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Merge pull request #129 from getwilds/cve-fixes
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CVE Fixes
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@tefirman
tefirman authored Oct 29, 2024
2 parents 5e8229c + d267b4a commit ab95c83
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Showing 21 changed files with 82 additions and 48 deletions.
2 changes: 1 addition & 1 deletion annovar/Dockerfile_hg19
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# Using the Ubuntu base image
FROM ubuntu:noble-20240114
FROM ubuntu:noble-20241011

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="annovar"
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2 changes: 1 addition & 1 deletion annovar/Dockerfile_hg38
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# Using the Ubuntu base image
FROM ubuntu:noble-20240114
FROM ubuntu:noble-20241011

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="annovar"
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2 changes: 1 addition & 1 deletion annovar/Dockerfile_latest
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# Using the Ubuntu base image
FROM ubuntu:noble-20240114
FROM ubuntu:noble-20241011

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="annovar"
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8 changes: 4 additions & 4 deletions bcftools/Dockerfile_1.11
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# Using the Ubuntu base image
FROM ubuntu:noble-20240114
FROM ubuntu:noble-20241011

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="bcftools"
Expand All @@ -15,9 +15,9 @@ LABEL org.opencontainers.image.licenses=MIT
# Installing prerequisites
RUN apt-get update \
&& apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1 liblzma-dev=5.6.1+really5.4.5-1 \
libssl-dev=3.0.13-0ubuntu3.1 libcurl4-gnutls-dev=8.5.0-2ubuntu10.1 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1build0.1 liblzma-dev=5.6.1+really5.4.5-1build0.1 \
libssl-dev=3.0.13-0ubuntu3.4 libcurl4-gnutls-dev=8.5.0-2ubuntu10.4 \
&& rm -rf /var/lib/apt/lists/*

# Pulling and extracting bcftools source code
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8 changes: 4 additions & 4 deletions bcftools/Dockerfile_1.19
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# Using the Ubuntu base image
FROM ubuntu:noble-20240114
FROM ubuntu:noble-20241011

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="bcftools"
Expand All @@ -15,9 +15,9 @@ LABEL org.opencontainers.image.licenses=MIT
# Installing prerequisites
RUN apt-get update \
&& apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1 liblzma-dev=5.6.1+really5.4.5-1 \
libssl-dev=3.0.13-0ubuntu3.1 libcurl4-gnutls-dev=8.5.0-2ubuntu10.1 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1build0.1 liblzma-dev=5.6.1+really5.4.5-1build0.1 \
libssl-dev=3.0.13-0ubuntu3.4 libcurl4-gnutls-dev=8.5.0-2ubuntu10.4 \
&& rm -rf /var/lib/apt/lists/*

# Pulling and extracting bcftools source code
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8 changes: 4 additions & 4 deletions bcftools/Dockerfile_latest
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# Using the Ubuntu base image
FROM ubuntu:noble-20240114
FROM ubuntu:noble-20241011

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="bcftools"
Expand All @@ -15,9 +15,9 @@ LABEL org.opencontainers.image.licenses=MIT
# Installing prerequisites
RUN apt-get update \
&& apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1 liblzma-dev=5.6.1+really5.4.5-1 \
libssl-dev=3.0.13-0ubuntu3.1 libcurl4-gnutls-dev=8.5.0-2ubuntu10.1 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1build0.1 liblzma-dev=5.6.1+really5.4.5-1build0.1 \
libssl-dev=3.0.13-0ubuntu3.4 libcurl4-gnutls-dev=8.5.0-2ubuntu10.4 \
&& rm -rf /var/lib/apt/lists/*

# Pulling and extracting bcftools source code
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2 changes: 1 addition & 1 deletion biobambam2/Dockerfile_2.0.185
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# Using the Ubuntu base image
FROM ubuntu:noble-20240114
FROM ubuntu:noble-20241011

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="biobambam2"
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2 changes: 1 addition & 1 deletion biobambam2/Dockerfile_latest
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# Using the Ubuntu base image
FROM ubuntu:noble-20240114
FROM ubuntu:noble-20241011

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="biobambam2"
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6 changes: 3 additions & 3 deletions picard/Dockerfile_3.1.1
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# Using the Ubuntu base image
FROM ubuntu:jammy-20240212
FROM ubuntu:oracular-20241009

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="picard"
Expand All @@ -17,8 +17,8 @@ ENV DEBIAN_FRONTEND noninteractive

# Installing Java
RUN apt-get update \
&& apt-get install -y --no-install-recommends openjdk-17-jdk=17.0.11+9-1~22.04.1 \
ant=1.10.12-1 wget=1.21.2-2ubuntu1 r-base=4.1.2-1ubuntu2 ca-certificates-java=20190909ubuntu1.2 \
&& apt-get install -y --no-install-recommends openjdk-17-jdk=17.0.12+7-2 \
ant=1.10.14-1 wget=1.24.5-1ubuntu2 r-base=4.4.1-1 ca-certificates-java=20240118 \
&& rm -rf /var/lib/apt/lists/* \
&& update-ca-certificates -f;
ENV JAVA_HOME /usr/lib/jvm/java-17-openjdk-amd64/
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6 changes: 3 additions & 3 deletions picard/Dockerfile_latest
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# Using the Ubuntu base image
FROM ubuntu:jammy-20240212
FROM ubuntu:oracular-20241009

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="picard"
Expand All @@ -17,8 +17,8 @@ ENV DEBIAN_FRONTEND noninteractive

# Installing Java
RUN apt-get update \
&& apt-get install -y --no-install-recommends openjdk-17-jdk=17.0.11+9-1~22.04.1 \
ant=1.10.12-1 wget=1.21.2-2ubuntu1 r-base=4.1.2-1ubuntu2 ca-certificates-java=20190909ubuntu1.2 \
&& apt-get install -y --no-install-recommends openjdk-17-jdk=17.0.12+7-2 \
ant=1.10.14-1 wget=1.24.5-1ubuntu2 r-base=4.4.1-1 ca-certificates-java=20240118 \
&& rm -rf /var/lib/apt/lists/* \
&& update-ca-certificates -f;
ENV JAVA_HOME /usr/lib/jvm/java-17-openjdk-amd64/
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6 changes: 3 additions & 3 deletions rnaseqc/Dockerfile_2.4.2
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# Using the Ubuntu base image
FROM ubuntu:jammy-20240212
FROM ubuntu:oracular-20241009

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="rnaseqc"
Expand All @@ -17,8 +17,8 @@ ENV DEBIAN_FRONTEND noninteractive

# Installing Java
RUN apt-get update \
&& apt-get install -y --no-install-recommends openjdk-17-jdk=17.0.11+9-1~22.04.1 \
ant=1.10.12-1 wget=1.21.2-2ubuntu1 r-base=4.1.2-1ubuntu2 ca-certificates-java=20190909ubuntu1.2 \
&& apt-get install -y --no-install-recommends openjdk-17-jdk=17.0.12+7-2 \
ant=1.10.14-1 wget=1.24.5-1ubuntu2 r-base=4.4.1-1 ca-certificates-java=20240118 \
&& rm -rf /var/lib/apt/lists/* \
&& update-ca-certificates -f;
ENV JAVA_HOME /usr/lib/jvm/java-17-openjdk-amd64/
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6 changes: 3 additions & 3 deletions rnaseqc/Dockerfile_latest
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# Using the Ubuntu base image
FROM ubuntu:jammy-20240212
FROM ubuntu:oracular-20241009

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="rnaseqc"
Expand All @@ -17,8 +17,8 @@ ENV DEBIAN_FRONTEND noninteractive

# Installing Java
RUN apt-get update \
&& apt-get install -y --no-install-recommends openjdk-17-jdk=17.0.11+9-1~22.04.1 \
ant=1.10.12-1 wget=1.21.2-2ubuntu1 r-base=4.1.2-1ubuntu2 ca-certificates-java=20190909ubuntu1.2 \
&& apt-get install -y --no-install-recommends openjdk-17-jdk=17.0.12+7-2 \
ant=1.10.14-1 wget=1.24.5-1ubuntu2 r-base=4.4.1-1 ca-certificates-java=20240118 \
&& rm -rf /var/lib/apt/lists/* \
&& update-ca-certificates -f;
ENV JAVA_HOME /usr/lib/jvm/java-17-openjdk-amd64/
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8 changes: 4 additions & 4 deletions samtools/Dockerfile_1.10
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# Using the Ubuntu base image
FROM ubuntu:noble-20240114
FROM ubuntu:noble-20241011

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="samtools"
Expand All @@ -15,9 +15,9 @@ LABEL org.opencontainers.image.licenses=MIT
# Installing prerequisites
RUN apt-get update \
&& apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1 liblzma-dev=5.6.1+really5.4.5-1 \
libssl-dev=3.0.13-0ubuntu3.1 libcurl4-gnutls-dev=8.5.0-2ubuntu10.1 bedtools=2.31.1+dfsg-2 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1build0.1 liblzma-dev=5.6.1+really5.4.5-1build0.1 \
libssl-dev=3.0.13-0ubuntu3.4 libcurl4-gnutls-dev=8.5.0-2ubuntu10.4 bedtools=2.31.1+dfsg-2 \
&& rm -rf /var/lib/apt/lists/*

# Pulling and extracting Samtools source code
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8 changes: 4 additions & 4 deletions samtools/Dockerfile_1.11
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@@ -1,6 +1,6 @@

# Using the Ubuntu base image
FROM ubuntu:noble-20240114
FROM ubuntu:noble-20241011

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="samtools"
Expand All @@ -15,9 +15,9 @@ LABEL org.opencontainers.image.licenses=MIT
# Installing prerequisites
RUN apt-get update \
&& apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1 liblzma-dev=5.6.1+really5.4.5-1 \
libssl-dev=3.0.13-0ubuntu3.1 libcurl4-gnutls-dev=8.5.0-2ubuntu10.1 bedtools=2.31.1+dfsg-2 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1build0.1 liblzma-dev=5.6.1+really5.4.5-1build0.1 \
libssl-dev=3.0.13-0ubuntu3.4 libcurl4-gnutls-dev=8.5.0-2ubuntu10.4 bedtools=2.31.1+dfsg-2 \
&& rm -rf /var/lib/apt/lists/*

# Pulling and extracting Samtools source code
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8 changes: 4 additions & 4 deletions samtools/Dockerfile_latest
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# Using the Ubuntu base image
FROM ubuntu:noble-20240114
FROM ubuntu:noble-20241011

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="samtools"
Expand All @@ -15,9 +15,9 @@ LABEL org.opencontainers.image.licenses=MIT
# Installing prerequisites
RUN apt-get update \
&& apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1 liblzma-dev=5.6.1+really5.4.5-1 \
libssl-dev=3.0.13-0ubuntu3.1 libcurl4-gnutls-dev=8.5.0-2ubuntu10.1 bedtools=2.31.1+dfsg-2 \
zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1build0.1 liblzma-dev=5.6.1+really5.4.5-1build0.1 \
libssl-dev=3.0.13-0ubuntu3.4 libcurl4-gnutls-dev=8.5.0-2ubuntu10.4 bedtools=2.31.1+dfsg-2 \
&& rm -rf /var/lib/apt/lists/*

# Pulling and extracting Samtools source code
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16 changes: 16 additions & 0 deletions scanpy/Dockerfile_1.10.2
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# Using Python base image
FROM python:3.12-slim

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="scanpy"
LABEL org.opencontainers.image.description="Container image for the use of Scanpy library for Single-Cell analysis in Python"
LABEL org.opencontainers.image.version="latest"
LABEL org.opencontainers.image.authors="wilds@fredhutch.org"
LABEL org.opencontainers.image.url=https://hutchdatascience.org/
LABEL org.opencontainers.image.documentation=https://getwilds.org/
LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library
LABEL org.opencontainers.image.licenses=MIT

# Installing packages via pip
RUN pip install --no-cache-dir scanpy==1.10.2 leiden-clustering==0.1.0
2 changes: 1 addition & 1 deletion scanpy/Dockerfile_latest
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@@ -1,6 +1,6 @@

# Using Python base image
FROM python:3.10-slim
FROM python:3.12-slim

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="scanpy"
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18 changes: 18 additions & 0 deletions scvi-tools/Dockerfile_1.1.6
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# Using Python base image
FROM python:3.12-slim

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="scvi-tools"
LABEL org.opencontainers.image.description="Container image for the use of scvi-tools library for Single-Cell analysis in Python"
LABEL org.opencontainers.image.version="latest"
LABEL org.opencontainers.image.authors="wilds@fredhutch.org"
LABEL org.opencontainers.image.url=https://hutchdatascience.org/
LABEL org.opencontainers.image.documentation=https://getwilds.org/
LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library
LABEL org.opencontainers.image.licenses=MIT

# Installing packages via pip
# For GPU enabled abilities (from https://pytorch.org/get-started/locally/) - torch, torchvision, torchaudio
RUN pip install --no-cache-dir scvi-tools==1.1.6 scanpy==1.10.2 leiden-clustering==0.1.0 scikit-misc==0.5.1 \
&& pip install --no-cache-dir torch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 --index-url https://download.pytorch.org/whl/cu118
2 changes: 1 addition & 1 deletion scvi-tools/Dockerfile_latest
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@@ -1,6 +1,6 @@

# Using Python base image
FROM python:3.10-slim
FROM python:3.12-slim

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="scvi-tools"
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6 changes: 3 additions & 3 deletions umitools/Dockerfile_1.0.1 → umitools/Dockerfile_1.1.6
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@@ -1,16 +1,16 @@

# Using the Ubuntu base image
FROM python:3.9.19-bookworm
FROM python:3.12-bookworm

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="umitools"
LABEL org.opencontainers.image.description="Container image for the use of umi_tools in FH DaSL's WILDS"
LABEL org.opencontainers.image.version="1.0.1"
LABEL org.opencontainers.image.version="1.1.6"
LABEL org.opencontainers.image.authors="wilds@fredhutch.org"
LABEL org.opencontainers.image.url=https://hutchdatascience.org/
LABEL org.opencontainers.image.documentation=https://getwilds.org/
LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library
LABEL org.opencontainers.image.licenses=MIT

# Installing umi_tools via pip
RUN pip install --no-cache-dir umi_tools==1.0.1
RUN pip install --no-cache-dir umi_tools==1.1.6
4 changes: 2 additions & 2 deletions umitools/Dockerfile_latest
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@@ -1,6 +1,6 @@

# Using the Ubuntu base image
FROM python:3.9.19-bookworm
FROM python:3.12-bookworm

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="umitools"
Expand All @@ -13,4 +13,4 @@ LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-l
LABEL org.opencontainers.image.licenses=MIT

# Installing umi_tools via pip
RUN pip install --no-cache-dir umi_tools==1.0.1
RUN pip install --no-cache-dir umi_tools==1.1.6

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