_dir + 'slurm_loopback.sh')
|
193
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+
else
|
194
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+
"echo SKIPPED SLURM lookback\necho"
|
180
195
|
end
|
181
196
|
}
|
182
197
|
|
@@ -185,7 +200,7 @@ echo "source /etc/rbbt_environment" >> /etc/profile
|
|
185
200
|
EOF
|
186
201
|
|
187
202
|
provision_script +=<<-EOF
|
188
|
-
echo "
|
203
|
+
echo "5. Configuring user"
|
189
204
|
EOF
|
190
205
|
|
191
206
|
if not SKIP_USER
|
@@ -198,43 +213,47 @@ if [[ '#{ USER }' == 'root' ]] ; then
|
|
198
213
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else
|
199
214
|
useradd -ms /bin/bash #{USER}
|
200
215
|
home_dir='/home/#{USER}'
|
216
|
+
|
217
|
+
if [ -d /usr/local/miniconda3 ]; then
|
218
|
+
chgrp #{USER} -R /usr/local/miniconda3
|
219
|
+
chmod g+rw -R /usr/local/miniconda3
|
220
|
+
fi
|
201
221
|
fi
|
202
222
|
|
203
223
|
user_script=$home_dir/.rbbt/bin/config_user
|
204
224
|
mkdir -p $(dirname $user_script)
|
205
|
-
chown -R #{USER}
|
206
|
-
|
225
|
+
chown -R #{USER} $home_dir/.rbbt/
|
207
226
|
|
208
227
|
# set user configuration script
|
209
228
|
cat > $user_script <<'EUSER'
|
210
229
|
|
211
230
|
. /etc/profile
|
212
231
|
|
213
|
-
echo "
|
232
|
+
echo "5.1. Loading custom variables"
|
214
233
|
#{
|
215
234
|
VARIABLES.collect do |variable,value|
|
216
235
|
"export " << ([variable,'"' << value.to_s << '"'] * "=")
|
217
236
|
end * "\n"
|
218
237
|
}
|
219
238
|
|
220
|
-
echo "
|
239
|
+
echo "5.2. Loading default variables"
|
221
240
|
#{File.read(script_dir + 'variables.sh')}
|
222
241
|
|
223
|
-
echo "
|
242
|
+
echo "5.3. Configuring rbbt"
|
224
243
|
#{File.read(script_dir + 'user_setup.sh')}
|
225
244
|
EUSER
|
226
245
|
|
227
|
-
echo "
|
246
|
+
echo "5.4. Running user configuration as '#{USER}'"
|
228
247
|
chown #{USER} $user_script;
|
229
248
|
su -l -c "bash $user_script" #{USER}
|
230
249
|
|
231
250
|
EOF
|
232
251
|
else
|
233
|
-
provision_script += "echo SKIPPED\necho\n\n"
|
252
|
+
provision_script += "echo SKIPPED user configuration\necho\n\n"
|
234
253
|
end
|
235
254
|
|
236
255
|
provision_script +=<<-EOF
|
237
|
-
echo "
|
256
|
+
echo "6. Bootstrapping workflows as '#{USER}'"
|
238
257
|
echo
|
239
258
|
EOF
|
240
259
|
|
@@ -252,21 +271,22 @@ user_script=$home_dir/.rbbt/bin/bootstrap
|
|
252
271
|
cat > $user_script <<'EUSER'
|
253
272
|
|
254
273
|
. /etc/profile
|
274
|
+
. /etc/rbbt_environment
|
255
275
|
|
256
|
-
echo "
|
276
|
+
echo "6.1. Loading custom variables"
|
257
277
|
#{
|
258
278
|
VARIABLES.collect do |variable,value|
|
259
279
|
"export " << ([variable,'"' << value.to_s << '"'] * "=")
|
260
280
|
end * "\n"
|
261
281
|
}
|
262
282
|
|
263
|
-
echo "
|
283
|
+
echo "6.2. Loading default variables"
|
264
284
|
#{File.read(script_dir + 'variables.sh')}
|
265
285
|
|
266
|
-
echo "
|
286
|
+
echo "6.3. Configuring rbbt"
|
267
287
|
#{File.read(script_dir + 'user_setup.sh')}
|
268
288
|
#
|
269
|
-
echo "
|
289
|
+
echo "6.4. Install and bootstrap"
|
270
290
|
#{File.read(script_dir + "bootstrap.sh")}
|
271
291
|
EUSER
|
272
292
|
|
@@ -275,7 +295,7 @@ su -l -c "bash $user_script" #{USER}
|
|
275
295
|
|
276
296
|
EOF
|
277
297
|
else
|
278
|
-
provision_script += "echo SKIPPED\necho\n\n"
|
298
|
+
provision_script += "echo SKIPPED User configuration\necho\n\n"
|
279
299
|
end
|
280
300
|
|
281
301
|
provision_script +=<<-EOF
|
@@ -302,7 +322,7 @@ EOF
|
|
302
322
|
|
303
323
|
|
304
324
|
if docker_image = options[:docker]
|
305
|
-
container_dependency = options[:container_dependency] || 'ubuntu:
|
325
|
+
container_dependency = options[:container_dependency] || 'ubuntu:focal'
|
306
326
|
dockerfile = options[:dockerfile] || File.join(root_dir, 'Dockerfile')
|
307
327
|
dockerfile_text = Open.read(dockerfile)
|
308
328
|
dockerfile_text.sub!(/^FROM.*/,'FROM ' + container_dependency) if container_dependency
|
@@ -339,7 +359,7 @@ end
|
|
339
359
|
|
340
360
|
if singularity_image = options[:singularity]
|
341
361
|
|
342
|
-
container_dependency = options[:container_dependency] || 'ubuntu:
|
362
|
+
container_dependency = options[:container_dependency] || 'ubuntu:focal'
|
343
363
|
TmpFile.with_file(nil, false) do |dir|
|
344
364
|
Path.setup(dir)
|
345
365
|
|
@@ -357,10 +377,12 @@ EOS
|
|
357
377
|
ln -s /etc/rbbt_environment /.singularity.d/env/99-rbbt_environment.sh
|
358
378
|
chmod +x /.singularity.d/env/99-rbbt_environment.sh
|
359
379
|
bash -c '[ -d /usr/local/share ] || mkdir -p /usr/local/share'
|
380
|
+
bash -c '[ -d /usr/local/workflows ] || mkdir -p /usr/local/workflows'
|
360
381
|
bash -c '[ -d /software/rbbt ] || mkdir -p /software/rbbt'
|
361
|
-
bash -c '[ -d /home/#{USER}/.rbbt/var/ ] && mv /home/#{USER}/.rbbt/var/ /var/rbbt' || echo -n ""
|
362
|
-
bash -c '[ -d /home/#{USER}/.rbbt/var/ ] &&
|
382
|
+
#bash -c '[ -d /home/#{USER}/.rbbt/var/ ] && mv /home/#{USER}/.rbbt/var/ /var/rbbt' || echo -n ""
|
383
|
+
bash -c '[ -d /home/#{USER}/.rbbt/var/ ] && rm -Rf /home/#{USER}/.rbbt/var/' || echo -n ""
|
363
384
|
bash -c '[ -d /home/#{USER}/.rbbt/share/ ] && mv /home/#{USER}/.rbbt/share/ /usr/local/share/rbbt' || echo -n ""
|
385
|
+
bash -c '[ -d /home/#{USER}/.rbbt/workflows/ ] && mv /home/#{USER}/.rbbt/workflows/ /usr/local/workflows/rbbt' || echo -n ""
|
364
386
|
bash -c '[ -d /home/#{USER}/.rbbt/software/opt ] && mv /home/#{USER}/.rbbt/software/opt /software/rbbt/opt' || echo -n ""
|
365
387
|
bash -c '[ -d /home/#{USER}/.rbbt/software/src ] && mv /home/#{USER}/.rbbt/software/src /software/rbbt/src' || echo -n ""
|
366
388
|
bash -c '[ -d /home/#{USER}/.rbbt/software/scm ] && mv /home/#{USER}/.rbbt/software/scm /software/rbbt/scm' || echo -n ""
|
@@ -374,11 +396,11 @@ EOF
|
|
374
396
|
cmd_boot = "singularity build #{singularity_image} '#{dir["singularity_bootstrap"]}'"
|
375
397
|
|
376
398
|
|
377
|
-
puts "**************"
|
378
|
-
puts "CREATING IMAGE: #{dir["singularity_bootstrap"].find}"
|
379
|
-
puts "**************"
|
380
|
-
puts cmd_create
|
381
|
-
CMD.cmd_log(cmd_create, :log => 4)
|
399
|
+
#puts "**************"
|
400
|
+
#puts "CREATING IMAGE: #{dir["singularity_bootstrap"].find}"
|
401
|
+
#puts "**************"
|
402
|
+
#puts cmd_create
|
403
|
+
#CMD.cmd_log(cmd_create, :log => 4)
|
382
404
|
|
383
405
|
puts "**************"
|
384
406
|
puts "BUILDING IMAGE: #{dir["singularity_bootstrap"].find}"
|
@@ -390,6 +412,7 @@ EOF
|
|
390
412
|
end
|
391
413
|
|
392
414
|
if options[:virtualbox]
|
415
|
+
container_dependency = options[:container_dependency] || 'ubuntu:focal'
|
393
416
|
TmpFile.with_file(nil, false) do |dir|
|
394
417
|
Path.setup(dir)
|
395
418
|
|
@@ -416,11 +439,9 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
|
|
416
439
|
end
|
417
440
|
EOF
|
418
441
|
|
442
|
+
Log.debug "Running vagrant on #{dir}"
|
419
443
|
Misc.in_dir(dir) do
|
420
|
-
|
421
|
-
while line = io.gets
|
422
|
-
puts line
|
423
|
-
end
|
444
|
+
CMD.cmd_log(:vagrant, "up")
|
424
445
|
end
|
425
446
|
end
|
426
447
|
end
|
@@ -37,10 +37,15 @@ R_install_packages 'digest' 'gtable' 'reshape2' 'scales' 'proto'
|
|
37
37
|
|
38
38
|
R_CMD_install 'https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_1.0.0.tar.gz' ggplot2
|
39
39
|
|
40
|
-
R_install_packages NMF Cairo drc
|
40
|
+
R_install_packages NMF Cairo drc gridSVG ggthemes mclust randomForest viper
|
41
|
+
|
42
|
+
echo 'install.packages("Rserve", repos="http://www.rforge.net/")' | R --vanilla
|
43
|
+
|
41
44
|
R_install_packages pheatmap VennDiagram Hmisc pls gridSVG
|
42
45
|
R_install_packages tidyverse
|
43
46
|
|
47
|
+
R_install_packages UpSetR
|
48
|
+
|
44
49
|
R_biocLite limma viper
|
45
50
|
|
46
51
|
R_install_packages pROC txtplot
|
@@ -5,13 +5,25 @@
|
|
5
5
|
|
6
6
|
for workflow in $BOOTSTRAP_WORKFLOWS; do
|
7
7
|
rbbt workflow install $workflow
|
8
|
+
|
9
|
+
pip_requirements_file=$(rbbt_find.rb -w $workflow requirements.pip --nocolor)
|
10
|
+
[ -f $pip_requirements_file ] && echo PIP $pip_requirements_file && pip install -r $pip_requirements_file
|
11
|
+
unset pip_requirements_file
|
12
|
+
|
13
|
+
pip_requirements_file2=$(rbbt_find.rb -w $workflow requirements.pip2 --nocolor)
|
14
|
+
[ -f $pip_requirements_file2 ] && pip install -r $pip_requirements_file2
|
15
|
+
unset pip_requirements_file2
|
16
|
+
|
17
|
+
pip_requirements_file3=$(rbbt_find.rb -w $workflow requirements.pip3 --nocolor)
|
18
|
+
[ -f $pip_requirements_file3 ] && pip install -r $pip_requirements_file3
|
19
|
+
unset pip_requirements_file3
|
8
20
|
done
|
9
21
|
|
10
22
|
export RBBT_WORKFLOW_AUTOINSTALL=true
|
11
|
-
export RBBT_LOG
|
23
|
+
export RBBT_LOG=0
|
12
24
|
|
13
25
|
for workflow in $BOOTSTRAP_WORKFLOWS; do
|
14
26
|
echo "Bootstrapping $workflow on $BOOTSTRAP_CPUS CPUs"
|
15
27
|
[ -d $HOME/.rbbt/tmp/ ] || mkdir -p $HOME/.rbbt/tmp/
|
16
|
-
rbbt workflow cmd $workflow bootstrap --cpus $BOOTSTRAP_CPUS
|
28
|
+
rbbt workflow cmd $workflow bootstrap --config_keys "cpus $BOOTSTRAP_CPUS bootstrap" > $HOME/.rbbt/tmp/${workflow}.bootstrap.log
|
17
29
|
done
|
@@ -27,14 +27,14 @@ echo "* Installing bulk gems and Rbbt"
|
|
27
27
|
gem install --no-document --force \
|
28
28
|
tokyocabinet \
|
29
29
|
ruby-prof \
|
30
|
-
rbbt-util rbbt-rest rbbt-dm rbbt-text rbbt-sources
|
30
|
+
rbbt-util rbbt-rest rbbt-dm rbbt-text rbbt-sources \
|
31
31
|
rserve-client \
|
32
32
|
|
33
33
|
# Get good version of lockfile
|
34
34
|
#wget http://ubio.bioinfo.cnio.es/people/mvazquezg/lockfile-2.1.4.gem -O /tmp/lockfile-2.1.4.gem
|
35
35
|
echo "* Installing our version of lockfile"
|
36
|
-
wget
|
37
|
-
gem install --no-document /tmp/lockfile-2.1.
|
36
|
+
wget https://github.com/mikisvaz/lockfile/raw/master/lockfile-2.1.6.gem -O /tmp/lockfile-2.1.6.gem
|
37
|
+
gem install --no-document /tmp/lockfile-2.1.6.gem
|
38
38
|
|
39
39
|
# Extra things for web interface
|
40
40
|
gem install --no-document --force \
|
@@ -42,5 +42,5 @@ gem install --no-document --force \
|
|
42
42
|
ruby-prof \
|
43
43
|
rbbt-util rbbt-rest rbbt-dm rbbt-text rbbt-sources rbbt-phgx rbbt-GE \
|
44
44
|
rserve-client \
|
45
|
-
uglifier therubyracer kramdown pandoc pandoc-ruby\
|
46
|
-
puma prawn prawn-svg
|
45
|
+
uglifier therubyracer kramdown pandoc pandoc-ruby \
|
46
|
+
puma prawn prawn-svg mimemagic
|
@@ -1,2 +1,2 @@
|
|
1
1
|
# For BNReduction work
|
2
|
-
ln -s /bin/sed /usr/bin/sed
|
2
|
+
#ln -s /bin/sed /usr/bin/sed
|
@@ -2,15 +2,24 @@ wget "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" -O
|
|
2
2
|
echo "# Python conda " >> /etc/rbbt_environment
|
3
3
|
|
4
4
|
bash /tmp/miniconda.sh -b -p /usr/local/miniconda3
|
5
|
+
|
5
6
|
ln -s /usr/local/miniconda3/bin/conda /usr/local/bin/conda
|
6
7
|
echo '_add_path "/usr/local/miniconda3/bin/"' >> /etc/rbbt_environment
|
7
8
|
|
8
9
|
conda create --yes -n python2 python=2.7 pip
|
9
10
|
|
10
|
-
conda create --yes -n python3 python=3 pip
|
11
|
+
conda create --yes -n python3 python=3.6 pip
|
11
12
|
|
12
13
|
echo '_add_path "/usr/local/miniconda3/envs/python2/bin/"' >> /etc/rbbt_environment
|
13
14
|
echo '_add_path "/usr/local/miniconda3/envs/python3/bin/"' >> /etc/rbbt_environment
|
15
|
+
echo '' >> /etc/rbbt_environment
|
16
|
+
echo '# Setup conda environment' >> /etc/rbbt_environment
|
17
|
+
echo 'export CONDA_PKGS_DIRS=~/tmp/conda/pkgs' >> /etc/rbbt_environment
|
18
|
+
echo '. /usr/local/miniconda3/etc/profile.d/conda.sh' >> /etc/rbbt_environment
|
14
19
|
|
15
20
|
rm -Rf /usr/local/miniconda3/pkgs
|
16
21
|
source /etc/rbbt_environment
|
22
|
+
|
23
|
+
pip install ansible
|
24
|
+
|
25
|
+
gem install pycall
|
@@ -13,7 +13,7 @@ cd /tmp/ruby-install
|
|
13
13
|
wget https://cache.ruby-lang.org/pub/ruby/$_small_version/ruby-${RUBY_VERSION}.tar.gz -O "ruby.tar.gz"
|
14
14
|
tar -xvzf ruby.tar.gz
|
15
15
|
cd ruby-*/
|
16
|
-
./configure --prefix=/usr/local
|
16
|
+
./configure --prefix=/usr/local --enable-shared
|
17
17
|
make && make install
|
18
18
|
|
19
19
|
unset _small_version
|
@@ -0,0 +1,45 @@
|
|
1
|
+
#!/bin/bash -x
|
2
|
+
|
3
|
+
# Prepare SLURM loopback
|
4
|
+
# ======================
|
5
|
+
|
6
|
+
cat <<'EOF' > /usr/local/bin/loopback_cmd
|
7
|
+
#!/bin/bash
|
8
|
+
|
9
|
+
if [ -z "$LOOPBACK_KEY" ]; then
|
10
|
+
LOOPBACK_KEY="$HOME/.ssh/slurm-loopback"
|
11
|
+
fi
|
12
|
+
|
13
|
+
if [ ! -f "$LOOPBACK_KEY" ]; then
|
14
|
+
echo "Prepare a ssh key on '$LOOPBACK_KEY' or point to it with environment variable LOOPBACK_KEY." >&2
|
15
|
+
exit -1
|
16
|
+
else
|
17
|
+
ssh localhost -i $LOOPBACK_KEY "$@"
|
18
|
+
fi
|
19
|
+
EOF
|
20
|
+
|
21
|
+
|
22
|
+
cat <<'EOF' > /usr/local/bin/squeue
|
23
|
+
#!/bin/bash
|
24
|
+
|
25
|
+
loopback_cmd squeue "$@"
|
26
|
+
EOF
|
27
|
+
|
28
|
+
|
29
|
+
cat <<'EOF' > /usr/local/bin/sbatch
|
30
|
+
#!/bin/bash
|
31
|
+
|
32
|
+
loopback_cmd sbatch "$@"
|
33
|
+
EOF
|
34
|
+
|
35
|
+
cat <<'EOF' > /usr/local/bin/sacct
|
36
|
+
#!/bin/bash
|
37
|
+
|
38
|
+
loopback_cmd sacct "$@"
|
39
|
+
EOF
|
40
|
+
|
41
|
+
chmod +x /usr/local/bin/loopback_cmd /usr/local/bin/squeue /usr/local/bin/sbatch /usr/local/bin/sacct
|
42
|
+
|
43
|
+
|
44
|
+
|
45
|
+
|
@@ -76,14 +76,16 @@ DEBIAN_FRONTEND=noninteractive apt-get -y install \
|
|
76
76
|
vim \
|
77
77
|
wget \
|
78
78
|
libc6 \
|
79
|
+
time numactl xvfb \
|
79
80
|
bison autoconf g++ libxslt1-dev make \
|
80
81
|
zlib1g-dev libbz2-dev libreadline-dev \
|
81
82
|
rsync wget curl git openssl libyaml-0-2 libyaml-dev \
|
82
83
|
openjdk-8-jdk \
|
83
84
|
libcairo2 libcairo2-dev r-base-core r-base-dev r-cran-rserve liblzma5 liblzma-dev libcurl4-openssl-dev \
|
84
85
|
build-essential zlib1g-dev libssl-dev libyaml-dev libffi-dev \
|
85
|
-
python3 python \
|
86
|
+
python3 python libtorch \
|
86
87
|
tcsh gawk \
|
88
|
+
ansible \
|
87
89
|
pandoc \
|
88
90
|
libtbb-dev
|
89
91
|
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-image
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.1.
|
4
|
+
version: 0.1.39
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2023-01-31 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rbbt-util
|
@@ -48,6 +48,7 @@ files:
|
|
48
48
|
- share/provision_scripts/perl_setup.sh
|
49
49
|
- share/provision_scripts/python_setup.sh
|
50
50
|
- share/provision_scripts/ruby_setup.sh
|
51
|
+
- share/provision_scripts/slurm_loopback.sh
|
51
52
|
- share/provision_scripts/tokyocabinet_setup.sh
|
52
53
|
- share/provision_scripts/ubuntu_setup.sh
|
53
54
|
- share/provision_scripts/user_setup.sh
|
@@ -71,7 +72,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
71
72
|
- !ruby/object:Gem::Version
|
72
73
|
version: '0'
|
73
74
|
requirements: []
|
74
|
-
rubygems_version: 3.
|
75
|
+
rubygems_version: 3.1.4
|
75
76
|
signing_key:
|
76
77
|
specification_version: 4
|
77
78
|
summary: Build docker and Vagrant (VM) images
|