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Verification Report [v12.0.2] #1204

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4 tasks done
ivadym opened this issue Jul 19, 2023 · 2 comments · Fixed by #1210
Closed
4 tasks done

Verification Report [v12.0.2] #1204

ivadym opened this issue Jul 19, 2023 · 2 comments · Fixed by #1210
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@khurrammaqbool @mathiasbio @ivadym @pbiology
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Verification Report Report for validating minor and patch releases

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@ivadym
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ivadym commented Jul 19, 2023 •
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Balsamic Verification Report

Release Information

  • Version: 12.0.2
  • Release Type: Patch
  • Release Commit: c62ec13
  • Release Date: 2023-07-24

Person(s) involved in the development of new release

Summary

After adding TIDDIT tumor normal filtering, a bug was identified in ticket Ticket #248220. Consequently, there are issues processing the SV VCF with other tools.

These are the goals of this verification:

  1. Validate the format of the header in the SV VCF (SV.somatic.<case-id>.svdb.clinical.filtered.pass.vcf.gz) to ensure its correctness (only relevant for WGS tumor normal analyses).
  2. Verify the integrity of the different analysis types after updating the balsamic and varcall-cnvkit containers.

Changelog

Type Pull Request Performed tests
Fixed #1203 Test: correctness of the SV VCF filtered file for WGS TN analysis
Changed #1206 Test: pydantic version is <2.0 in S_balsamic environment
Changed #1206 Test: rules using the edit_vcf_info.py script behave as expected
Changed #1207 Test: rules using varcall-cnvkit container behave as expected

Pre-Verification Checklist

Before proceeding with the verification process, ensure that the following tasks have been completed:

  • Install Balsamic in stage and production environments in hasta and build its cache.

  • Confirm the availability of necessary resources, such as test cases.

  • Review the changelog and ensure all changes and updates are documented:

    Document Sections to Be Updated Pull Request
    Balsamic Documentation N/A N/A
    Atlas Documentation N/A N/A

  • Set up the stage environment with the necessary software and configurations:

    Software Current Version Pull Request with the Required Updates
    CG Version 40.1.2 N/A
    Servers Version 16.1.3 N/A
    Hermes Version 1.12.1 N/A

Verification Results

Workflow Integrity Verification Cases

Case ID Analysis type Expected QC Status
acetuna QC, tumor-only Pass Pass
civilsole WGS, tumor-only Fail (PCT_60X=0.004532) Pass
fleetjay WGS, tumor-normal Fail (PCT_60X=0.00836) Pass
setamoeba TGA, tumor-only Pass Pass
unitedbeagle TGA, tumor-normal Pass Pass
uphippo UMI, tumor-only Fail (GC dropout=1.650392 and PCT_TARGET_BASES_1000X=0.861996) Pass
equalbug UMI, tumor-normal Fail (GC_DROPOUT=1.087173 and RELATEDNESS=-0.524) Pass

Test: correctness of the SV VCF filtered file for WGS TN analysis

Case ID Description Expected outcome Status
fleetjay Look at header lines in the final SV VCF for INFO AF_N_MAX, AF_T_MAX, and BND_ID It should have the "Number=. " field between the "ID" and "Type" field. Pass

Test: pydantic version is <2.0 in S_balsamic environment

Case ID Description Expected outcome Status
N/A Pydantic version has been locked The version should be <2.0 Pass (v1.10.10)

Test: rules using the edit_vcf_info.py script behave as expected

Case ID Description Expected outcome Status
setamoeba Look for FOUND_IN in INFO field in {var_type}.somatic.{case_name}.vardict.research.filtered.pass.vcf.gz and compare file-sizes past and current version The FOUND_IN field should be added properly to INFO field and size of VCF should be identical Pass
unitedbeagle Look for FOUND_IN in INFO field in {var_type}.somatic.{case_name}.vardict.research.filtered.pass.vcf.gz, and compare file-sizes past and current version The FOUND_IN field should be added properly to INFO field and size of VCF should be identical Pass

Test: rules using varcall-cnvkit container behave as expected

Case ID Description Expected Outcome Status
setamoeba Updated CNVkit dependencies, keeping the same CNVkit version. CNVkit tumor-only output should remain unaffected. Output files identical to those in version 12.0.1. Pass
unitedbeagle Updated CNVkit dependencies, keeping the same CNVkit version. CNVkit tumor-normal output should remain unaffected. Output files identical to those in version 12.0.1. Pass
uphippo Updated CNVkit dependencies, keeping the same CNVkit version. CNVkit UMI tumor-only output should remain unaffected. Output files identical to those in version 12.0.1. Pass
equalbug Updated CNVkit dependencies, keeping the same CNVkit version. CNVkit UMI tumor-normal output should remain unaffected. Output files identical to those in version 12.0.1. Pass

Issues Identified

No issues identified.

Recommendations

Conclusion

The verification process for Balsamic v12.0.2 was conducted to ensure the integrity and correctness of the patch. The primary objective was to validate the format of the header in the SV VCF (SV.somatic.<case-id>.svdb.clinical.filtered.pass.vcf.gz) for WGS tumor-normal analyses and to verify the integrity of different analysis types after updating the balsamic and varcall-cnvkit containers.

Furthermore, no issues were identified during the verification process. As a result, the Balsamic Version 12.0.2 patch release is ready for deployment.

Approval

  • Verification review: Anders Lind, @pbiology
  • Date: 2023-07-26

Deployment

  • Responsible: VI, @ivadym
  • Date: 2023-07-27
@ivadym ivadym added the Verification Report Report for validating minor and patch releases label Jul 19, 2023
@ivadym ivadym added this to BALSAMIC Jul 19, 2023
@github-project-automation github-project-automation bot moved this to Todo in BALSAMIC Jul 19, 2023
@ivadym ivadym linked a pull request Jul 21, 2023 that will close this issue
feat: Release 12.0.2 #1210
Merged
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@github-project-automation github-project-automation bot moved this from Todo to Completed in BALSAMIC Jul 24, 2023
@ivadym ivadym reopened this Jul 24, 2023
@ivadym ivadym moved this from Completed to Review in BALSAMIC Jul 24, 2023
@pbiology
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Looks great, approved!

@ivadym ivadym moved this from Review to Testing in BALSAMIC Jul 26, 2023
@ivadym
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ivadym commented Jul 27, 2023

Deployed:

θ62° 16d [hiseq.clinical@hasta:~] [P_base] $ conda activate P_balsamic
θ67° 16d [hiseq.clinical@hasta:~] [P_balsamic] $ balsamic --version
balsamic, version 12.0.1
θ65° 16d [hiseq.clinical@hasta:~] [P_balsamic] 8s $ pip uninstall balsamic
Found existing installation: BALSAMIC 12.0.1
Uninstalling BALSAMIC-12.0.1:
  Would remove:
    /home/proj/production/bin/miniconda3/envs/P_balsamic/bin/balsamic
    /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages/BALSAMIC-12.0.1.dist-info/*
    /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages/BALSAMIC/*
    /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages/tests/*
Proceed (Y/n)? Y
  Successfully uninstalled BALSAMIC-12.0.1
θ61° 16d [hiseq.clinical@hasta:~] [P_balsamic] 9s $ balsamic --version
-bash: /home/proj/production/bin/miniconda3/envs/P_balsamic/bin/balsamic: No such file or directory
θ63° 16d [hiseq.clinical@hasta:~] [P_balsamic] 127 $ ll /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages/BALSAMIC/
ls: cannot access /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages/BALSAMIC/: No such file or directory
θ62° 16d [hiseq.clinical@hasta:~] [P_balsamic] 2 $ pip install --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC
Collecting git+https://github.com/Clinical-Genomics/BALSAMIC
  Cloning https://github.com/Clinical-Genomics/BALSAMIC to ./tmp/pip-req-build-0z1rn5_y
  Running command git clone --quiet https://github.com/Clinical-Genomics/BALSAMIC /home/hiseq.clinical/tmp/pip-req-build-0z1rn5_y
  Resolved https://github.com/Clinical-Genomics/BALSAMIC to commit c62ec134971c402858891bb805e3e30f39cd3aae
  Preparing metadata (setup.py) ... done
Requirement already satisfied: click==8.1.3 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (8.1.3)
Requirement already satisfied: colorclass>=2.2.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (2.2.2)
Requirement already satisfied: coloredlogs>=14.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (15.0.1)
Requirement already satisfied: graphviz==0.16 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (0.16)
Requirement already satisfied: gsutil==5.23 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (5.23)
Requirement already satisfied: jinja2>=2.11.2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (3.1.2)
Requirement already satisfied: matplotlib==3.5.2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (3.5.2)
Requirement already satisfied: networkx>=2.6.3 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (2.6.3)
Requirement already satisfied: numpy>=1.21.6 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (1.21.6)
Requirement already satisfied: pandas>=1.1.5 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (1.1.5)
Requirement already satisfied: psutil>=5.7.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (5.9.5)
Requirement already satisfied: pydantic<2.0,>=1.9.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (1.10.9)
Requirement already satisfied: pygments>=2.6.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (2.15.1)
Requirement already satisfied: pyyaml>=5.3.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (6.0)
Requirement already satisfied: six>=1.12.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (1.16.0)
Requirement already satisfied: snakemake==6.5.3 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (6.5.3)
Requirement already satisfied: yapf>=0.30.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (0.40.1)
Requirement already satisfied: h5py>=3.6.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (3.8.0)
Requirement already satisfied: PyPDF2>=1.26.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (3.0.1)
Requirement already satisfied: markdown==3.3.3 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (3.3.3)
Requirement already satisfied: cryptography==40.0.2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (40.0.2)
Requirement already satisfied: tabulate==0.8.10 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (0.8.10)
Requirement already satisfied: toml==0.10.2 in ./.local/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (0.10.2)
Collecting cyvcf2==0.30.22 (from BALSAMIC==12.0.2)
  Downloading cyvcf2-0.30.22-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.1/7.1 MB 15.2 MB/s eta 0:00:00
Requirement already satisfied: importlib-metadata in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from click==8.1.3->BALSAMIC==12.0.2) (6.7.0)
Requirement already satisfied: cffi>=1.12 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from cryptography==40.0.2->BALSAMIC==12.0.2) (1.15.1)
Requirement already satisfied: argcomplete>=1.9.4 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (3.1.1)
Requirement already satisfied: crcmod>=1.7 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (1.7)
Requirement already satisfied: fasteners>=0.14.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (0.18)
Requirement already satisfied: gcs-oauth2-boto-plugin>=3.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (3.0)
Requirement already satisfied: google-apitools>=0.5.32 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (0.5.32)
Requirement already satisfied: httplib2==0.20.4 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (0.20.4)
Requirement already satisfied: google-reauth>=0.1.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (0.1.1)
Requirement already satisfied: monotonic>=1.4 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (1.6)
Requirement already satisfied: pyOpenSSL>=0.13 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (23.2.0)
Requirement already satisfied: retry-decorator>=1.0.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (1.1.1)
Requirement already satisfied: google-auth[aiohttp]>=2.5.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (2.21.0)
Requirement already satisfied: cycler>=0.10 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (4.38.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (1.4.4)
Requirement already satisfied: packaging>=20.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (23.1)
Requirement already satisfied: pillow>=6.2.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (9.5.0)
Requirement already satisfied: pyparsing>=2.2.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (3.1.0)
Requirement already satisfied: python-dateutil>=2.7 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (2.8.2)
Requirement already satisfied: wrapt in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (1.15.0)
Requirement already satisfied: requests in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (2.31.0)
Requirement already satisfied: ratelimiter in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (1.2.0.post0)
Requirement already satisfied: configargparse in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (1.5.5)
Requirement already satisfied: appdirs in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (1.4.4)
Requirement already satisfied: datrie in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (0.8.2)
Requirement already satisfied: jsonschema in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (4.17.3)
Requirement already satisfied: docutils in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (0.20.1)
Requirement already satisfied: gitpython in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (3.1.31)
Requirement already satisfied: nbformat in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (5.8.0)
Requirement already satisfied: toposort in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (1.10)
Requirement already satisfied: connection-pool>=0.0.3 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (0.0.3)
Requirement already satisfied: pulp>=2.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (2.7.0)
Requirement already satisfied: smart-open>=3.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (6.3.0)
Requirement already satisfied: filelock in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (3.12.2)
Requirement already satisfied: stopit in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (1.1.2)
Requirement already satisfied: humanfriendly>=9.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from coloredlogs>=14.0->BALSAMIC==12.0.2) (10.0)
Requirement already satisfied: MarkupSafe>=2.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from jinja2>=2.11.2->BALSAMIC==12.0.2) (2.1.3)
Requirement already satisfied: pytz>=2017.2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from pandas>=1.1.5->BALSAMIC==12.0.2) (2023.3)
Requirement already satisfied: typing-extensions>=4.2.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from pydantic<2.0,>=1.9.0->BALSAMIC==12.0.2) (4.6.3)
Requirement already satisfied: platformdirs>=3.5.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from yapf>=0.30.0->BALSAMIC==12.0.2) (3.8.0)
Requirement already satisfied: tomli>=2.0.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from yapf>=0.30.0->BALSAMIC==12.0.2) (2.0.1)
Requirement already satisfied: pycparser in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from cffi>=1.12->cryptography==40.0.2->BALSAMIC==12.0.2) (2.21)
Requirement already satisfied: rsa==4.7.2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gcs-oauth2-boto-plugin>=3.0->gsutil==5.23->BALSAMIC==12.0.2) (4.7.2)
Requirement already satisfied: boto>=2.29.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gcs-oauth2-boto-plugin>=3.0->gsutil==5.23->BALSAMIC==12.0.2) (2.49.0)
Requirement already satisfied: oauth2client>=2.2.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gcs-oauth2-boto-plugin>=3.0->gsutil==5.23->BALSAMIC==12.0.2) (4.1.3)
Requirement already satisfied: pyasn1>=0.1.3 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from rsa==4.7.2->gcs-oauth2-boto-plugin>=3.0->gsutil==5.23->BALSAMIC==12.0.2) (0.5.0)
Requirement already satisfied: cachetools<6.0,>=2.0.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (5.3.1)
Requirement already satisfied: pyasn1-modules>=0.2.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (0.3.0)
Requirement already satisfied: urllib3<2.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (1.26.16)
Requirement already satisfied: aiohttp<4.0.0.dev0,>=3.6.2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (3.8.4)
Requirement already satisfied: pyu2f in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from google-reauth>=0.1.0->gsutil==5.23->BALSAMIC==12.0.2) (0.1.5)
Requirement already satisfied: zipp>=0.5 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from importlib-metadata->click==8.1.3->BALSAMIC==12.0.2) (3.15.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from requests->snakemake==6.5.3->BALSAMIC==12.0.2) (3.1.0)
Requirement already satisfied: idna<4,>=2.5 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from requests->snakemake==6.5.3->BALSAMIC==12.0.2) (3.4)
Requirement already satisfied: certifi>=2017.4.17 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from requests->snakemake==6.5.3->BALSAMIC==12.0.2) (2023.5.7)
Requirement already satisfied: gitdb<5,>=4.0.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gitpython->snakemake==6.5.3->BALSAMIC==12.0.2) (4.0.10)
Requirement already satisfied: attrs>=17.4.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from jsonschema->snakemake==6.5.3->BALSAMIC==12.0.2) (23.1.0)
Requirement already satisfied: importlib-resources>=1.4.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from jsonschema->snakemake==6.5.3->BALSAMIC==12.0.2) (5.12.0)
Requirement already satisfied: pkgutil-resolve-name>=1.3.10 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from jsonschema->snakemake==6.5.3->BALSAMIC==12.0.2) (1.3.10)
Requirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from jsonschema->snakemake==6.5.3->BALSAMIC==12.0.2) (0.19.3)
Requirement already satisfied: fastjsonschema in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from nbformat->snakemake==6.5.3->BALSAMIC==12.0.2) (2.17.1)
Requirement already satisfied: jupyter-core in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from nbformat->snakemake==6.5.3->BALSAMIC==12.0.2) (4.12.0)
Requirement already satisfied: traitlets>=5.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from nbformat->snakemake==6.5.3->BALSAMIC==12.0.2) (5.9.0)
Requirement already satisfied: multidict<7.0,>=4.5 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (6.0.4)
Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (4.0.2)
Requirement already satisfied: yarl<2.0,>=1.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (1.9.2)
Requirement already satisfied: frozenlist>=1.1.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (1.3.3)
Requirement already satisfied: aiosignal>=1.1.2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (1.3.1)
Requirement already satisfied: asynctest==0.13.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (0.13.0)
Requirement already satisfied: smmap<6,>=3.0.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gitdb<5,>=4.0.1->gitpython->snakemake==6.5.3->BALSAMIC==12.0.2) (5.0.0)
Building wheels for collected packages: BALSAMIC
  Building wheel for BALSAMIC (setup.py) ... done
  Created wheel for BALSAMIC: filename=BALSAMIC-12.0.2-py3-none-any.whl size=92795234 sha256=513c5bee959610236600547fa612aa6dc74210f5c71a067156e77cc96d76ee08
  Stored in directory: /home/hiseq.clinical/tmp/pip-ephem-wheel-cache-kd62n9e5/wheels/67/53/85/a9b1f8619ee7ad1b4c3cdae9f0949db7479f041b1a560b9a80
Successfully built BALSAMIC
Installing collected packages: cyvcf2, BALSAMIC
  Attempting uninstall: cyvcf2
    Found existing installation: cyvcf2 0.9.0
    Uninstalling cyvcf2-0.9.0:
      Successfully uninstalled cyvcf2-0.9.0
Successfully installed BALSAMIC-12.0.2 cyvcf2-0.30.22
θ62° 16d [hiseq.clinical@hasta:~] [P_balsamic] 41s $ balsamic --version
balsamic, version 12.0.2

@ivadym ivadym closed this as completed Jul 27, 2023
@github-project-automation github-project-automation bot moved this from Testing to Completed in BALSAMIC Jul 27, 2023
@mathiasbio mathiasbio mentioned this issue Jul 27, 2023
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@khurrammaqbool khurrammaqbool

@mathiasbio mathiasbio

@ivadym ivadym

@pbiology pbiology

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Verification Report Report for validating minor and patch releases
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feat: Release 12.0.2 Clinical-Genomics/BALSAMIC
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@khurrammaqbool @mathiasbio @ivadym @pbiology