diff --git a/.ebextensions/01_download_data.config b/.ebextensions/01_download_data.config index e1358921..8ee01fd2 100644 --- a/.ebextensions/01_download_data.config +++ b/.ebextensions/01_download_data.config @@ -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"