Merge pull request #2 from getwilds/df-reorg

Reorganizing Dockerfiles into Subdirectories
getwilds · Feb 23, 2024 · 69eb86b · 69eb86b
2 parents c33c455 + 799c9cd
commit 69eb86b
Show file tree

Hide file tree

Showing 14 changed files with 253 additions and 25 deletions.
diff --git a/.github/workflows/docker-images.yml b/.github/workflows/docker-images.yml
@@ -32,12 +32,18 @@ jobs:
       -
         name: Build and Push
         run: |
-          docker build --platform linux/amd64 -t ghcr.io/getwilds/samtools:latest -f Dockerfile_samtools --push .
-          docker build --platform linux/amd64 -t ghcr.io/getwilds/gatk:latest -f Dockerfile_gatk --push .
-          docker build --platform linux/amd64 -t ghcr.io/getwilds/bwa:latest -f Dockerfile_bwa --push .
-          docker build --platform linux/amd64 -t ghcr.io/getwilds/picard:latest -f Dockerfile_picard --push .
-          docker build --platform linux/amd64 -t ghcr.io/getwilds/biobambam2:latest -f Dockerfile_biobambam2 --push .
-          docker build --platform linux/amd64 -t ghcr.io/getwilds/annovar:latest -f Dockerfile_annovar --push .
+          for TOOL in *
+          do
+              if [ -d $TOOL ]; then
+                  for TAG in $TOOL/*
+                  do 
+                      if [[ $TAG =~ Dockerfile_* ]]; then
+                          IFS="_" read -ra newarr <<< "$TAG"
+                          docker build --platform linux/amd64 -t ghcr.io/getwilds/$TOOL:${newarr[1]} -f $TOOL/$TAG --push .
+                      fi
+                  done
+              fi
+          done
 
 
 
diff --git a/Dockerfile_annovar → annovar/Dockerfile_hg19 b/Dockerfile_annovar → annovar/Dockerfile_hg19
@@ -4,12 +4,11 @@ FROM ubuntu:noble-20240114
 
 # Adding labels for the GitHub Container Registry
 LABEL org.opencontainers.image.title="annovar"
-LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library
 LABEL org.opencontainers.image.description="Container image for the use of Annovar using hg19 in FH DaSL's WILDS"
 LABEL org.opencontainers.image.version="hg19"
-LABEL org.opencontainers.image.authors="tfirman@fredhutch.org"
-LABEL org.opencontainers.image.url=https://github.com/getwilds/wilds-docker-library
-LABEL org.opencontainers.image.documentation=https://github.com/getwilds/wilds-docker-library
+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
 

diff --git a/annovar/Dockerfile_hg38 b/annovar/Dockerfile_hg38
@@ -0,0 +1,35 @@
+
+# Using the Ubuntu base image
+FROM ubuntu:noble-20240114
+
+# Adding labels for the GitHub Container Registry
+LABEL org.opencontainers.image.title="annovar"
+LABEL org.opencontainers.image.description="Container image for the use of Annovar using hg38 in FH DaSL's WILDS"
+LABEL org.opencontainers.image.version="hg38"
+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 prerequisites
+RUN apt-get update \
+  && apt-get install -y build-essential wget perl \
+  && rm -rf /var/lib/apt/lists/*
+
+# Pulling and extracting Annovar source code
+RUN wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz
+RUN tar -xvf annovar.latest.tar.gz
+ENV PATH="${PATH}:/annovar"
+
+# Downloading GRCh38 resources
+RUN annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGene /annovar/humandb/
+RUN annotate_variation.pl -buildver hg38 -downdb -webfrom annovar knownGene /annovar/humandb/
+RUN annotate_variation.pl -buildver hg38 -downdb -webfrom annovar cosmic70 /annovar/humandb/
+RUN annotate_variation.pl -buildver hg38 -downdb -webfrom annovar esp6500siv2_all /annovar/humandb/
+RUN annotate_variation.pl -buildver hg38 -downdb -webfrom annovar clinvar_20180603 /annovar/humandb/
+RUN annotate_variation.pl -buildver hg38 -downdb -webfrom annovar gnomad211_exome /annovar/humandb/
+
+# Cleanup
+RUN rm /annovar/humandb/hg19_*
+RUN rm -rf annovar.latest.tar.gz
diff --git a/annovar/Dockerfile_latest b/annovar/Dockerfile_latest
@@ -0,0 +1,34 @@
+
+# Using the Ubuntu base image
+FROM ubuntu:noble-20240114
+
+# Adding labels for the GitHub Container Registry
+LABEL org.opencontainers.image.title="annovar"
+LABEL org.opencontainers.image.description="Container image for the use of Annovar using hg19 in FH DaSL's WILDS"
+LABEL org.opencontainers.image.version="latest"
+LABEL org.opencontainers.image.authors="[email protected]"
+LABEL org.opencontainers.image.url=https://hutchdatascience.org/
+LABEL org.opencontainers.image.documentation=https://getwilds.org/
+LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library
+LABEL org.opencontainers.image.licenses=MIT
+
+# Installing prerequisites
+RUN apt-get update \
+  && apt-get install -y build-essential wget perl \
+  && rm -rf /var/lib/apt/lists/*
+
+# Pulling and extracting Annovar source code
+RUN wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz
+RUN tar -xvf annovar.latest.tar.gz
+ENV PATH="${PATH}:/annovar"
+
+# Downloading GRCh38 resources
+RUN annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene /annovar/humandb/
+RUN annotate_variation.pl -buildver hg19 -downdb -webfrom annovar knownGene /annovar/humandb/
+RUN annotate_variation.pl -buildver hg19 -downdb -webfrom annovar cosmic70 /annovar/humandb/
+RUN annotate_variation.pl -buildver hg19 -downdb -webfrom annovar esp6500siv2_all /annovar/humandb/
+RUN annotate_variation.pl -buildver hg19 -downdb -webfrom annovar clinvar_20180603 /annovar/humandb/
+RUN annotate_variation.pl -buildver hg19 -downdb -webfrom annovar gnomad211_exome /annovar/humandb/
+
+# Cleanup
+RUN rm -rf annovar.latest.tar.gz
diff --git a/Dockerfile_biobambam2 → biobambam2/Dockerfile_2.0.185 b/Dockerfile_biobambam2 → biobambam2/Dockerfile_2.0.185
@@ -6,9 +6,9 @@ FROM ubuntu:noble-20240114
 LABEL org.opencontainers.image.title="biobambam2"
 LABEL org.opencontainers.image.description="Container image for the use of biobambam2 in FH DaSL's WILDS"
 LABEL org.opencontainers.image.version="2.0.185"
-LABEL org.opencontainers.image.authors="tfirman@fredhutch.org"
-LABEL org.opencontainers.image.url=https://github.com/getwilds/wilds-docker-library
-LABEL org.opencontainers.image.documentation=https://github.com/getwilds/wilds-docker-library
+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
 

diff --git a/biobambam2/Dockerfile_latest b/biobambam2/Dockerfile_latest
@@ -0,0 +1,18 @@
+
+# Using the Ubuntu base image
+FROM ubuntu:noble-20240114
+
+# Adding labels for the GitHub Container Registry
+LABEL org.opencontainers.image.title="biobambam2"
+LABEL org.opencontainers.image.description="Container image for the use of biobambam2 in FH DaSL's WILDS"
+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 biobambam2 via apt-get
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends biobambam2 \
+  && rm -rf /var/lib/apt/lists/*
diff --git a/Dockerfile_bwa → bwa/Dockerfile_0.7.17 b/Dockerfile_bwa → bwa/Dockerfile_0.7.17
@@ -6,9 +6,9 @@ FROM ubuntu:noble-20240114
 LABEL org.opencontainers.image.title="bwa"
 LABEL org.opencontainers.image.description="Container image for the use of bwa in FH DaSL's WILDS"
 LABEL org.opencontainers.image.version="0.7.17"
-LABEL org.opencontainers.image.authors="tfirman@fredhutch.org"
-LABEL org.opencontainers.image.url=https://github.com/getwilds/wilds-docker-library
-LABEL org.opencontainers.image.documentation=https://github.com/getwilds/wilds-docker-library
+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
 

diff --git a/bwa/Dockerfile_latest b/bwa/Dockerfile_latest
@@ -0,0 +1,40 @@
+
+# Using the Ubuntu base image
+FROM ubuntu:noble-20240114
+
+# Adding labels for the GitHub Container Registry
+LABEL org.opencontainers.image.title="bwa"
+LABEL org.opencontainers.image.description="Container image for the use of bwa in FH DaSL's WILDS"
+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 prerequisites
+RUN apt-get update \
+  && apt-get install -y build-essential wget zlib1g-dev autoconf automake libncurses5-dev libbz2-dev liblzma-dev libssl-dev libcurl4-gnutls-dev \
+  && rm -rf /var/lib/apt/lists/*
+
+# Pulling and extracting bwa source code
+RUN wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2
+RUN tar -jxf bwa-0.7.17.tar.bz2
+
+# Installing bwa
+WORKDIR /bwa-0.7.17
+RUN make CC='gcc -fcommon'
+WORKDIR /
+ENV PATH="${PATH}:/bwa-0.7.17"
+
+# Pulling and extracting Samtools source code
+RUN wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
+RUN tar -jxf samtools-1.11.tar.bz2
+
+# Installing Samtools
+WORKDIR /samtools-1.11
+RUN ./configure && make && make install
+WORKDIR /
+
+# Cleanup
+RUN rm -rf samtools-1.11 samtools-1.11.tar.bz2
diff --git a/Dockerfile_gatk → gatk/Dockerfile_4.3.0.0 b/Dockerfile_gatk → gatk/Dockerfile_4.3.0.0
@@ -6,9 +6,9 @@ FROM continuumio/miniconda3
 LABEL org.opencontainers.image.title="gatk"
 LABEL org.opencontainers.image.description="Container image for the use of GATK in FH DaSL's WILDS"
 LABEL org.opencontainers.image.version="4.3.0.0"
-LABEL org.opencontainers.image.authors="tfirman@fredhutch.org"
-LABEL org.opencontainers.image.url=https://github.com/getwilds/wilds-docker-library
-LABEL org.opencontainers.image.documentation=https://github.com/getwilds/wilds-docker-library
+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
 

diff --git a/gatk/Dockerfile_latest b/gatk/Dockerfile_latest
@@ -0,0 +1,33 @@
+
+# Using the Miniconda base image
+FROM continuumio/miniconda3
+
+# Adding labels for the GitHub Container Registry
+LABEL org.opencontainers.image.title="gatk"
+LABEL org.opencontainers.image.description="Container image for the use of GATK in FH DaSL's WILDS"
+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 GATK via conda
+RUN conda install -c bioconda gatk4=4.3.0.0
+
+# Installing Samtools prerequisites
+RUN apt-get update \
+  && apt-get install -y build-essential wget zlib1g-dev autoconf automake libncurses5-dev libbz2-dev liblzma-dev libssl-dev libcurl4-gnutls-dev \
+  && rm -rf /var/lib/apt/lists/*
+
+# Pulling and extracting Samtools source code
+RUN wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
+RUN tar -jxf samtools-1.11.tar.bz2
+
+# Installing Samtools
+WORKDIR /samtools-1.11
+RUN ./configure && make && make install
+WORKDIR /
+
+# Cleanup
+RUN rm -rf samtools-1.11 samtools-1.11.tar.bz2
diff --git a/Dockerfile_picard → picard/Dockerfile_3.1.1 b/Dockerfile_picard → picard/Dockerfile_3.1.1
@@ -6,9 +6,9 @@ FROM ubuntu:noble-20240114
 LABEL org.opencontainers.image.title="picard"
 LABEL org.opencontainers.image.description="Container image for the use of Picard in FH DaSL's WILDS"
 LABEL org.opencontainers.image.version="3.1.1"
-LABEL org.opencontainers.image.authors="tfirman@fredhutch.org"
-LABEL org.opencontainers.image.url=https://github.com/getwilds/wilds-docker-library
-LABEL org.opencontainers.image.documentation=https://github.com/getwilds/wilds-docker-library
+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
 

diff --git a/picard/Dockerfile_latest b/picard/Dockerfile_latest
@@ -0,0 +1,33 @@
+
+# Using the Ubuntu base image
+FROM ubuntu:noble-20240114
+
+# Adding labels for the GitHub Container Registry
+LABEL org.opencontainers.image.title="picard"
+LABEL org.opencontainers.image.description="Container image for the use of Picard in FH DaSL's WILDS"
+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 Java
+RUN apt-get update && \
+    apt-get install -y openjdk-17-jdk && \
+    apt-get install -y ant && \
+    apt-get install -y wget && \
+    apt-get install -y r-base && \
+    apt-get clean;
+
+# Updating Java certificates
+RUN apt-get update && \
+    apt-get install ca-certificates-java && \
+    apt-get clean && \
+    update-ca-certificates -f;
+ENV JAVA_HOME /usr/lib/jvm/java-17-openjdk-amd64/
+RUN export JAVA_HOME
+
+# Pulling Picard jar to a location that will persist in Apptainer
+RUN mkdir /usr/picard
+RUN wget -P /usr/picard/ https://github.com/broadinstitute/picard/releases/download/3.1.1/picard.jar
diff --git a/Dockerfile_samtools → samtools/Dockerfile_1.11 b/Dockerfile_samtools → samtools/Dockerfile_1.11
@@ -6,9 +6,9 @@ FROM ubuntu:noble-20240114
 LABEL org.opencontainers.image.title="samtools"
 LABEL org.opencontainers.image.description="Container image for the use of Samtools in FH DaSL's WILDS"
 LABEL org.opencontainers.image.version="1.11"
-LABEL org.opencontainers.image.authors="tfirman@fredhutch.org"
-LABEL org.opencontainers.image.url=https://github.com/getwilds/wilds-docker-library
-LABEL org.opencontainers.image.documentation=https://github.com/getwilds/wilds-docker-library
+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
 

diff --git a/samtools/Dockerfile_latest b/samtools/Dockerfile_latest
@@ -0,0 +1,30 @@
+
+# Using the Ubuntu base image
+FROM ubuntu:noble-20240114
+
+# Adding labels for the GitHub Container Registry
+LABEL org.opencontainers.image.title="samtools"
+LABEL org.opencontainers.image.description="Container image for the use of Samtools in FH DaSL's WILDS"
+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 prerequisites
+RUN apt-get update \
+  && apt-get install -y build-essential wget zlib1g-dev autoconf automake libncurses5-dev libbz2-dev liblzma-dev libssl-dev libcurl4-gnutls-dev \
+  && rm -rf /var/lib/apt/lists/*
+
+# Pulling and extracting Samtools source code
+RUN wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
+RUN tar -jxf samtools-1.11.tar.bz2
+
+# Installing Samtools
+WORKDIR /samtools-1.11
+RUN ./configure && make && make install
+WORKDIR /
+
+# Cleanup
+RUN rm -rf samtools-1.11 samtools-1.11.tar.bz2