From 76a631184c1cca86bfd04aada9cd0f74d3c9127d Mon Sep 17 00:00:00 2001
From: Taylor Firman <tefirman@gmail.com>
Date: Fri, 23 Feb 2024 09:04:39 -0800
Subject: [PATCH 01/11] Moving Annovar Dockerfiles to their own directory

---
 Dockerfile_annovar => annovar/Dockerfile_latest | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename Dockerfile_annovar => annovar/Dockerfile_latest (100%)

diff --git a/Dockerfile_annovar b/annovar/Dockerfile_latest
similarity index 100%
rename from Dockerfile_annovar
rename to annovar/Dockerfile_latest

From b1873b218f79b44e3dcf2c9d7dda20951b83f1dd Mon Sep 17 00:00:00 2001
From: Taylor Firman <tefirman@gmail.com>
Date: Fri, 23 Feb 2024 09:54:52 -0800
Subject: [PATCH 02/11] Moving biobambam2 Dockerfiles to their own directory

---
 Dockerfile_biobambam2 => biobambam2/Dockerfile_latest | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename Dockerfile_biobambam2 => biobambam2/Dockerfile_latest (100%)

diff --git a/Dockerfile_biobambam2 b/biobambam2/Dockerfile_latest
similarity index 100%
rename from Dockerfile_biobambam2
rename to biobambam2/Dockerfile_latest

From 113fc5611d9641c0f1e839750823edd997640806 Mon Sep 17 00:00:00 2001
From: Taylor Firman <tefirman@gmail.com>
Date: Fri, 23 Feb 2024 10:18:17 -0800
Subject: [PATCH 03/11] Moving bwa Dockerfiles to their own directory

---
 Dockerfile_bwa => bwa/Dockerfile_latest | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename Dockerfile_bwa => bwa/Dockerfile_latest (100%)

diff --git a/Dockerfile_bwa b/bwa/Dockerfile_latest
similarity index 100%
rename from Dockerfile_bwa
rename to bwa/Dockerfile_latest

From 821552d56137c013a734445fd4696d7ac457f98d Mon Sep 17 00:00:00 2001
From: Taylor Firman <tefirman@gmail.com>
Date: Fri, 23 Feb 2024 10:37:10 -0800
Subject: [PATCH 04/11] Moving gatk Dockerfiles to their own directory

---
 Dockerfile_gatk => gatk/Dockerfile_latest | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename Dockerfile_gatk => gatk/Dockerfile_latest (100%)

diff --git a/Dockerfile_gatk b/gatk/Dockerfile_latest
similarity index 100%
rename from Dockerfile_gatk
rename to gatk/Dockerfile_latest

From 61005b4698f5fecca7dca41e0c5cdadbf146f54c Mon Sep 17 00:00:00 2001
From: Taylor Firman <tefirman@gmail.com>
Date: Fri, 23 Feb 2024 10:47:06 -0800
Subject: [PATCH 05/11] Moving picard Dockerfiles to their own directory

---
 Dockerfile_picard => picard/Dockerfile_latest | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename Dockerfile_picard => picard/Dockerfile_latest (100%)

diff --git a/Dockerfile_picard b/picard/Dockerfile_latest
similarity index 100%
rename from Dockerfile_picard
rename to picard/Dockerfile_latest

From 3a8e372232956652b479de1c19b6b8bcc51d4a89 Mon Sep 17 00:00:00 2001
From: Taylor Firman <tefirman@gmail.com>
Date: Fri, 23 Feb 2024 10:51:43 -0800
Subject: [PATCH 06/11] Moving samtools Dockerfiles to their own directory

---
 Dockerfile_samtools => samtools/Dockerfile_latest | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename Dockerfile_samtools => samtools/Dockerfile_latest (100%)

diff --git a/Dockerfile_samtools b/samtools/Dockerfile_latest
similarity index 100%
rename from Dockerfile_samtools
rename to samtools/Dockerfile_latest

From cd90ecaf8fd40484cdc3cf8071d86374aa646b74 Mon Sep 17 00:00:00 2001
From: Taylor Firman <tefirman@gmail.com>
Date: Fri, 23 Feb 2024 11:34:43 -0800
Subject: [PATCH 07/11] Adding version-tagged Dockerfiles for each tool

---
 annovar/Dockerfile_hg19       | 35 ++++++++++++++++++++++++++++++
 biobambam2/Dockerfile_2.0.185 | 18 ++++++++++++++++
 bwa/Dockerfile_0.7.17         | 40 +++++++++++++++++++++++++++++++++++
 gatk/Dockerfile_4.3.0.0       | 33 +++++++++++++++++++++++++++++
 picard/Dockerfile_3.1.1       | 33 +++++++++++++++++++++++++++++
 samtools/Dockerfile_1.11      | 30 ++++++++++++++++++++++++++
 6 files changed, 189 insertions(+)
 create mode 100644 annovar/Dockerfile_hg19
 create mode 100644 biobambam2/Dockerfile_2.0.185
 create mode 100644 bwa/Dockerfile_0.7.17
 create mode 100644 gatk/Dockerfile_4.3.0.0
 create mode 100644 picard/Dockerfile_3.1.1
 create mode 100644 samtools/Dockerfile_1.11

diff --git a/annovar/Dockerfile_hg19 b/annovar/Dockerfile_hg19
new file mode 100644
index 0000000..cb50107
--- /dev/null
+++ b/annovar/Dockerfile_hg19
@@ -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.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.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/biobambam2/Dockerfile_2.0.185 b/biobambam2/Dockerfile_2.0.185
new file mode 100644
index 0000000..9d61a7a
--- /dev/null
+++ b/biobambam2/Dockerfile_2.0.185
@@ -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="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.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/bwa/Dockerfile_0.7.17 b/bwa/Dockerfile_0.7.17
new file mode 100644
index 0000000..9c56584
--- /dev/null
+++ b/bwa/Dockerfile_0.7.17
@@ -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="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.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/gatk/Dockerfile_4.3.0.0 b/gatk/Dockerfile_4.3.0.0
new file mode 100644
index 0000000..dc7a9b5
--- /dev/null
+++ b/gatk/Dockerfile_4.3.0.0
@@ -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="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.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/picard/Dockerfile_3.1.1 b/picard/Dockerfile_3.1.1
new file mode 100644
index 0000000..290688e
--- /dev/null
+++ b/picard/Dockerfile_3.1.1
@@ -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="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.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/samtools/Dockerfile_1.11 b/samtools/Dockerfile_1.11
new file mode 100644
index 0000000..d2429bc
--- /dev/null
+++ b/samtools/Dockerfile_1.11
@@ -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="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.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

From c1eb146778cfb8add1b39a0b9fd1bbacbb9bf465 Mon Sep 17 00:00:00 2001
From: Taylor Firman <tefirman@gmail.com>
Date: Fri, 23 Feb 2024 14:07:24 -0800
Subject: [PATCH 08/11] Adding version tagged Dockerfiles, updating labels, and
 generalizing the build-and-push GitHub Action

---
 annovar/Dockerfile_hg19       | 7 +++----
 annovar/Dockerfile_latest     | 9 ++++-----
 biobambam2/Dockerfile_2.0.185 | 6 +++---
 biobambam2/Dockerfile_latest  | 8 ++++----
 bwa/Dockerfile_0.7.17         | 6 +++---
 bwa/Dockerfile_latest         | 8 ++++----
 gatk/Dockerfile_4.3.0.0       | 6 +++---
 gatk/Dockerfile_latest        | 8 ++++----
 picard/Dockerfile_3.1.1       | 6 +++---
 picard/Dockerfile_latest      | 8 ++++----
 samtools/Dockerfile_1.11      | 6 +++---
 samtools/Dockerfile_latest    | 8 ++++----
 12 files changed, 42 insertions(+), 44 deletions(-)

diff --git a/annovar/Dockerfile_hg19 b/annovar/Dockerfile_hg19
index cb50107..2d2942d 100644
--- a/annovar/Dockerfile_hg19
+++ b/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_latest b/annovar/Dockerfile_latest
index cb50107..41a02d3 100644
--- a/annovar/Dockerfile_latest
+++ b/annovar/Dockerfile_latest
@@ -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.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
 
diff --git a/biobambam2/Dockerfile_2.0.185 b/biobambam2/Dockerfile_2.0.185
index 9d61a7a..93d6bf7 100644
--- a/biobambam2/Dockerfile_2.0.185
+++ b/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
index 9d61a7a..3f09718 100644
--- a/biobambam2/Dockerfile_latest
+++ b/biobambam2/Dockerfile_latest
@@ -5,10 +5,10 @@ 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="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.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
 
diff --git a/bwa/Dockerfile_0.7.17 b/bwa/Dockerfile_0.7.17
index 9c56584..5ad15ea 100644
--- a/bwa/Dockerfile_0.7.17
+++ b/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
index 9c56584..2fe510a 100644
--- a/bwa/Dockerfile_latest
+++ b/bwa/Dockerfile_latest
@@ -5,10 +5,10 @@ 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="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.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
 
diff --git a/gatk/Dockerfile_4.3.0.0 b/gatk/Dockerfile_4.3.0.0
index dc7a9b5..7e41d46 100644
--- a/gatk/Dockerfile_4.3.0.0
+++ b/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
index dc7a9b5..a86f2e2 100644
--- a/gatk/Dockerfile_latest
+++ b/gatk/Dockerfile_latest
@@ -5,10 +5,10 @@ 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="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.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
 
diff --git a/picard/Dockerfile_3.1.1 b/picard/Dockerfile_3.1.1
index 290688e..18e3c13 100644
--- a/picard/Dockerfile_3.1.1
+++ b/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
index 290688e..b9f65e5 100644
--- a/picard/Dockerfile_latest
+++ b/picard/Dockerfile_latest
@@ -5,10 +5,10 @@ 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="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.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
 
diff --git a/samtools/Dockerfile_1.11 b/samtools/Dockerfile_1.11
index d2429bc..e989821 100644
--- a/samtools/Dockerfile_1.11
+++ b/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
index d2429bc..6372447 100644
--- a/samtools/Dockerfile_latest
+++ b/samtools/Dockerfile_latest
@@ -5,10 +5,10 @@ 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="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.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
 

From 4a83de0dc4aba39e868725cb79debdc551b68684 Mon Sep 17 00:00:00 2001
From: Taylor Firman <tefirman@gmail.com>
Date: Fri, 23 Feb 2024 14:08:49 -0800
Subject: [PATCH 09/11] Generalizing the build-and-push GitHub Action

---
 .github/workflows/docker-images.yml | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/docker-images.yml b/.github/workflows/docker-images.yml
index 2ce2f9d..988b196 100644
--- a/.github/workflows/docker-images.yml
+++ b/.github/workflows/docker-images.yml
@@ -32,12 +32,16 @@ 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 $TOOL/*
+                  do 
+                      IFS="_" read -ra newarr <<< "$TAG"
+                      docker build --platform linux/amd64 -t ghcr.io/getwilds/$TOOL:${newarr[1]} -f $TOOL/$TAG --push .
+                  done
+              fi
+          done
 
 
 

From ac6ed5d432868dd5681d678a4a9cafbc01549b4d Mon Sep 17 00:00:00 2001
From: Taylor Firman <tefirman@gmail.com>
Date: Fri, 23 Feb 2024 14:14:19 -0800
Subject: [PATCH 10/11] Adding hg38 version of Annovar

---
 annovar/Dockerfile_hg38 | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 annovar/Dockerfile_hg38

diff --git a/annovar/Dockerfile_hg38 b/annovar/Dockerfile_hg38
new file mode 100644
index 0000000..d201b6d
--- /dev/null
+++ 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="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 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

From 799c9cdcfa1201cfb70f04eb0608eac3f32c67c2 Mon Sep 17 00:00:00 2001
From: Taylor Firman <tefirman@gmail.com>
Date: Fri, 23 Feb 2024 14:26:34 -0800
Subject: [PATCH 11/11] Adding Dockerfile string logic to the build-and-push
 GitHub Action

---
 .github/workflows/docker-images.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker-images.yml b/.github/workflows/docker-images.yml
index 988b196..a20100a 100644
--- a/.github/workflows/docker-images.yml
+++ b/.github/workflows/docker-images.yml
@@ -37,8 +37,10 @@ jobs:
               if [ -d $TOOL ]; then
                   for TAG in $TOOL/*
                   do 
-                      IFS="_" read -ra newarr <<< "$TAG"
-                      docker build --platform linux/amd64 -t ghcr.io/getwilds/$TOOL:${newarr[1]} -f $TOOL/$TAG --push .
+                      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