adding usher version 0.6.3

Program_Licenses.md

@@ -180,6 +180,7 @@ The licenses of the open-source software that is contained in these Docker image
 | Trimmomatic | GNU GPLv3 | https://github.com/usadellab/Trimmomatic/blob/main/distSrc/LICENSE |
 | Trycycler | GNU GPLv3 | https://github.com/rrwick/Trycycler/blob/master/LICENSE |
 | Unicycler | GNU GPLv3 | https://github.com/rrwick/Unicycler/blob/master/LICENSE |
+| UShER | MIT | https://github.com/yatisht/usher/blob/master/LICENSE |
 | VADR | Public Domain | https://github.com/nawrockie/vadr/blob/master/LICENSE |
 | Verkko | Public Domain | https://github.com/marbl/verkko/blob/master/README.licenses |
 | VIBRANT | GNU GPLv3 | https://github.com/AnantharamanLab/VIBRANT/blob/master/LICENSE |

README.md

@@ -287,6 +287,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Trimmomatic](https://hub.docker.com/r/staphb/trimmomatic/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/trimmomatic)](https://hub.docker.com/r/staphb/trimmomatic) | <ul><li>0.38</li><li>0.39</li></ul> | http://www.usadellab.org/cms/?page=trimmomatic </br>https://github.com/usadellab/Trimmomatic |
 | [Trycycler](https://hub.docker.com/r/staphb/trycycler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/trycycler)](https://hub.docker.com/r/staphb/trycycler) | <ul><li>[0.3.1](./trycycler/0.3.1/)</li><li>[0.3.2](./trycycler/0.3.2/)</li><li>[0.3.3](./trycycler/0.3.3/)</li><li>[0.5.0](./trycycler/0.5.0/)</li><li>[0.5.3](./trycycler/0.5.3/)</li><li>[0.5.4](./trycycler/0.5.4/)</li><li>[0.5.5](./trycycler/0.5.5/)</li></ul> | https://github.com/rrwick/Trycycler |
 | [Unicycler](https://hub.docker.com/r/staphb/unicycler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/unicycler)](https://hub.docker.com/r/staphb/unicycler) | <ul><li>0.4.7</li><li>0.4.8</li><li>0.4.9</li><li>0.5.0</li></ul> | https://github.com/rrwick/Unicycler |
+| [UShER](https://hub.docker.com/r/staphb/usher/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/usher)](https://hub.docker.com/r/staphb/usher) | <ul><li>[0.6.3](./usher/0.6.3/)</li></ul> | https://github.com/yatisht/usher |
 | [VADR](https://hub.docker.com/r/staphb/vadr/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/vadr)](https://hub.docker.com/r/staphb/vadr) | <ul><li>1.1</li><li>1.1.2</li><li>1.1.3</li><li>1.2</li><li>1.2.1</li><li>1.3 & SARS-CoV-2 models 1.3-1</li><li>1.3 & SARS-CoV-2 models 1.3-2</li><li>1.4 & SARS-CoV-2 models 1.3-2</li><li>1.4.1 & SARS-CoV-2 models 1.3-2</li><li>[1.4.2 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1](vadr/1.4.2/)</li><li>[1.5 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1](vadr/1.5/)</li><li>[1.5.1 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2](vadr/1.5.1/)</li><li>[1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-1](vadr/1.6.3/)</li><li>[1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-1, HAV v1.0.0](vadr/1.6.3-hav/)</li><li>[1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-2, HAV v1.0.0](vadr/1.6.3-hav-flu2/)</li></ul> | https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr) </br>https://github.com/ncbi/vadr |
 | [Verkko](https://hub.docker.com/r/staphb/verkko/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/verkko)](https://hub.docker.com/r/staphb/verkko) | <ul><li>[2.0](./verkko/2.0/)</li><li>[2.1](./verkko/2.1/)</li></ul> | https://github.com/marbl/verkko |
 | [VIBRANT](https://hub.docker.com/r/staphb/vibrant/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/vibrant)](https://hub.docker.com/r/staphb/vibrant) | <ul><li>1.2.1</li></ul> | https://github.com/AnantharamanLab/VIBRANT |

usher/0.6.3/Dockerfile

@@ -0,0 +1,102 @@
+ARG USHER_VER="0.6.3"
+
+FROM ubuntu:jammy as builder
+
+ARG USHER_VER
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps \
+    python3 \
+    mafft \
+    libisal-dev \
+    libtbb-dev \
+    python3-pip \
+    sudo \
+    cmake \
+    make \
+    gcc \
+    g++ \
+    protobuf-compiler \
+    libprotobuf-dev \
+    openmpi-bin \
+    openmpi-common \
+    libopenmpi-dev && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget -q https://github.com/yatisht/usher/archive/refs/tags/v${USHER_VER}.tar.gz && \
+    tar -xvf v${USHER_VER}.tar.gz && \
+    rm v${USHER_VER}.tar.gz && \
+    cd /usher-${USHER_VER} && \
+    ./install/installUbuntu.sh 
+
+FROM ubuntu:jammy as app
+
+ARG USHER_VER
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="UShER"
+LABEL software.version="${USHER_VER}"
+LABEL description="Ultrafast Sample Placement on Existing Trees."
+LABEL website="https://github.com/yatisht/usher"
+LABEL license="https://github.com/yatisht/usher/blob/master/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="eriny@utah.gov"
+
+# 'RUN' executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps \
+    python3 \
+    mafft \
+    libisal-dev \
+    libtbb-dev \
+    python3-pip \
+    libboost-all-dev \
+    libtbb-dev && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+COPY --from=builder /usher-${USHER_VER}/build/* /usher/build/
+COPY --from=builder /usher-${USHER_VER}/scripts/* /usher/scripts/
+
+RUN wget -q http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faSomeRecords -O /usr/local/bin/faSomeRecords && \
+    wget -q http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faSize -O /usr/local/bin/faSize && \
+    wget -q http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToVcf -O /usr/local/bin/faToVcf && \
+    chmod 775 /usr/local/bin/faSize /usr/local/bin/faSomeRecords /usr/local/bin/faToVcf
+
+ENV PATH="/usher/build/:/usher/scripts/:$PATH" \
+    LC_ALL=C \
+    LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
+
+RUN ls /usr/lib/x86_64-linux-gnu && ln -s /usr/lib/x86_64-linux-gnu/libtbb_preview.so.12 /usr/lib/x86_64-linux-gnu/libtbb_preview.so.2
+
+CMD [ "usher", "--help" ]
+
+WORKDIR /data
+
+FROM app as test
+
+ARG USHER_VER
+
+WORKDIR /usher-${USHER_VER}
+
+RUN usher --help && \
+    usher --version
+
+# https://usher-wiki.readthedocs.io/en/latest/UShER.html
+RUN usher -t test/global_phylo.nh -v test/global_samples.vcf -o global_assignments.pb -d output/
+
+RUN usher -t test/global_phylo.nh -v test/global_samples.vcf -o global_assignments.pb -c -d output2/
+
+RUN usher -t test/global_phylo.nh -v test/global_samples.vcf -o global_assignments.pb -c -u -d output3/
+
+RUN usher -i global_assignments.pb -v test/new_samples.vcf -u -d output4/
+
+RUN usher -i global_assignments.pb -v test/new_samples.vcf -u -k 20 -d output5/
+
+RUN usher -i global_assignments.pb -v test/new_samples.vcf -u -o new_global_assignments.pb -d output6/

usher/0.6.3/README.md

@@ -0,0 +1,29 @@
+# UShER container
+
+Main tool: [UShER](https://usher-wiki.readthedocs.io/en/latest/)
+
+Code repository: https://github.com/yatisht/usher
+
+Basic information on how to use this tool:
+- executable: usher
+- help: --help
+- version: NA
+- description: |
+> UShER is a program for rapid, accurate placement of samples to existing phylogenies. 
+
+Full documentation: https://usher-wiki.readthedocs.io/en/latest/
+
+Also contains (same version):
+- matUtils
+- matOptimize
+- ripples
+
+## Example Usage
+
+```bash
+# create mutation annotated tree object
+usher --tree global_phylo.nh --vcf global_samples.vcf --collapse-tree --save-mutation-annotated-tree global_phylo.pb
+
+# place samples onto tree
+usher --vcf new_samples.vcf --load-mutation-annotated-tree global_phylo.pb --write-uncondensed-final-tree
+```