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Clinical-Genomics / genotype

Simple genotype comparison of VCF files
http://taboo.readthedocs.org/en/latest/
MIT License
8 stars 2 forks source link

Update DEPLOYMENT.md #59

Closed henrikstranneheim closed 1 year ago

henrikstranneheim commented 1 year ago

This PR adds/fixes ...

How to prepare for test:

Review:

This version is a:

Implementation plan:

sonarcloud[bot] commented 1 year ago

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

henrikstranneheim commented 1 year ago

Deployed on Hasta:

[henrik.stranneheim@hasta:~] [P_base] $ bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-prod.sh -e P_genotype -t genotype -b master
Collecting git+https://github.com/Clinical-Genomics/genotype@master
  Running command git clone --quiet https://github.com/Clinical-Genomics/genotype /home/henrik.stranneheim/tmp/pip-req-build-q7j9km2j
  Cloning https://github.com/Clinical-Genomics/genotype (to revision master) to ./tmp/pip-req-build-q7j9km2j
  Resolved https://github.com/Clinical-Genomics/genotype to commit 9141f76383510210e52e190da05c35596e442539
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: genotype
  Building wheel for genotype (pyproject.toml): started
  Building wheel for genotype (pyproject.toml): finished with status 'done'
  Created wheel for genotype: filename=genotype-4.1.2-py3-none-any.whl size=31297 sha256=3ae3e532cb6c33f70bb1b8cb64a74a5a1e667c0ee0b1b7df88ebdb4891ec27ad
  Stored in directory: /home/henrik.stranneheim/tmp/pip-ephem-wheel-cache-m0gwvee2/wheels/01/16/ea/57ccaf0014013064dba677747cfca144721c057caa9bbc6734
Successfully built genotype
Installing collected packages: genotype
  Attempting uninstall: genotype
    Found existing installation: genotype 4.1.1
    Uninstalling genotype-4.1.1:
      Successfully uninstalled genotype-4.1.1
Successfully installed genotype-4.1.2
Collecting git+https://github.com/Clinical-Genomics/genotype@master
  Running command git clone --quiet https://github.com/Clinical-Genomics/genotype /home/henrik.stranneheim/tmp/pip-req-build-yg1kbofb
  Cloning https://github.com/Clinical-Genomics/genotype (to revision master) to ./tmp/pip-req-build-yg1kbofb
  Resolved https://github.com/Clinical-Genomics/genotype to commit 9141f76383510210e52e190da05c35596e442539
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: Flask-Security in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (3.0.0)
Requirement already satisfied: Flask-Login==0.5.0 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (0.5.0)
Requirement already satisfied: gunicorn in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (20.1.0)
Requirement already satisfied: Flask-Alchy in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (0.5.0)
Requirement already satisfied: Flask-Bootstrap in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (3.3.7.1)
Requirement already satisfied: coloredlogs in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (15.0.1)
Requirement already satisfied: numpy==1.19.2 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (1.19.2)
Requirement already satisfied: Flask-SQLAlchemy==2.1 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (2.1)
Requirement already satisfied: SQLAlchemy<1.4 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (1.3.24)
Requirement already satisfied: cyvcf2 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (0.30.18)
Requirement already satisfied: Alchy in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (2.2.2)
Requirement already satisfied: pysam in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (0.19.1)
Requirement already satisfied: werkzeug<1.0.0 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (0.16.1)
Requirement already satisfied: jinja2==2.11.2 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (2.11.2)
Requirement already satisfied: xlrd==1.2.0 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (1.2.0)
Requirement already satisfied: pyyaml in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (6.0)
Requirement already satisfied: ruamel.yaml in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (0.17.21)
Requirement already satisfied: markupsafe==1.1.1 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (1.1.1)
Requirement already satisfied: itsdangerous==1.1.0 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (1.1.0)
Requirement already satisfied: click in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (8.1.3)
Requirement already satisfied: Flask==1.1.1 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (1.1.1)
Requirement already satisfied: cython in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (0.29.32)
Requirement already satisfied: pymysql in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (1.0.2)
Requirement already satisfied: Flask-Dance==3.0.0 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (3.0.0)
Requirement already satisfied: wheel in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (0.37.1)
Requirement already satisfied: Flask-Reverse-Proxy in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from genotype==4.1.2) (0.2.0.2)
Requirement already satisfied: six in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Dance==3.0.0->genotype==4.1.2) (1.16.0)
Requirement already satisfied: oauthlib in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Dance==3.0.0->genotype==4.1.2) (3.2.2)
Requirement already satisfied: requests-oauthlib>=1.0.0 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Dance==3.0.0->genotype==4.1.2) (1.3.1)
Requirement already satisfied: requests>=2.0 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Dance==3.0.0->genotype==4.1.2) (2.28.1)
Requirement already satisfied: urlobject in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Dance==3.0.0->genotype==4.1.2) (2.4.3)
Requirement already satisfied: importlib-metadata in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from click->genotype==4.1.2) (5.0.0)
Requirement already satisfied: pydash>=3.4.7 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Alchy->genotype==4.1.2) (5.1.1)
Requirement already satisfied: humanfriendly>=9.1 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from coloredlogs->genotype==4.1.2) (10.0)
Requirement already satisfied: visitor in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Bootstrap->genotype==4.1.2) (0.1.3)
Requirement already satisfied: dominate in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Bootstrap->genotype==4.1.2) (2.7.0)
Requirement already satisfied: Flask-Principal>=0.3.3 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Security->genotype==4.1.2) (0.4.0)
Requirement already satisfied: Flask-Mail>=0.7.3 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Security->genotype==4.1.2) (0.9.1)
Requirement already satisfied: passlib>=1.7 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Security->genotype==4.1.2) (1.7.4)
Requirement already satisfied: Flask-WTF>=0.13.1 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Security->genotype==4.1.2) (1.0.1)
Requirement already satisfied: Flask-BabelEx>=0.9.3 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Security->genotype==4.1.2) (0.9.4)
Requirement already satisfied: setuptools>=3.0 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from gunicorn->genotype==4.1.2) (65.5.0)
Requirement already satisfied: ruamel.yaml.clib>=0.2.6 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from ruamel.yaml->genotype==4.1.2) (0.2.7)
Requirement already satisfied: Babel>=1.0 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-BabelEx>=0.9.3->Flask-Security->genotype==4.1.2) (2.10.3)
Requirement already satisfied: speaklater>=1.2 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-BabelEx>=0.9.3->Flask-Security->genotype==4.1.2) (1.3)
Requirement already satisfied: blinker in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-Mail>=0.7.3->Flask-Security->genotype==4.1.2) (1.5)
Requirement already satisfied: WTForms in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Flask-WTF>=0.13.1->Flask-Security->genotype==4.1.2) (3.0.1)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from requests>=2.0->Flask-Dance==3.0.0->genotype==4.1.2) (1.26.12)
Requirement already satisfied: certifi>=2017.4.17 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from requests>=2.0->Flask-Dance==3.0.0->genotype==4.1.2) (2022.9.24)
Requirement already satisfied: idna<4,>=2.5 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from requests>=2.0->Flask-Dance==3.0.0->genotype==4.1.2) (3.4)
Requirement already satisfied: charset-normalizer<3,>=2 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from requests>=2.0->Flask-Dance==3.0.0->genotype==4.1.2) (2.1.1)
Requirement already satisfied: zipp>=0.5 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from importlib-metadata->click->genotype==4.1.2) (3.10.0)
Requirement already satisfied: typing-extensions>=3.6.4 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from importlib-metadata->click->genotype==4.1.2) (4.4.0)
Requirement already satisfied: pytz>=2015.7 in /home/proj/production/bin/miniconda3/envs/P_genotype/lib/python3.7/site-packages (from Babel>=1.0->Flask-BabelEx>=0.9.3->Flask-Security->genotype==4.1.2) (2022.5)
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
repository is clean
Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/henrik.stranneheim
done.
Log deploy... done.
genotype, version 4.1.2