Revert all Docker restructuring (#384)

* giving up on docker restructuring for now

* skip non-standard ClinVar chromosomes

* Bump version: 3.2.2 → 3.2.3

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.2.2
+current_version = 3.2.3
 commit = True
 tag = False
 
@@ -13,6 +13,10 @@ replace = VERSION: {new_version}
 search = cpg_aip:{current_version}
 replace = cpg_aip:{new_version}
 
+[bumpversion:file:.github/workflows/index_page_builder.yaml]
+search = cpg_aip:{current_version}
+replace = cpg_aip:{new_version}
+
 [bumpversion:file:reanalysis/version.py]
 search = __version__ = '{current_version}'
 replace = __version__ = '{new_version}'

.github/workflows/clinvar_runner.yaml

@@ -32,5 +32,5 @@ jobs:
           curl --fail --silent --show-error -X POST \
               -H "Authorization: Bearer $TOKEN" \
               -H "Content-Type:application/json" \
-              -d '{"output": "generate_clinvar_${{ steps.date.outputs.date }}", "dataset": "talos", "accessLevel": "full", "repo": "automated-interpretation-pipeline", "commit": "${{ github.sha }}", "cwd": "reanalysis", "script": ["./clinvar_runner.py"], "description": "Generate Latest Clinvar Summaries", "image": "australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:3.2.2", "config": {"workflow": {"sequencing_type": "genome"}, "cohorts": {"talos": {"clinvar_filter": ["victorian clinical genetics services, murdoch childrens research institute"]}}}, "wait": false}' \
+              -d '{"output": "generate_clinvar_${{ steps.date.outputs.date }}", "dataset": "talos", "accessLevel": "full", "repo": "automated-interpretation-pipeline", "commit": "${{ github.sha }}", "cwd": "reanalysis", "script": ["./clinvar_runner.py"], "description": "Generate Latest Clinvar Summaries", "image": "australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:3.2.3", "config": {"workflow": {"sequencing_type": "genome"}, "cohorts": {"talos": {"clinvar_filter": ["victorian clinical genetics services, murdoch childrens research institute"]}}}, "wait": false}' \
               https://server-a2pko7ameq-ts.a.run.app

.github/workflows/docker.yaml

@@ -14,7 +14,7 @@ permissions:
   contents: read
 
 env:
-  VERSION: 3.2.2
+  VERSION: 3.2.3
 
 jobs:
   docker-prod:

.github/workflows/index_page_builder.yaml

@@ -34,5 +34,5 @@ jobs:
           curl --fail --silent --show-error -X POST \
               -H "Authorization: Bearer $TOKEN" \
               -H "Content-Type:application/json" \
-              -d '{"output": "report_index_${{ steps.date.outputs.date }}", "dataset": "talos", "image": "australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:latest", "accessLevel": "full", "repo": "automated-interpretation-pipeline", "commit": "${{ github.sha }}", "cwd": "helpers", "script": ["./report_hunter.py"], "description": "Locate Latest AIP Reports", "wait": false}' \
+              -d '{"output": "report_index_${{ steps.date.outputs.date }}", "dataset": "talos", "image": "australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:3.2.3", "accessLevel": "full", "repo": "automated-interpretation-pipeline", "commit": "${{ github.sha }}", "cwd": "helpers", "script": ["./report_hunter.py"], "description": "Locate Latest AIP Reports", "wait": false}' \
               https://server-a2pko7ameq-ts.a.run.app

Dockerfile

@@ -1,38 +1,10 @@
-FROM python:3.10-bullseye
-
-ARG HAIL_SHA=${HAIL_SHA:-8f6797b033d2e102575c40166cf0c977e91f834e}
-
-RUN apt update && apt install -y \
-        apt-transport-https \
-        bash \
-        build-essential \
-        bzip2 \
-        ca-certificates \
-        curl \
-        g++ \
-        gcc \
-        git \
-        gnupg \
-        liblapack3 \
-        libopenblas-base \
-        make \
-        openjdk-11-jdk-headless \
-        rsync \
-        software-properties-common \
-        wget \
-        zip && \
-    rm -r /var/lib/apt/lists/* && \
-    rm -r /var/cache/apt/*
-
-# Install Hail from the CPG fork.
-RUN git clone https://github.com/populationgenomics/hail.git && \
-    cd hail && \
-    git checkout $HAIL_SHA && \
-    cd hail && \
-    # Install locally, avoiding the need for a pip package.
-    make install && \
-    cd ../.. && \
-    rm -rf hail
-
-COPY . /
+FROM australia-southeast1-docker.pkg.dev/analysis-runner/images/driver:latest
+
+COPY requirements.txt .
+COPY requirements-dev.txt .
+RUN pip install -r requirements.txt
+COPY README.md .
+COPY setup.py .
+COPY helpers helpers/
+COPY reanalysis reanalysis/
 RUN pip install .

reanalysis/reanalysis_global.toml

@@ -71,7 +71,7 @@ default_memory = 'highmem'
 
 [images]
 gatk = 'australia-southeast1-docker.pkg.dev/cpg-common/images/gatk:4.2.6.1'
-aip = 'australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:3.2.2'
+aip = 'australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:3.2.3'
 vep_110 = "australia-southeast1-docker.pkg.dev/cpg-common/images/vep_110:release_110.1"
 cpg_workflows = "australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_workflows:latest"
 

reanalysis/summarise_clinvar_entries.py

@@ -131,6 +131,10 @@ def get_allele_locus_map(summary_file: str) -> dict:
         ref = line[32]
         alt = line[33]
 
+        # skip non-standard chromosomes
+        if chromosome not in ORDERED_ALLELES:
+            continue
+
         # skip chromosomal deletions and insertions, mito, or massive indels
         if (
             ref == 'na'

reanalysis/version.py

@@ -3,4 +3,4 @@
 """
 
 # Do not edit this file manually
-__version__ = '3.2.2'
+__version__ = '3.2.3'

setup.py

@@ -26,7 +26,7 @@ def read_reqs(filename: str) -> list[str]:
     name='automated-interpretation-pipeline',
     description='CPG Variant Prioritisation',
     long_description=readme,
-    version='3.2.2',
+    version='3.2.3',
     author='Matthew Welland, CPG',
     author_email=('[email protected], ' '[email protected]'),
     package_data={'reanalysis': ['templates/*.jinja', 'reanalysis_global.toml']},