From 766cb82f8667e983502889e8ab8de10eedbb55b8 Mon Sep 17 00:00:00 2001
From: taylorpaisie <tpaisie91@gmail.com>
Date: Thu, 21 Nov 2024 10:41:15 -0500
Subject: [PATCH 01/19] adding hostile to new branch

---
 hostile/1.1.0/Dockerfile | 73 ++++++++++++++++++++++++++++++++++++++++
 hostile/1.1.0/README.md  | 43 +++++++++++++++++++++++
 2 files changed, 116 insertions(+)
 create mode 100644 hostile/1.1.0/Dockerfile
 create mode 100644 hostile/1.1.0/README.md

diff --git a/hostile/1.1.0/Dockerfile b/hostile/1.1.0/Dockerfile
new file mode 100644
index 000000000..5ee8c8f50
--- /dev/null
+++ b/hostile/1.1.0/Dockerfile
@@ -0,0 +1,73 @@
+# Set global variables
+ARG HOSTILE_VER="1.1.0"
+
+# Stage 1: Build Dockerfile
+FROM ubuntu:focal AS builder
+ARG HOSTILE_VER
+
+# Metadata
+LABEL base.image="ubuntu:focal" 
+LABEL dockerfile.version="1" 
+LABEL software="hostile"
+LABEL software.version="${HOSTILE_VER}"
+LABEL description="Precise host read removal."
+LABEL website="https://github.com/bede/hostile"
+LABEL license.url="https://github.com/bede/hostile?tab=MIT-1-ov-file#readme"
+LABEL maintainer="Taylor K. Paisie"
+LABEL maintainer.email="ltj8@cdc.gov"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    software-properties-common && \
+    add-apt-repository ppa:deadsnakes/ppa && \
+    apt-get update && apt-get install -y --no-install-recommends \
+    python3.10 python3.10-distutils build-essential \
+    wget unzip samtools minimap2 bedtools gawk ca-certificates && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+
+# Install pip for Python 3.10
+RUN wget https://bootstrap.pypa.io/get-pip.py && python3.10 get-pip.py && \
+    rm get-pip.py && pip install --no-cache-dir setuptools pytest && \
+    ln -sf /usr/bin/python3.10 /usr/bin/python3 && \
+    ln -sf /usr/local/bin/pip /usr/bin/pip
+
+# Install bowtie2 and ensure all executables are accessible
+RUN wget https://github.com/BenLangmead/bowtie2/releases/download/v2.5.1/bowtie2-2.5.1-linux-x86_64.zip && \
+    unzip bowtie2-2.5.1-linux-x86_64.zip && \
+    mv bowtie2-2.5.1-linux-x86_64 /usr/local/bowtie2 && \
+    ln -s /usr/local/bowtie2/bowtie2* /usr/bin/ && \
+    rm -f bowtie2-2.5.1-linux-x86_64.zip
+
+# Install hostile
+RUN wget https://github.com/bede/hostile/archive/refs/tags/${HOSTILE_VER}.tar.gz && \
+    tar -xzvf ${HOSTILE_VER}.tar.gz && cd hostile-${HOSTILE_VER} && \
+    pip install --no-cache-dir . && \
+    pytest && \
+    cd .. && rm -rf ${HOSTILE_VER}.tar.gz
+
+
+
+# Stage 2: Final image
+FROM ubuntu:focal AS app
+
+COPY --from=builder /usr/ /usr/
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    ca-certificates && update-ca-certificates && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Optional stage: Test data
+FROM app AS test
+
+WORKDIR /data/test
+
+
+RUN wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R1.fastq.gz \
+    --no-check-certificate && \
+    wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R2.fastq.gz \
+    --no-check-certificate
+
+#     hostile fetch && \
+#     hostile clean --fastq1 test_miniburk_R1.fastq.gz --fastq2 test_miniburk_R2.fastq.gz
+
+WORKDIR /data
\ No newline at end of file
diff --git a/hostile/1.1.0/README.md b/hostile/1.1.0/README.md
new file mode 100644
index 000000000..29cc2b1e9
--- /dev/null
+++ b/hostile/1.1.0/README.md
@@ -0,0 +1,43 @@
+# hostile
+
+Main tool: [hostile](https://github.com/bede/hostile)
+  
+Code repository: https://github.com/bede/hostile
+
+Basic information on how to use this tool:
+- executable: |
+```
+usage: hostile [-h] [--version] {clean,mask,fetch} ...
+
+positional arguments:
+  {clean,mask,fetch}
+    clean             Remove reads aligning to an index from fastq[.gz] input files
+    mask              Mask reference genome against target genome(s)
+    fetch             Download and cache indexes from object storage for use with hostile clean
+
+options:
+  -h, --help          show this help message and exit
+  --version           show program's version number and exit
+```
+
+- help: `hostile --help`
+- version: `hostle --version`
+- description: | 
+> Hostile accurately removes host sequences from short and long read (meta)genomes, consuming single-read or paired fastq input.
+
+  
+Full documentation: https://github.com/bede/hostile
+
+
+# Testing hostile analysis
+```
+# Downloading test dataset
+wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R1.fastq.gz --no-check-certificate
+wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R2.fastq.gz --no-check-certificate
+
+# Fetching human host indexes    
+hostile fetch
+
+# Running hostile clean on test dataset
+hostile clean --fastq1 test_miniburk_R1.fastq.gz --fastq2 test_miniburk_R2.fastq.gz
+```
\ No newline at end of file

From 80e04d8cab999c8c75fb107c4e0397e3ca86a732 Mon Sep 17 00:00:00 2001
From: taylorpaisie <tpaisie91@gmail.com>
Date: Thu, 21 Nov 2024 12:06:47 -0500
Subject: [PATCH 02/19] editing hostile readme and test in dockerfile

---
 hostile/1.1.0/Dockerfile | 7 +++----
 hostile/1.1.0/README.md  | 4 +---
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/hostile/1.1.0/Dockerfile b/hostile/1.1.0/Dockerfile
index 5ee8c8f50..396e8e79f 100644
--- a/hostile/1.1.0/Dockerfile
+++ b/hostile/1.1.0/Dockerfile
@@ -51,6 +51,7 @@ RUN wget https://github.com/bede/hostile/archive/refs/tags/${HOSTILE_VER}.tar.gz
 FROM ubuntu:focal AS app
 
 COPY --from=builder /usr/ /usr/
+COPY --from=builder /hostile-1.1.0/tests/data/sars-cov-2 /data/test/sars-cov-2/
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
     ca-certificates && update-ca-certificates && \
@@ -65,9 +66,7 @@ WORKDIR /data/test
 RUN wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R1.fastq.gz \
     --no-check-certificate && \
     wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R2.fastq.gz \
-    --no-check-certificate
-
-#     hostile fetch && \
-#     hostile clean --fastq1 test_miniburk_R1.fastq.gz --fastq2 test_miniburk_R2.fastq.gz
+    --no-check-certificate && \
+    hostile clean --index /data/test/sars-cov-2/sars-cov-2 --fastq1 test_miniburk_R1.fastq.gz --fastq2 test_miniburk_R2.fastq.gz
 
 WORKDIR /data
\ No newline at end of file
diff --git a/hostile/1.1.0/README.md b/hostile/1.1.0/README.md
index 29cc2b1e9..4e419c350 100644
--- a/hostile/1.1.0/README.md
+++ b/hostile/1.1.0/README.md
@@ -35,9 +35,7 @@ Full documentation: https://github.com/bede/hostile
 wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R1.fastq.gz --no-check-certificate
 wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R2.fastq.gz --no-check-certificate
 
-# Fetching human host indexes    
-hostile fetch
 
 # Running hostile clean on test dataset
-hostile clean --fastq1 test_miniburk_R1.fastq.gz --fastq2 test_miniburk_R2.fastq.gz
+hostile clean --index /data/test/sars-cov-2/sars-cov-2 --fastq1 test_miniburk_R1.fastq.gz --fastq2 test_miniburk_R2.fastq.gz
 ```
\ No newline at end of file

From 8d625d152ff83457eb7f6d04efec9911612b1ab2 Mon Sep 17 00:00:00 2001
From: taylorpaisie <tpaisie91@gmail.com>
Date: Thu, 21 Nov 2024 14:08:16 -0500
Subject: [PATCH 03/19] making edits to readme and hostile dockerfile

---
 hostile/1.1.0/Dockerfile | 3 +--
 hostile/1.1.0/README.md  | 1 -
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/hostile/1.1.0/Dockerfile b/hostile/1.1.0/Dockerfile
index 396e8e79f..52988c7ff 100644
--- a/hostile/1.1.0/Dockerfile
+++ b/hostile/1.1.0/Dockerfile
@@ -51,7 +51,7 @@ RUN wget https://github.com/bede/hostile/archive/refs/tags/${HOSTILE_VER}.tar.gz
 FROM ubuntu:focal AS app
 
 COPY --from=builder /usr/ /usr/
-COPY --from=builder /hostile-1.1.0/tests/data/sars-cov-2 /data/test/sars-cov-2/
+COPY --from=builder /hostile-1.1.0/tests/data/ /data/test/
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
     ca-certificates && update-ca-certificates && \
@@ -62,7 +62,6 @@ FROM app AS test
 
 WORKDIR /data/test
 
-
 RUN wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R1.fastq.gz \
     --no-check-certificate && \
     wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R2.fastq.gz \
diff --git a/hostile/1.1.0/README.md b/hostile/1.1.0/README.md
index 4e419c350..008602b23 100644
--- a/hostile/1.1.0/README.md
+++ b/hostile/1.1.0/README.md
@@ -35,7 +35,6 @@ Full documentation: https://github.com/bede/hostile
 wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R1.fastq.gz --no-check-certificate
 wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R2.fastq.gz --no-check-certificate
 
-
 # Running hostile clean on test dataset
 hostile clean --index /data/test/sars-cov-2/sars-cov-2 --fastq1 test_miniburk_R1.fastq.gz --fastq2 test_miniburk_R2.fastq.gz
 ```
\ No newline at end of file

From e454d82a6cc55d1a1ca5d2c6262be532178120c6 Mon Sep 17 00:00:00 2001
From: taylorpaisie <tpaisie91@gmail.com>
Date: Fri, 22 Nov 2024 10:47:30 -0500
Subject: [PATCH 04/19] adding hostile tag to readme

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 01e1407e8..5eee7ceea 100644
--- a/README.md
+++ b/README.md
@@ -166,6 +166,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [heatcluster](https://hub.docker.com/r/staphb/heatcluster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/heatcluster)](https://hub.docker.com/r/staphb/heatcluster) | <ul><li>[1.0.2c](./heatcluster/1.0.2c/)</li></ul> | https://github.com/DrB-S/heatcluster/tree/main |
 | [hmmer](https://hub.docker.com/r/staphb/hmmer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | <ul><li>[3.3](hmmer/3.3/)</li><li>[3.3.2](hmmer/3.3.2/)</li></ul> | http://hmmer.org/ |
 | [homopolish](https://hub.docker.com/r/staphb/homopolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | <ul><li>0.4.1</li></ul> | https://github.com/ythuang0522/homopolish/ |
+| [hostile](https://github.com/bede/hostile) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hostile)](https://hub.docker.com/r/staphb/hostile | <ul><li>1.1.0</li></ul> | https://github.com/bede/hostile |
 | [htslib](https://hub.docker.com/r/staphb/htslib) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | <ul><li>[1.14](./htslib/1.14)</li><li>[1.15](./htslib/1.15)</li><li>[1.16](./htslib/1.16)</li><li>[1.17](./htslib/1.17)</li><li>[1.18](./htslib/1.18/)</li><li>[1.19](./htslib/1.19/)</li></ul> | https://www.htslib.org/ |
 | [iqtree](https://hub.docker.com/r/staphb/iqtree/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | <ul><li>1.6.7</li></ul> | http://www.iqtree.org/ |
 | [iqtree2](https://hub.docker.com/r/staphb/iqtree2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | <ul><li>2.1.2</li><li>2.2.2.2</li><li>[2.2.2.6](iqtree2/2.2.2.6/)</li><li>[2.2.2.7](iqtree2/2.2.2.7/)</li></ul> | http://www.iqtree.org/ |

From b74548bd02255cdeac627dab883b9a704612f1a3 Mon Sep 17 00:00:00 2001
From: taylorpaisie <tpaisie91@gmail.com>
Date: Fri, 22 Nov 2024 10:59:44 -0500
Subject: [PATCH 05/19] edited hostile dockerfile

---
 hostile/1.1.0/Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/hostile/1.1.0/Dockerfile b/hostile/1.1.0/Dockerfile
index 52988c7ff..4f9b9693c 100644
--- a/hostile/1.1.0/Dockerfile
+++ b/hostile/1.1.0/Dockerfile
@@ -46,7 +46,6 @@ RUN wget https://github.com/bede/hostile/archive/refs/tags/${HOSTILE_VER}.tar.gz
     cd .. && rm -rf ${HOSTILE_VER}.tar.gz
 
 
-
 # Stage 2: Final image
 FROM ubuntu:focal AS app
 

From 0ecd8846717bafed4068709a277060267def83eb Mon Sep 17 00:00:00 2001
From: taylorpaisie <tpaisie91@gmail.com>
Date: Fri, 22 Nov 2024 12:58:03 -0500
Subject: [PATCH 06/19] minor edits to dockerfile and hostile readme

---
 hostile/1.1.0/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/hostile/1.1.0/Dockerfile b/hostile/1.1.0/Dockerfile
index 4f9b9693c..798d74418 100644
--- a/hostile/1.1.0/Dockerfile
+++ b/hostile/1.1.0/Dockerfile
@@ -25,6 +25,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
 
+
 # Install pip for Python 3.10
 RUN wget https://bootstrap.pypa.io/get-pip.py && python3.10 get-pip.py && \
     rm get-pip.py && pip install --no-cache-dir setuptools pytest && \
@@ -50,7 +51,7 @@ RUN wget https://github.com/bede/hostile/archive/refs/tags/${HOSTILE_VER}.tar.gz
 FROM ubuntu:focal AS app
 
 COPY --from=builder /usr/ /usr/
-COPY --from=builder /hostile-1.1.0/tests/data/ /data/test/
+COPY --from=builder /hostile-1.1.0/tests/data/sars-cov-2/ /data/test/sars-cov-2/
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
     ca-certificates && update-ca-certificates && \

From 3afa2986b849f20c116eb82071dbcf73621c360f Mon Sep 17 00:00:00 2001
From: taylorpaisie <tpaisie91@gmail.com>
Date: Fri, 22 Nov 2024 13:02:10 -0500
Subject: [PATCH 07/19] updaing workflows

---
 .github/workflows/update_pango_aliasor.yml | 84 ++++++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 .github/workflows/update_pango_aliasor.yml

diff --git a/.github/workflows/update_pango_aliasor.yml b/.github/workflows/update_pango_aliasor.yml
new file mode 100644
index 000000000..003dfb545
--- /dev/null
+++ b/.github/workflows/update_pango_aliasor.yml
@@ -0,0 +1,84 @@
+##### ------------------------------------------------------------------------------------------------ #####
+##### This caller workflow tests, builds, and pushes the image to Docker Hub and Quay using the most   #####
+##### recent version of pango_aliasor and downloads the current pangolin lineages.                     #####
+##### It takes no manual input.                                                                        #####
+##### ------------------------------------------------------------------------------------------------ #####
+
+name: Update pango aliasor
+
+on: 
+  workflow_dispatch:
+  schedule:
+    - cron: '30 7 * * 1'
+
+run-name: Updating pango aliasor
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    steps:
+          
+      - name: pull repo
+        uses: actions/checkout@v4
+
+      - name: set pango_aliasor version
+        id: latest_version
+        run: |
+          version=0.3.0
+          echo "version=$version" >> $GITHUB_OUTPUT 
+          
+          file=pango_aliasor/0.3.0/Dockerfile
+          ls $file
+          echo "file=$file" >> $GITHUB_OUTPUT
+
+      - name: set up docker buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: build to test
+        id: docker_build_to_test
+        uses: docker/build-push-action@v5
+        with:
+          context: pango_aliasor/${{ steps.latest_version.outputs.version }}
+          target: test
+          load: true
+          push: false
+          tags: pango_aliasor:update
+
+      - name: Get current date
+        id: date
+        run: |
+          date=$(date '+%Y-%m-%d')
+          echo "the date is $date"
+          echo "date=$date" >> $GITHUB_OUTPUT
+      
+      - name: Login to DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Login to Quay
+        uses: docker/login-action@v3
+        with:
+          registry: quay.io
+          username: ${{ secrets.QUAY_USERNAME }}
+          password: ${{ secrets.QUAY_ROBOT_TOKEN }}
+
+      - name: Build and push user-defined tag to DockerHub
+        id: docker_build_user_defined_tag
+        uses: docker/build-push-action@v5
+        with:
+          file: ${{ steps.latest_version.outputs.file }}
+          target: app
+          push: true
+          tags: |
+            staphb/pango_aliasor:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
+            staphb/pango_aliasor:latest
+            quay.io/staphb/pango_aliasor:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date 
+}}
+            quay.io/staphb/pango_aliasor:latest
+
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}
+

From bcc09f204590aa42f0d371df5d5e1db6b6f859c9 Mon Sep 17 00:00:00 2001
From: taylorpaisie <tpaisie91@gmail.com>
Date: Fri, 22 Nov 2024 13:12:28 -0500
Subject: [PATCH 08/19] making changes on branch to match master branch

---
 .github/workflows/main.yml          | 137 ----------------------------
 .github/workflows/update_freyja.yml |  88 ++++--------------
 2 files changed, 20 insertions(+), 205 deletions(-)
 delete mode 100644 .github/workflows/main.yml

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
deleted file mode 100644
index 09a300dee..000000000
--- a/.github/workflows/main.yml
+++ /dev/null
@@ -1,137 +0,0 @@
-
-##### ------------------------------------------------------------------------------------------------ #####
-##### This caller workflow tests, builds, and pushes the image to Docker Hub and Quay using the most   #####
-##### recent version of Freyja and downloading the most recent variant information.                    #####
-##### It takes no manual input.                                                                        #####
-##### ------------------------------------------------------------------------------------------------ #####
-
-name: Update Freyja
-
-on: 
-  workflow_dispatch:
-  schedule:
-    - cron: '30 7 * * *'
-
-run-name: Updating Freyja
-
-jobs:
-  update:
-    runs-on: ubuntu-latest
-    steps:
-
-# Keeping here in case we want to use it to keep Freyja's version up-to-date as well
-#      - name: Get latest release
-#        uses: rez0n/actions-github-release@main
-#        id: latest_release
-#        with:
-#          token: ${{ secrets.GITHUB_TOKEN }}
-#          repository: andersen-lab/Freyja
-#          type: "stable"
-#      - name: Remove V
-#        id: strip
-#        run: |
-#          version=$(echo "${{ steps.latest_release.outputs.release }}" | sed 's/V//g' | sed 's/v//g' )
-#          echo "The version is $version"
-#          echo "version=$version" >> $GITHUB_OUTPUT
-          
-      - name: pull repo
-        uses: actions/checkout@v3
-
-# Keeping here in case we want to figure out why this doesn't work      
-#      - name: get latest version of freyja in docker-builds repo
-#        id: latest_version
-#        run: | 
-#          file=$(git log -1 --name-only --format=%cd --date=iso freyja/*/Dockerfile | grep Dockerfile | head -n 1 )
-#          echo "the latest file is $file"
-#          echo "file=$file" >> $GITHUB_OUTPUT
-#
-#          version=$(echo $file | cut -f 2 -d "/" | cut -f 1 -d "_")
-#          echo "the latest version is $version"
-#          echo "version=$version" >> $GITHUB_OUTPUT      
-
-      - name: set freyja version
-        id: latest_version
-        run: |
-          version=1.4.8
-          echo "version=$version" >> $GITHUB_OUTPUT 
-          
-          file=freyja/$version/Dockerfile
-          ls $file
-          echo "file=$file" >> $GITHUB_OUTPUT
-      - name: set up docker buildx
-        id: buildx
-        uses: docker/setup-buildx-action@v2
-
-      - name: cache docker layers
-        uses: actions/cache@v3
-        with:
-          path: /tmp/.buildx-cache-freyja
-          key: ${{ runner.os }}-buildx-freyja-${{ github.sha }}
-          restore-keys: ${{ runner.os }}-buildx-freyja
-
-      - name: build to test
-        id: docker_build_to_test
-        uses: docker/build-push-action@v3
-        with:
-          file: ${{ steps.latest_version.outputs.file }}
-          target: test
-          load: true
-          push: false
-          cache-from: type=local,src=/tmp/.buildx-cache-freyja
-          cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new
-          tags: freyja:update
-
-      - name: get freyja database version
-        id: db_version
-        run: |
-          docker run freyja:update freyja demix --version
-          version=$(docker run freyja:update freyja demix --version | grep . | grep -v Barcode | head -n 1)
-          echo "the latest version is $version"
-          echo "version=$version" >> $GITHUB_OUTPUT
-      - name: Get current date
-        id: date
-        run: |
-          date=$(date '+%Y-%m-%d')
-          echo "the date is $date"
-          echo "date=$date" >> $GITHUB_OUTPUT
-      
-      # - name: Login to DockerHub
-      #   uses: docker/login-action@v2
-      #   with:
-      #     username: ${{ secrets.DOCKER_HUB_USERNAME }}
-      #     password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
-
-      - name: Login to Quay
-        uses: docker/login-action@v2
-        with:
-          registry: quay.io
-          username: ${{ secrets.QUAY_USERNAME }}
-          password: ${{ secrets.QUAY_ROBOT_TOKEN }}
-
-      - name: Build and push user-defined tag to DockerHub
-        id: docker_build_user_defined_tag
-        uses: docker/build-push-action@v3
-        with:
-          file: ${{ steps.latest_version.outputs.file }}
-          target: app
-          push: true
-          cache-from: type=local,src=/tmp/.buildx-cache-freyja
-          cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new # mode=max means export layers from all stage to cache
-          tags: staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
-            
-      - name: Build and push to Quay
-        id: build
-        uses: docker/build-push-action@v3
-        with:
-          file: ${{ steps.latest_version.outputs.file }}
-          target: app
-          push: true
-          cache-from: type=local,src=/tmp/.buildx-cache-freyja
-          cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new # mode=max means export 
-          tags: quay.io/staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
-
-      - name: Move cache # apparently prevents the cache from growing in size forever
-        run: |
-          rm -rf /tmp/.buildx-cache-freyja
-          mv /tmp/.buildx-cache-freyja-new /tmp/.buildx-cache-freyja
-      - name: Image digest
diff --git a/.github/workflows/update_freyja.yml b/.github/workflows/update_freyja.yml
index 35a1f67ec..f89acb4c1 100644
--- a/.github/workflows/update_freyja.yml
+++ b/.github/workflows/update_freyja.yml
@@ -9,49 +9,21 @@ name: Update Freyja
 on: 
   workflow_dispatch:
   schedule:
-    - cron: '30 7 * * *'
+    - cron: '30 7 * * 1'
 
 run-name: Updating Freyja
 
 jobs:
   update:
     runs-on: ubuntu-latest
-    steps:
-
-# Keeping here in case we want to use it to keep Freyja's version up-to-date as well
-#      - name: Get latest release
-#        uses: rez0n/actions-github-release@main
-#        id: latest_release
-#        with:
-#          token: ${{ secrets.GITHUB_TOKEN }}
-#          repository: andersen-lab/Freyja
-#          type: "stable"
-#      - name: Remove V
-#        id: strip
-#        run: |
-#          version=$(echo "${{ steps.latest_release.outputs.release }}" | sed 's/V//g' | sed 's/v//g' )
-#          echo "The version is $version"
-#          echo "version=$version" >> $GITHUB_OUTPUT
-          
+    steps:    
       - name: pull repo
-        uses: actions/checkout@v3
-
-# Keeping here in case we want to figure out why this doesn't work      
-#      - name: get latest version of freyja in docker-builds repo
-#        id: latest_version
-#        run: | 
-#          file=$(git log -1 --name-only --format=%cd --date=iso freyja/*/Dockerfile | grep Dockerfile | head -n 1 )
-#          echo "the latest file is $file"
-#          echo "file=$file" >> $GITHUB_OUTPUT
-#
-#          version=$(echo $file | cut -f 2 -d "/" | cut -f 1 -d "_")
-#          echo "the latest version is $version"
-#          echo "version=$version" >> $GITHUB_OUTPUT      
+        uses: actions/checkout@v4     
 
       - name: set freyja version
         id: latest_version
         run: |
-          version=1.4.9
+          version=1.5.2
           echo "version=$version" >> $GITHUB_OUTPUT 
           
           file=freyja/$version/Dockerfile
@@ -60,25 +32,16 @@ jobs:
 
       - name: set up docker buildx
         id: buildx
-        uses: docker/setup-buildx-action@v2
-
-      - name: cache docker layers
-        uses: actions/cache@v3
-        with:
-          path: /tmp/.buildx-cache-freyja
-          key: ${{ runner.os }}-buildx-freyja-${{ github.sha }}
-          restore-keys: ${{ runner.os }}-buildx-freyja
+        uses: docker/setup-buildx-action@v3
 
       - name: build to test
         id: docker_build_to_test
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           file: ${{ steps.latest_version.outputs.file }}
           target: test
           load: true
           push: false
-          cache-from: type=local,src=/tmp/.buildx-cache-freyja
-          cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new
           tags: freyja:update
 
       - name: get freyja database version
@@ -97,44 +60,33 @@ jobs:
           echo "date=$date" >> $GITHUB_OUTPUT
       
       - name: Login to DockerHub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
 
       - name: Login to Quay
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: quay.io
           username: ${{ secrets.QUAY_USERNAME }}
           password: ${{ secrets.QUAY_ROBOT_TOKEN }}
 
-      - name: Build and push user-defined tag to DockerHub
-        id: docker_build_user_defined_tag
-        uses: docker/build-push-action@v3
-        with:
-          file: ${{ steps.latest_version.outputs.file }}
-          target: app
-          push: true
-          cache-from: type=local,src=/tmp/.buildx-cache-freyja
-          cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new # mode=max means export layers from all stage to cache
-          tags: staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
-            
-      - name: Build and push to Quay
-        id: build
-        uses: docker/build-push-action@v3
+      - name: Build and push Dockerfile
+        id: docker_build_and_push
+        uses: docker/build-push-action@v5
         with:
           file: ${{ steps.latest_version.outputs.file }}
           target: app
           push: true
-          cache-from: type=local,src=/tmp/.buildx-cache-freyja
-          cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new # mode=max means export 
-          tags: quay.io/staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
-
-      - name: Move cache # apparently prevents the cache from growing in size forever
-        run: |
-          rm -rf /tmp/.buildx-cache-freyja
-          mv /tmp/.buildx-cache-freyja-new /tmp/.buildx-cache-freyja
+          tags: |
+            staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version 
+}}-${{ steps.date.outputs.date }}
+            staphb/freyja:latest
+            quay.io/staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ 
+steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
+            quay.io/staphb/freyja:latest
 
       - name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}
+        run: echo ${{ steps.docker_build_user_defined_tag.outputs.digest }}
+

From ba84ae91991ed3b3d33d0d2e3956c2303c1f3eaa Mon Sep 17 00:00:00 2001
From: taylorpaisie <tpaisie91@gmail.com>
Date: Fri, 22 Nov 2024 15:37:55 -0500
Subject: [PATCH 09/19] updated program licenses with hostile

---
 Program_Licenses.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Program_Licenses.md b/Program_Licenses.md
index fd5fbcec7..8bdb4b262 100644
--- a/Program_Licenses.md
+++ b/Program_Licenses.md
@@ -62,6 +62,7 @@ The licenses of the open-source software that is contained in these Docker image
 | HeatCluster | GPL-3.0 | https://github.com/DrB-S/heatcluster/blob/main/LICENSE |
 | Hmmer | BSD-3 | http://eddylab.org/software/hmmer/Userguide.pdf |
 | homopolish | GNU GPLv3 | https://github.com/ythuang0522/homopolish/blob/master/LICENSE |
+| hostile | MIT | https://github.com/bede/hostile?tab=MIT-1-ov-file#readme |
 | htslib | MIT | https://github.com/samtools/htslib/blob/develop/LICENSE |
 | iqtree | GNU GPLv2 | https://github.com/Cibiv/IQ-TREE/blob/master/LICENSE |
 | iqtree2 | GNU GPLv2 | https://github.com/iqtree/iqtree2/blob/master/LICENSE |

From a1ea237d969e8aeba30c26c26fa52b1069413818 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 3 Dec 2024 12:38:30 -0700
Subject: [PATCH 10/19] Added hyperlink

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 92e5cd6bc..2a03fda77 100644
--- a/README.md
+++ b/README.md
@@ -181,7 +181,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [heatcluster](https://hub.docker.com/r/staphb/heatcluster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/heatcluster)](https://hub.docker.com/r/staphb/heatcluster) | <ul><li>[1.0.2c](./heatcluster/1.0.2c/)</li></ul> | https://github.com/DrB-S/heatcluster/tree/main |
 | [hmmer](https://hub.docker.com/r/staphb/hmmer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | <ul><li>[3.3](hmmer/3.3/)</li><li>[3.3.2](hmmer/3.3.2/)</li><li>[3.4](./hmmer/3.4/)</li></ul> | http://hmmer.org/ |
 | [homopolish](https://hub.docker.com/r/staphb/homopolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | <ul><li>0.4.1</li></ul> | https://github.com/ythuang0522/homopolish/ |
-| [hostile](https://github.com/bede/hostile) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hostile)](https://hub.docker.com/r/staphb/hostile | <ul><li>1.1.0</li></ul> | https://github.com/bede/hostile |
+| [hostile](https://github.com/bede/hostile) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hostile)](https://hub.docker.com/r/staphb/hostile | <ul><li>[1.1.0](./hostile/1.1.0)</li></ul> | https://github.com/bede/hostile |
 | [htslib](https://hub.docker.com/r/staphb/htslib) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | <ul><li>[1.14](./htslib/1.14)</li><li>[1.15](./htslib/1.15)</li><li>[1.16](./htslib/1.16)</li><li>[1.17](./htslib/1.17)</li><li>[1.18](./htslib/1.18/)</li><li>[1.19](./htslib/1.19/)</li><li>[1.20](./htslib/1.20/)</li><li>[1.20.c](./htslib/1.20.c/)</li><li>[1.21](./htslib/1.21/)</li></ul> | https://www.htslib.org/ |
 | [Integron Finder](https://hub.docker.com/r/staphb/integron_finder/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/integron_finder)](https://hub.docker.com/r/staphb/integron_finder) | <ul><li>[2.0.5](./integron_finder/2.0.5/)</li></ul> | https://github.com/gem-pasteur/Integron_Finder |
 | [iqtree](https://hub.docker.com/r/staphb/iqtree/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | <ul><li>1.6.7</li></ul> | http://www.iqtree.org/ |

From f0b0fcb2dd5d902eefb21df10025f4cf9d37d945 Mon Sep 17 00:00:00 2001
From: Taylor Paisie <tpaisie91@gmail.com>
Date: Wed, 4 Dec 2024 11:22:49 -0500
Subject: [PATCH 11/19] moving labels and hostile help command to app stage in
 dockerfile

---
 hostile/1.1.0/Dockerfile | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/hostile/1.1.0/Dockerfile b/hostile/1.1.0/Dockerfile
index 798d74418..179423966 100644
--- a/hostile/1.1.0/Dockerfile
+++ b/hostile/1.1.0/Dockerfile
@@ -5,17 +5,6 @@ ARG HOSTILE_VER="1.1.0"
 FROM ubuntu:focal AS builder
 ARG HOSTILE_VER
 
-# Metadata
-LABEL base.image="ubuntu:focal" 
-LABEL dockerfile.version="1" 
-LABEL software="hostile"
-LABEL software.version="${HOSTILE_VER}"
-LABEL description="Precise host read removal."
-LABEL website="https://github.com/bede/hostile"
-LABEL license.url="https://github.com/bede/hostile?tab=MIT-1-ov-file#readme"
-LABEL maintainer="Taylor K. Paisie"
-LABEL maintainer.email="ltj8@cdc.gov"
-
 RUN apt-get update && apt-get install -y --no-install-recommends \
     software-properties-common && \
     add-apt-repository ppa:deadsnakes/ppa && \
@@ -24,8 +13,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     wget unzip samtools minimap2 bedtools gawk ca-certificates && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
-
-
 # Install pip for Python 3.10
 RUN wget https://bootstrap.pypa.io/get-pip.py && python3.10 get-pip.py && \
     rm get-pip.py && pip install --no-cache-dir setuptools pytest && \
@@ -50,6 +37,16 @@ RUN wget https://github.com/bede/hostile/archive/refs/tags/${HOSTILE_VER}.tar.gz
 # Stage 2: Final image
 FROM ubuntu:focal AS app
 
+LABEL base.image="ubuntu:focal" 
+LABEL dockerfile.version="1" 
+LABEL software="hostile"
+LABEL software.version="${HOSTILE_VER}"
+LABEL description="Precise host read removal."
+LABEL website="https://github.com/bede/hostile"
+LABEL license.url="https://github.com/bede/hostile?tab=MIT-1-ov-file#readme"
+LABEL maintainer="Taylor K. Paisie"
+LABEL maintainer.email="ltj8@cdc.gov"
+
 COPY --from=builder /usr/ /usr/
 COPY --from=builder /hostile-1.1.0/tests/data/sars-cov-2/ /data/test/sars-cov-2/
 
@@ -57,6 +54,9 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     ca-certificates && update-ca-certificates && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
+CMD hostile --help
+WORKDIR /data
+
 # Optional stage: Test data
 FROM app AS test
 
@@ -68,4 +68,4 @@ RUN wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_d
     --no-check-certificate && \
     hostile clean --index /data/test/sars-cov-2/sars-cov-2 --fastq1 test_miniburk_R1.fastq.gz --fastq2 test_miniburk_R2.fastq.gz
 
-WORKDIR /data
\ No newline at end of file
+WORKDIR /data

From 84ac86e475a0d5fdaae77e811403c1ee399f53bf Mon Sep 17 00:00:00 2001
From: Taylor Paisie <tpaisie91@gmail.com>
Date: Wed, 4 Dec 2024 11:31:14 -0500
Subject: [PATCH 12/19] adding bowtie2 version arg to dockerfile

---
 hostile/1.1.0/Dockerfile | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/hostile/1.1.0/Dockerfile b/hostile/1.1.0/Dockerfile
index 179423966..044af930b 100644
--- a/hostile/1.1.0/Dockerfile
+++ b/hostile/1.1.0/Dockerfile
@@ -1,5 +1,6 @@
 # Set global variables
 ARG HOSTILE_VER="1.1.0"
+ARG BOWTIE2_VER="2.5.1"
 
 # Stage 1: Build Dockerfile
 FROM ubuntu:focal AS builder
@@ -20,11 +21,11 @@ RUN wget https://bootstrap.pypa.io/get-pip.py && python3.10 get-pip.py && \
     ln -sf /usr/local/bin/pip /usr/bin/pip
 
 # Install bowtie2 and ensure all executables are accessible
-RUN wget https://github.com/BenLangmead/bowtie2/releases/download/v2.5.1/bowtie2-2.5.1-linux-x86_64.zip && \
-    unzip bowtie2-2.5.1-linux-x86_64.zip && \
-    mv bowtie2-2.5.1-linux-x86_64 /usr/local/bowtie2 && \
+RUN wget https://github.com/BenLangmead/bowtie2/releases/download/v${BOWTIE2_VER}/bowtie2-${BOWTIE2_VER}-linux-x86_64.zip && \
+    unzip bowtie2-${BOWTIE2_VER}-linux-x86_64.zip && \
+    mv bowtie2-${BOWTIE2_VER}-linux-x86_64 /usr/local/bowtie2 && \
     ln -s /usr/local/bowtie2/bowtie2* /usr/bin/ && \
-    rm -f bowtie2-2.5.1-linux-x86_64.zip
+    rm -f bowtie2-${BOWTIE2_VER}-linux-x86_64.zip
 
 # Install hostile
 RUN wget https://github.com/bede/hostile/archive/refs/tags/${HOSTILE_VER}.tar.gz && \

From fed5b82cd9f22ea294af9f92c2d74d463fa0c4a2 Mon Sep 17 00:00:00 2001
From: Taylor Paisie <tpaisie91@gmail.com>
Date: Thu, 5 Dec 2024 14:03:57 -0500
Subject: [PATCH 13/19] Updated Dockerfile with ubuntu:jammy

---
 hostile/1.1.0/Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hostile/1.1.0/Dockerfile b/hostile/1.1.0/Dockerfile
index 044af930b..d3ecf6415 100644
--- a/hostile/1.1.0/Dockerfile
+++ b/hostile/1.1.0/Dockerfile
@@ -3,7 +3,7 @@ ARG HOSTILE_VER="1.1.0"
 ARG BOWTIE2_VER="2.5.1"
 
 # Stage 1: Build Dockerfile
-FROM ubuntu:focal AS builder
+FROM ubuntu:jammy AS builder
 ARG HOSTILE_VER
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
@@ -36,7 +36,7 @@ RUN wget https://github.com/bede/hostile/archive/refs/tags/${HOSTILE_VER}.tar.gz
 
 
 # Stage 2: Final image
-FROM ubuntu:focal AS app
+FROM ubuntu:jammy AS app
 
 LABEL base.image="ubuntu:focal" 
 LABEL dockerfile.version="1" 

From f2e25422513d0255681725edefbcd98d160f0dbe Mon Sep 17 00:00:00 2001
From: Taylor Paisie <tpaisie91@gmail.com>
Date: Thu, 5 Dec 2024 14:09:39 -0500
Subject: [PATCH 14/19] changed dockerfile back to ubuntu:focal

---
 hostile/1.1.0/Dockerfile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/hostile/1.1.0/Dockerfile b/hostile/1.1.0/Dockerfile
index d3ecf6415..7b4d10d09 100644
--- a/hostile/1.1.0/Dockerfile
+++ b/hostile/1.1.0/Dockerfile
@@ -3,8 +3,9 @@ ARG HOSTILE_VER="1.1.0"
 ARG BOWTIE2_VER="2.5.1"
 
 # Stage 1: Build Dockerfile
-FROM ubuntu:jammy AS builder
+FROM ubuntu:focal AS builder
 ARG HOSTILE_VER
+ARG BOWTIE2_VER
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
     software-properties-common && \
@@ -36,7 +37,7 @@ RUN wget https://github.com/bede/hostile/archive/refs/tags/${HOSTILE_VER}.tar.gz
 
 
 # Stage 2: Final image
-FROM ubuntu:jammy AS app
+FROM ubuntu:focal AS app
 
 LABEL base.image="ubuntu:focal" 
 LABEL dockerfile.version="1" 

From f25b3b246a74f7c6d61d8f6cf4b583c5c246a20b Mon Sep 17 00:00:00 2001
From: Taylor Paisie <tpaisie91@gmail.com>
Date: Fri, 6 Dec 2024 14:42:23 -0500
Subject: [PATCH 15/19] updated dockerfile with hostile ver arg and hostile
 test paths

---
 hostile/1.1.0/Dockerfile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/hostile/1.1.0/Dockerfile b/hostile/1.1.0/Dockerfile
index 7b4d10d09..9b589b106 100644
--- a/hostile/1.1.0/Dockerfile
+++ b/hostile/1.1.0/Dockerfile
@@ -38,11 +38,12 @@ RUN wget https://github.com/bede/hostile/archive/refs/tags/${HOSTILE_VER}.tar.gz
 
 # Stage 2: Final image
 FROM ubuntu:focal AS app
+ARG HOSTILE_VER
 
 LABEL base.image="ubuntu:focal" 
 LABEL dockerfile.version="1" 
 LABEL software="hostile"
-LABEL software.version="${HOSTILE_VER}"
+LABEL software.version=${HOSTILE_VER}
 LABEL description="Precise host read removal."
 LABEL website="https://github.com/bede/hostile"
 LABEL license.url="https://github.com/bede/hostile?tab=MIT-1-ov-file#readme"
@@ -50,7 +51,7 @@ LABEL maintainer="Taylor K. Paisie"
 LABEL maintainer.email="ltj8@cdc.gov"
 
 COPY --from=builder /usr/ /usr/
-COPY --from=builder /hostile-1.1.0/tests/data/sars-cov-2/ /data/test/sars-cov-2/
+COPY --from=builder /hostile-${HOSTILE_VER}/tests/data/sars-cov-2/ /data/test/sars-cov-2/
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
     ca-certificates && update-ca-certificates && \

From 920cc16909bd809b55c0d31c81efe2d0cd8f5d22 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Mon, 9 Dec 2024 14:17:27 -0700
Subject: [PATCH 16/19] Update update_pango_aliasor.yml

---
 .github/workflows/update_pango_aliasor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/update_pango_aliasor.yml b/.github/workflows/update_pango_aliasor.yml
index 7993fa3f6..cc3e46ed2 100644
--- a/.github/workflows/update_pango_aliasor.yml
+++ b/.github/workflows/update_pango_aliasor.yml
@@ -79,4 +79,4 @@ jobs:
             quay.io/staphb/pango_aliasor:latest
 
       - name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}
\ No newline at end of file
+        run: echo ${{ steps.docker_build.outputs.digest }}

From 1548ab2ba672cd0d5b9310c9e0732792f0d42661 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Mon, 9 Dec 2024 14:17:58 -0700
Subject: [PATCH 17/19] Update update_pango_aliasor.yml

---
 .github/workflows/update_pango_aliasor.yml | 43 +++++++++++++---------
 1 file changed, 25 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/update_pango_aliasor.yml b/.github/workflows/update_pango_aliasor.yml
index cc3e46ed2..367599a20 100644
--- a/.github/workflows/update_pango_aliasor.yml
+++ b/.github/workflows/update_pango_aliasor.yml
@@ -1,33 +1,32 @@
 ##### ------------------------------------------------------------------------------------------------ #####
 ##### This caller workflow tests, builds, and pushes the image to Docker Hub and Quay using the most   #####
-##### recent version of pango_aliasor and downloads the current pangolin lineages.                     #####
+##### recent version of Freyja and downloading the most recent variant information.                    #####
 ##### It takes no manual input.                                                                        #####
 ##### ------------------------------------------------------------------------------------------------ #####
 
-name: Update pango aliasor
+name: Update Freyja
 
 on: 
   workflow_dispatch:
   schedule:
     - cron: '30 7 * * 1'
 
-run-name: Updating pango aliasor
+run-name: Updating Freyja
 
 jobs:
   update:
     runs-on: ubuntu-latest
-    steps:
-          
+    steps:    
       - name: pull repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4     
 
-      - name: set pango_aliasor version
+      - name: set freyja version
         id: latest_version
         run: |
-          version=0.3.0
+          version=1.5.2
           echo "version=$version" >> $GITHUB_OUTPUT 
           
-          file=pango_aliasor/0.3.0/Dockerfile
+          file=freyja/$version/Dockerfile
           ls $file
           echo "file=$file" >> $GITHUB_OUTPUT
 
@@ -39,11 +38,19 @@ jobs:
         id: docker_build_to_test
         uses: docker/build-push-action@v5
         with:
-          context: pango_aliasor/${{ steps.latest_version.outputs.version }}
+          file: ${{ steps.latest_version.outputs.file }}
           target: test
           load: true
           push: false
-          tags: pango_aliasor:update
+          tags: freyja:update
+
+      - name: get freyja database version
+        id: db_version
+        run: |
+          docker run freyja:update freyja demix --version
+          version=$(docker run freyja:update freyja demix --version | grep . | grep -v Barcode | head -n 1)
+          echo "the latest version is $version"
+          echo "version=$version" >> $GITHUB_OUTPUT
 
       - name: Get current date
         id: date
@@ -65,18 +72,18 @@ jobs:
           username: ${{ secrets.QUAY_USERNAME }}
           password: ${{ secrets.QUAY_ROBOT_TOKEN }}
 
-      - name: Build and push user-defined tag to DockerHub
-        id: docker_build_user_defined_tag
+      - name: Build and push Dockerfile
+        id: docker_build_and_push
         uses: docker/build-push-action@v5
         with:
           file: ${{ steps.latest_version.outputs.file }}
           target: app
           push: true
           tags: |
-            staphb/pango_aliasor:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
-            staphb/pango_aliasor:latest
-            quay.io/staphb/pango_aliasor:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
-            quay.io/staphb/pango_aliasor:latest
+            staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
+            staphb/freyja:latest
+            quay.io/staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
+            quay.io/staphb/freyja:latest
 
       - name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}
+        run: echo ${{ steps.docker_build_user_defined_tag.outputs.digest }}

From d4de03336239e9764508195c0dd623d474f195f2 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Mon, 9 Dec 2024 14:18:39 -0700
Subject: [PATCH 18/19] Update update_pango_aliasor.yml


From 940a168189f587e99be35363501d35cd6cf5c615 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Mon, 9 Dec 2024 14:19:36 -0700
Subject: [PATCH 19/19] Delete .github/workflows/update_pango_aliasor.yml

---
 .github/workflows/update_pango_aliasor.yml | 89 ----------------------
 1 file changed, 89 deletions(-)
 delete mode 100644 .github/workflows/update_pango_aliasor.yml

diff --git a/.github/workflows/update_pango_aliasor.yml b/.github/workflows/update_pango_aliasor.yml
deleted file mode 100644
index 367599a20..000000000
--- a/.github/workflows/update_pango_aliasor.yml
+++ /dev/null
@@ -1,89 +0,0 @@
-##### ------------------------------------------------------------------------------------------------ #####
-##### This caller workflow tests, builds, and pushes the image to Docker Hub and Quay using the most   #####
-##### recent version of Freyja and downloading the most recent variant information.                    #####
-##### It takes no manual input.                                                                        #####
-##### ------------------------------------------------------------------------------------------------ #####
-
-name: Update Freyja
-
-on: 
-  workflow_dispatch:
-  schedule:
-    - cron: '30 7 * * 1'
-
-run-name: Updating Freyja
-
-jobs:
-  update:
-    runs-on: ubuntu-latest
-    steps:    
-      - name: pull repo
-        uses: actions/checkout@v4     
-
-      - name: set freyja version
-        id: latest_version
-        run: |
-          version=1.5.2
-          echo "version=$version" >> $GITHUB_OUTPUT 
-          
-          file=freyja/$version/Dockerfile
-          ls $file
-          echo "file=$file" >> $GITHUB_OUTPUT
-
-      - name: set up docker buildx
-        id: buildx
-        uses: docker/setup-buildx-action@v3
-
-      - name: build to test
-        id: docker_build_to_test
-        uses: docker/build-push-action@v5
-        with:
-          file: ${{ steps.latest_version.outputs.file }}
-          target: test
-          load: true
-          push: false
-          tags: freyja:update
-
-      - name: get freyja database version
-        id: db_version
-        run: |
-          docker run freyja:update freyja demix --version
-          version=$(docker run freyja:update freyja demix --version | grep . | grep -v Barcode | head -n 1)
-          echo "the latest version is $version"
-          echo "version=$version" >> $GITHUB_OUTPUT
-
-      - name: Get current date
-        id: date
-        run: |
-          date=$(date '+%Y-%m-%d')
-          echo "the date is $date"
-          echo "date=$date" >> $GITHUB_OUTPUT
-      
-      - name: Login to DockerHub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ secrets.DOCKER_HUB_USERNAME }}
-          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
-
-      - name: Login to Quay
-        uses: docker/login-action@v3
-        with:
-          registry: quay.io
-          username: ${{ secrets.QUAY_USERNAME }}
-          password: ${{ secrets.QUAY_ROBOT_TOKEN }}
-
-      - name: Build and push Dockerfile
-        id: docker_build_and_push
-        uses: docker/build-push-action@v5
-        with:
-          file: ${{ steps.latest_version.outputs.file }}
-          target: app
-          push: true
-          tags: |
-            staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
-            staphb/freyja:latest
-            quay.io/staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
-            quay.io/staphb/freyja:latest
-
-      - name: Image digest
-        run: echo ${{ steps.docker_build_user_defined_tag.outputs.digest }}