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chore: add fasta-checksum-utils to containers #58

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merged 3 commits into from
Nov 17, 2023
Merged

chore: add fasta-checksum-utils to containers #58

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8514b6e
chore: add fasta-checksum-utils to containers
davidlougheed Nov 17, 2023
fe6e8fb
chore: update dependencies
davidlougheed Nov 17, 2023
7d518cb
chore: bump version to 0.12.1
davidlougheed Nov 17, 2023
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12 changes: 8 additions & 4 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,17 @@ FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.11.10 AS base-de

SHELL ["/bin/bash", "-c"]

WORKDIR /

# Install system packages for HTSLib + SAMtools + curl and jq for workflows
# OpenJDK is for running WOMtool/Cromwell
# Then, boostrap dependencies for setting up and running the Python application
# Then, install dependencies for running the Python server + Python workflow dependencies
COPY container.requirements.txt .
RUN apt-get update -y && \
apt-get install -y samtools tabix bcftools curl jq openjdk-17-jre && \
rm -rf /var/lib/apt/lists/* && \
pip install --no-cache-dir gunicorn==21.2.0 "pysam>=0.22.0,<0.23.0"
pip install --no-cache-dir -r /container.requirements.txt && \
rm /container.requirements.txt

WORKDIR /
ENV CROMWELL_VERSION=86
Expand All @@ -22,8 +26,8 @@ FROM base-deps AS build-install
RUN mkdir -p /wes/tmp && mkdir -p /data
WORKDIR /wes

COPY pyproject.toml pyproject.toml
COPY poetry.lock poetry.lock
COPY pyproject.toml .
COPY poetry.lock .

# Install production dependencies
# Without --no-root, we get errors related to the code not being copied in yet.
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3 changes: 3 additions & 0 deletions container.requirements.txt
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@@ -0,0 +1,3 @@
gunicorn==21.2.0
pysam>=0.22.0,<0.23.0
fasta-checksum-utils>=0.3.1,<0.4
6 changes: 4 additions & 2 deletions dev.Dockerfile
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Expand Up @@ -15,11 +15,13 @@ SHELL ["/bin/bash", "-c"]

# Install system packages for HTSLib + SAMtools + curl and jq for workflows
# OpenJDK is for running WOMtool/Cromwell
# Then, bootstrap dependencies for setting up and running the Python application
# Then, install dependencies for running the Python server + Python workflow dependencies
COPY container.requirements.txt .
RUN apt-get update -y && \
apt-get install -y samtools tabix bcftools curl jq openjdk-17-jre && \
rm -rf /var/lib/apt/lists/* && \
pip install --no-cache-dir gunicorn==21.2.0 "pysam>=0.22.0,<0.23.0"
pip install --no-cache-dir -r /container.requirements.txt && \
rm /container.requirements.txt

WORKDIR /
ENV CROMWELL_VERSION=86
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