Revision 54a97578981a27b4af5c4d62681c233fd89b9f65 authored by Forrest Tanaka on 04 May 2016, 22:38:42 UTC, committed by Forrest Tanaka on 04 May 2016, 22:38:42 UTC
Now concatenate biosample.construct and biosample.model_organism_donor_construct arrays to display them all together in the biosample summary panel.
1 parent 12710d5
cloud-config.yml
#cloud-config
# Instance
apt_sources:
- source: "ppa:webupd8team/java"
- source: "deb http://packages.elasticsearch.org/elasticsearch/1.7/debian stable main"
key: |
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- source: "deb https://deb.nodesource.com/node_4.x trusty main"
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bootcmd:
- set -ex
- cloud-init-per once ssh-users-ca echo "TrustedUserCAKeys /etc/ssh/users_ca.pub" >> /etc/ssh/sshd_config
- cloud-init-per once accepted-oracle-license-v1-1 echo "oracle-java8-installer shared/accepted-oracle-license-v1-1 select true" | debconf-set-selections
- cloud-init-per once fallocate-swapfile fallocate -l 4G /swapfile
- cloud-init-per once chmod-swapfile chmod 600 /swapfile
- cloud-init-per once mkswap-swapfile mkswap /swapfile
- MEMGIGS=$(awk '/MemTotal/{printf "%%.0f", $2 / 1024**2}' /proc/meminfo)
- if [ "$MEMGIGS" -gt 32 ]
- then
- echo "ES_HEAP_SIZE=16g" > /etc/default/elasticsearch
- elif [ "$MEMGIGS" -gt 12 ]
- then
- echo "ES_HEAP_SIZE=8g" > /etc/default/elasticsearch
- else
- echo "ES_HEAP_SIZE=4g" > /etc/default/elasticsearch
- sysctl "vm.swappiness=1"
- swapon /swapfile
- fi
package_upgrade: true
packages:
- apache2-mpm-worker
- bsdtar
- build-essential
- elasticsearch
- git
- graphviz
- libapache2-mod-wsgi-py3
- libevent-dev
- libfreetype6-dev
- libjpeg-dev
- liblcms2-dev
- libmagic-dev
- libpq-dev
- libssl-dev
- libtiff5-dev
- libwebp-dev
- libxml2-dev
- libxslt1-dev
- lzop
- nodejs
- ntp
- oracle-java8-installer
- oracle-java8-set-default
- postgresql-9.3
- pv
- python2.7-dev
- python3.4-dev
- python-software-properties
- python-virtualenv
- ruby-dev
- unattended-upgrades
- update-notifier-common
- zlib1g-dev
power_state:
mode: reboot
output:
all: '| tee -a /var/log/cloud-init-output.log'
runcmd:
# Ideally this would build as a different user so encoded only has read
# permissions
- set -ex
- update-rc.d elasticsearch defaults
- service elasticsearch start
- chown postgres:postgres /etc/postgresql/9.3/main/*.conf
- echo "include 'custom.conf'" >> /etc/postgresql/9.3/main/postgresql.conf
- if test "%(ROLE)s" = "demo"
- then
- echo "standby_mode = off" >> /etc/postgresql/9.3/main/recovery.conf
- echo "include 'demo.conf'" >> /etc/postgresql/9.3/main/postgresql.conf
- fi
- sudo -u postgres createuser encoded
- sudo -u postgres createdb --owner=encoded encoded
- mkdir /srv/encoded
- chown encoded:encoded /srv/encoded
- cd /srv/encoded
- sudo -u encoded git clone --no-checkout https://github.com/ENCODE-DCC/encoded.git .
- sudo -u encoded git checkout %(COMMIT)s
- mkdir /opt/cloudwatchmon
- chown build:build /opt/cloudwatchmon
- sudo -u build virtualenv --python=python2.7 /opt/cloudwatchmon
- sudo -u build /opt/cloudwatchmon/bin/pip install -r cloudwatchmon-requirements.txt
- mkdir /opt/wal-e
- chown postgres:postgres /opt/wal-e
- sudo -u postgres virtualenv --python=python2.7 /opt/wal-e
- sudo -u postgres /opt/wal-e/bin/pip install -r wal-e-requirements.txt
- /etc/init.d/postgresql stop
- sudo -u postgres /opt/wal-e/bin/wal-e --aws-instance-profile --s3-prefix="$(cat /etc/postgresql/9.3/main/wale_s3_prefix)" backup-fetch /var/lib/postgresql/9.3/main LATEST
- sudo -u postgres ln -s /etc/postgresql/9.3/main/recovery.conf /var/lib/postgresql/9.3/main/
- /etc/init.d/postgresql start
- sudo -u encoded python3.4 bootstrap.py --buildout-version 2.4.1 --setuptools-version 18.1
- sudo -u encoded LANG=en_US.UTF-8 bin/buildout -c %(ROLE)s.cfg
- sudo -u encoded bin/aws s3 cp --recursive s3://encoded-conf-prod/.aws .aws
- until sudo -u postgres psql postgres -c ""; do sleep 10; done
- sudo -u encoded sh -c 'cat /dev/urandom | head -c 256 | base64 > session-secret.b64'
- sudo -u encoded bin/create-mapping production.ini --app-name app
- sudo -u encoded bin/index-annotations production.ini --app-name app
- ln -s /srv/encoded/etc/encoded-apache.conf /etc/apache2/sites-available/encoded.conf
- ln -s /srv/encoded/etc/logging-apache.conf /etc/apache2/conf-available/logging.conf
- a2enmod headers
- a2enmod proxy_http
- a2enmod rewrite
- a2enmod ssl
- a2ensite encoded.conf
- a2dissite 000-default
- a2enconf logging
- a2disconf charset
- a2disconf security
- a2disconf localized-error-pages
- a2disconf other-vhosts-access-log
- a2disconf serve-cgi-bin
- if test "%(ROLE)s" = "demo"
- then
- sudo -i -u encoded bin/batchupgrade production.ini --app-name app
- fi
# - sleep 10
# - sudo -u postgres echo "include 'master.conf'" >> /etc/postgresql/9.3/main/postgresql.conf
# - pg_ctlcluster 9.3 main reload
# - pg_ctlcluster 9.3 main promote
# - sudo -u encoded bin/update-keys-links production.ini --app-name app
# - sudo -u encoded bin/upgrade production.ini --app-name app
# - sudo -i -u postgres /opt/wal-e/bin/envfile --config ~postgres/.aws/credentials --section default --upper -- /opt/wal-e/bin/wal-e --s3-prefix="$(cat /etc/postgresql/9.3/main/wale_s3_prefix)" backup-push /var/lib/postgresql/9.3/main
# - sleep 60
# - sudo -i -u encoded PATH="/usr/share/elasticsearch/bin:/usr/lib/postgresql/9.3/bin:$PATH" bin/test -m "not bdd" > tests.out
users:
- default
- name: build
gecos: Build user
inactive: true
system: true
- name: encoded
gecos: ENCODE Metadata Database daemon user
inactive: true
system: true
# Specified homedir must exist
# https://github.com/rubygems/rubygems/issues/689
homedir: /srv/encoded
write_files:
- path: /etc/apt/apt.conf.d/20auto-upgrades
content: |
APT::Periodic::Update-Package-Lists "1";
APT::Periodic::Unattended-Upgrade "1";
- path: /etc/apt/apt.conf.d/50unattended-upgrades
content: |
Unattended-Upgrade::Allowed-Origins {
"${distro_id} ${distro_codename}-security";
};
Unattended-Upgrade::Automatic-Reboot "true";
- path: /etc/cron.d/cloudwatchmon
content: |
*/5 * * * * nobody /opt/cloudwatchmon/bin/mon-put-instance-stats.py --mem-util --swap-util --disk-space-util --disk-path=/ --from-cron
- path: /etc/elasticsearch/elasticsearch.yml
content: |
index.search.slowlog.threshold.query.warn: 8s
index.search.slowlog.threshold.fetch.warn: 1s
index.indexing.slowlog.threshold.index.warn: 25s
- path: /etc/postgresql/9.3/main/custom.conf
content: |
hot_standby = on
max_standby_archive_delay = -1
wal_level = hot_standby
archive_mode = on
archive_timeout = 60
# http://www.postgresql.org/message-id/CAOycyLTm6X3mVLz+sLCex+W==WSMgu9giteV7efPoPXYDhPtzQ@mail.gmail.com
checkpoint_timeout = 1h
- path: /etc/postgresql/9.3/main/demo.conf
content: |
archive_mode = off
- path: /etc/postgresql/9.3/main/master.conf
content: |
archive_command = '/opt/wal-e/bin/envfile --config ~postgres/.aws/credentials --section default --upper -- /opt/wal-e/bin/wal-e --s3-prefix="$(cat /etc/postgresql/9.3/main/wale_s3_prefix)" wal-push "%%p"'
- path: /etc/postgresql/9.3/main/recovery.conf
content: |
# recovery.conf must be linked into data dir to do anything
recovery_target_timeline = 'latest'
restore_command = '/opt/wal-e/bin/wal-e --aws-instance-profile --s3-prefix="$(cat /etc/postgresql/9.3/main/wale_s3_prefix)" wal-fetch "%%f" "%%p"'
standby_mode = on
- path: /etc/postgresql/9.3/main/wale_s3_prefix
content: "%(WALE_S3_PREFIX)s"
- path: /etc/ssh/users_ca.pub
content: ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAv/ymOcnN4LhM4NACc3Or116XXJ6KytuOgB/+1qNkOFBqBosrn7cmJ35rsoNHRgYNrCsRE9ch74RKsN6H72FtSJgBhGh/9oUK7Os6Fqt3/ZZXxgxIx6ubs/MTgrxrAnujiBxUXMXQhLKMriNMpo8mt4nGYVtLk9PBjiyfncaS8H9ZKoNio9dhP8bmTuYvioAI35dqKdSlVLyzr/XkZxia8Ki+pQ0N6uuiEwMR3ToM+LSp8wpFOOAiu4PEAujRW7us/+1hlpKWfn0J7/V3826joHE+I967Vg/+ikcVhF77JjK1nib879VgCWfmn1HPQosIpk4yJfVgGvRVI7I2nfBPVw== encoded@demo-l.encodedcc.org
Computing file changes ...
