Merge pull request #129 from getwilds/cve-fixes

CVE Fixes
getwilds · Oct 29, 2024 · ab95c83 · ab95c83
2 parents 5e8229c + d267b4a
commit ab95c83
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diff --git a/annovar/Dockerfile_hg19 b/annovar/Dockerfile_hg19
@@ -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="annovar"

diff --git a/annovar/Dockerfile_hg38 b/annovar/Dockerfile_hg38
@@ -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="annovar"

diff --git a/annovar/Dockerfile_latest b/annovar/Dockerfile_latest
@@ -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="annovar"

diff --git a/bcftools/Dockerfile_1.11 b/bcftools/Dockerfile_1.11
@@ -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="bcftools"
@@ -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

diff --git a/bcftools/Dockerfile_1.19 b/bcftools/Dockerfile_1.19
@@ -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="bcftools"
@@ -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

diff --git a/bcftools/Dockerfile_latest b/bcftools/Dockerfile_latest
@@ -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="bcftools"
@@ -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

diff --git a/biobambam2/Dockerfile_2.0.185 b/biobambam2/Dockerfile_2.0.185
@@ -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="biobambam2"

diff --git a/biobambam2/Dockerfile_latest b/biobambam2/Dockerfile_latest
@@ -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="biobambam2"

diff --git a/picard/Dockerfile_3.1.1 b/picard/Dockerfile_3.1.1
@@ -1,6 +1,6 @@
 
 # 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"
@@ -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/

diff --git a/picard/Dockerfile_latest b/picard/Dockerfile_latest
@@ -1,6 +1,6 @@
 
 # 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"
@@ -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/

diff --git a/rnaseqc/Dockerfile_2.4.2 b/rnaseqc/Dockerfile_2.4.2
@@ -1,6 +1,6 @@
 
 # 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"
@@ -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/

diff --git a/rnaseqc/Dockerfile_latest b/rnaseqc/Dockerfile_latest
@@ -1,6 +1,6 @@
 
 # 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"
@@ -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/

diff --git a/samtools/Dockerfile_1.10 b/samtools/Dockerfile_1.10
@@ -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"
@@ -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

diff --git a/samtools/Dockerfile_1.11 b/samtools/Dockerfile_1.11
@@ -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"
@@ -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

diff --git a/samtools/Dockerfile_latest b/samtools/Dockerfile_latest
@@ -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"
@@ -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

diff --git a/scanpy/Dockerfile_1.10.2 b/scanpy/Dockerfile_1.10.2
@@ -0,0 +1,16 @@
+
+# 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="[email protected]"
+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
diff --git a/scanpy/Dockerfile_latest b/scanpy/Dockerfile_latest
@@ -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"

diff --git a/scvi-tools/Dockerfile_1.1.6 b/scvi-tools/Dockerfile_1.1.6
@@ -0,0 +1,18 @@
+
+# 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="[email protected]"
+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
diff --git a/scvi-tools/Dockerfile_latest b/scvi-tools/Dockerfile_latest
@@ -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"

diff --git a/umitools/Dockerfile_1.0.1 → umitools/Dockerfile_1.1.6 b/umitools/Dockerfile_1.0.1 → umitools/Dockerfile_1.1.6
@@ -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="[email protected]"
 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
diff --git a/umitools/Dockerfile_latest b/umitools/Dockerfile_latest
@@ -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"
@@ -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