cicd: update elastic beanstalk commands (#280)

* switch to using python 3.11, cool-seq-tool, and p7zip

.ebextensions/02_app_config.config → .ebextensions/01_app_config.config

@@ -3,25 +3,25 @@ commands:
         command: "yum install -y python-devel postgresql-devel"
     02_install_aws_cli:
         command: "yum install -y awscli"
-    03_install_unzip:
-        command: "yum install -y unzip"
+    03_install_p7zip:
+        command: "yum install -y p7zip"
     04_eb_packages:
        command: "/var/app/venv/staging-LQM1lest/bin/pip install uvloop websockets httptools typing-extensions"
     05_export_eb_env_var:
         command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)"
 
 container_commands:
-    01_uta_permissions:
-        test: test -d "/var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/uta_tools"
-        command: "chmod -R 777 /var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/uta_tools/data"
+    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"
 
     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"
 
-    03_unzip_seqrepo:
+    03_p7zip_seqrepo:
         test: test -f "/usr/local/share/seqrepo.zip"
-        command: "unzip /usr/local/share/seqrepo.zip -d /usr/local/share"
+        command: "7za x /usr/local/share/seqrepo.zip -o/usr/local/share -y"
 
     04_seqrepo_permission:
         test: test -d "/usr/local/share/seqrepo"