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chore: update ebextensions for downloading latest seqrepo instance (#292
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,46 +1,22 @@ | ||
| commands: | ||
| 01_install_postgresql_devel: | ||
| command: "yum install -y python-devel postgresql-devel" | ||
| 02_install_aws_cli: | ||
| 01_install_aws_cli: | ||
| command: "yum install -y awscli" | ||
| 03_install_p7zip: | ||
| command: "yum install -y p7zip" | ||
| 04_export_eb_env_var: | ||
| 02_export_eb_env_var: | ||
| command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)" | ||
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| container_commands: | ||
| 01_cool_seq_tool_permissions: | ||
| test: test -d "/var/app/venv/staging-LQM1lest/lib/python3.11/site-packages/cool_seq_tool" | ||
| command: "chmod -R 777 /var/app/venv/staging-LQM1lest/lib/python3.11/site-packages/cool_seq_tool/data" | ||
| 01_s3_download: | ||
| test: test ! -d "/usr/local/share/seqrepo/2024-02-20" | ||
| command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} /usr/local/share/seqrepo.tar.gz --region us-east-2" | ||
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| 02_seqrepo_download: | ||
| test: test ! -d "/usr/local/share/seqrepo" | ||
| command: "aws s3 cp s3://${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" | ||
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| 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" | ||
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| 04_seqrepo_permission: | ||
| test: test -d "/usr/local/share/seqrepo" | ||
| command: "chmod -R 777 /usr/local/share/seqrepo" | ||
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| 05_macosx_permission: | ||
| test: test -d "/usr/local/share/__MACOSX" | ||
| command: "chmod -R +wr /usr/local/share/__MACOSX" | ||
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| 06_seqrepo_zip_permission: | ||
| test: test -f "/usr/local/share/seqrepo.zip" | ||
| command: "chmod +wr /usr/local/share/seqrepo.zip" | ||
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| 07_remove_macosx: | ||
| test: test -d "/usr/local/share/__MACOSX" | ||
| command: "rm -R /usr/local/share/__MACOSX" | ||
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| 08_remove_seqrepo_zip: | ||
| test: test -f "/usr/local/share/seqrepo.zip" | ||
| command: "rm /usr/local/share/seqrepo.zip" | ||
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| 09_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" |