Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

chore: update ebextensions for downloading latest seqrepo instance #564

Merged
merged 13 commits into from
Jul 16, 2024
Merged

chore: update ebextensions for downloading latest seqrepo instance #564

Changes from all commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
cf00328
chore: update ebextensions for downloading latest seqrepo instance
korikuzma Jul 16, 2024
80e8a05
fix path
korikuzma Jul 16, 2024
18610d8
test
korikuzma Jul 16, 2024
a17af67
Merge branch 'staging' into eb-extensions
korikuzma Jul 16, 2024
cbb94db
fix: TypeError for params that accept union of enums
korikuzma Jul 16, 2024
4de1a07
style: ruff format
korikuzma Jul 16, 2024
ff24bca
Merge branch 'ruff' into fixes
korikuzma Jul 16, 2024
8fd4680
ruff
korikuzma Jul 16, 2024
f12482a
Merge branch 'fixes' into eb-extensions
korikuzma Jul 16, 2024
067a4c3
fix
korikuzma Jul 16, 2024
25e7432
Merge branch 'staging' into fixes
korikuzma Jul 16, 2024
8dad18b
Merge branch 'fixes' into eb-extensions
korikuzma Jul 16, 2024
fb3b484
Merge branch 'staging' into eb-extensions
korikuzma Jul 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
50 changes: 14 additions & 36 deletions .ebextensions/01_download_data.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,46 +3,24 @@ commands:
command: "yum install -y python-devel postgresql-devel"
02_install_aws_cli:
command: "yum install -y awscli"
03_install_p7zip:
command: "yum install -y p7zip"
04_eb_packages:
03_eb_packages:
command: "/var/app/venv/staging-LQM1lest/bin/pip install uvloop websockets httptools typing-extensions"
05_export_eb_env_var:
04_export_eb_env_var:
command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)"

container_commands:
01_cool_seq_tool_permissions:
test: test -d "/var/app/venv/staging-LQM1lest/lib/python3.11/site-packages/cool_seq_tool"
command: "chmod -R 777 /var/app/venv/staging-LQM1lest/lib/python3.11/site-packages/cool_seq_tool/data"
01_s3_download:
test: test ! -d "/usr/local/share/seqrepo/2024-02-20"
command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} /usr/local/share/seqrepo.tar.gz --region us-east-2"

02_s3_download:
test: test ! -d "/usr/local/share/seqrepo"
command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} /usr/local/share/seqrepo.zip --region us-east-2"
02_extract_seqrepo:
test: test -f "/usr/local/share/seqrepo.tar.gz"
command: "mkdir -p /usr/local/share/seqrepo/2024-02-20 && tar -xzvf /usr/local/share/seqrepo.tar.gz -C /usr/local/share/seqrepo/2024-02-20"

03_p7zip_seqrepo:
test: test -f "/usr/local/share/seqrepo.zip"
command: "7za x /usr/local/share/seqrepo.zip -o/usr/local/share -y"
03_seqrepo_zip_permission:
test: test -f "/usr/local/share/seqrepo.tar.gz"
command: "chmod +wr /usr/local/share/seqrepo.tar.gz"

04_seqrepo_permission:
test: test -d "/usr/local/share/seqrepo"
command: "chmod -R 777 /usr/local/share/seqrepo"

05_macosx_permission:
test: test -d "/usr/local/share/__MACOSX"
command: "chmod -R +wr /usr/local/share/__MACOSX"

06_seqrepo_zip_permission:
test: test -f "/usr/local/share/seqrepo.zip"
command: "chmod +wr /usr/local/share/seqrepo.zip"

07_remove_macosx:
test: test -d "/usr/local/share/__MACOSX"
command: "rm -R /usr/local/share/__MACOSX"

08_remove_seqrepo_zip:
test: test -f "/usr/local/share/seqrepo.zip"
command: "rm /usr/local/share/seqrepo.zip"

9_data_permission:
test: test -d "/usr/local/share/seqrepo"
command: "chmod -R +wrx /usr/local/share/seqrepo"
04_remove_seqrepo_zip:
test: test -f "/usr/local/share/seqrepo.tar.gz"
command: "rm /usr/local/share/seqrepo.tar.gz"