adding autocycler 0.2.1

Program_Licenses.md

@@ -16,6 +16,7 @@ The licenses of the open-source software that is contained in these Docker image
 | assembly_snptyper | MIT | https://github.com/boasvdp/assembly_snptyper/blob/main/LICENSE |
 | Augur | GNU Affero GPLv3 | https://github.com/nextstrain/augur/blob/master/LICENSE.txt |
 | Auspice | GNU Affero GPLv3 | https://github.com/nextstrain/auspice/blob/master/LICENSE.txt |
+| Autocycler | GNU General Public License v3.0 | https://github.com/rrwick/Autocycler/blob/main/LICENSE |
 | Bakta | GNU GPLv3 | https://github.com/oschwengers/bakta/blob/main/LICENSE |
 | Bandage | GNU GPLv3 | https://github.com/rrwick/Bandage?tab=GPL-3.0-1-ov-file#readme |
 | BBTools | non-standard - see `licence.txt` and `legal.txt` that is included in docker image under `/bbmap/docs/`; Also on sourceforge repo for BBTools | https://jgi.doe.gov/disclaimer/ |

README.md

@@ -121,6 +121,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [assembly_snptyper](https://hub.docker.com/r/staphb/assembly_snptyperh) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/assembly_snptyper)](https://hub.docker.com/r/staphb/assembly_snptyper) | <ul><li>[0.1.1](./assembly_snptyper/0.1.1/)</li></ul> | https://github.com/boasvdp/assembly_snptyper |
 | [Augur](https://hub.docker.com/r/staphb/augur) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/augur)](https://hub.docker.com/r/staphb/augur) | <ul><li>[6.3.0](./build-files/augur/6.3.0/)</li><li>[7.0.2](./build-files/augur/7.0.2/)</li><li>[8.0.0](./build-files/augur/8.0.0/)</li><li>[9.0.0](./build-files/augur/9.0.0/)</li><li>[16.0.3](./build-files/augur/16.0.3/)</li><li>[24.2.2](./build-files/augur/24.2.2/)</li><li>[24.2.3](./build-files/augur/24.2.3/)</li><li>[24.3.0](./build-files/augur/24.3.0/)</li><li>[24.4.0](./build-files/augur/24.4.0/)</li><li>[26.0.0](./build-files/augur/26.0.0/)</li><li>[27.0.0](./build-files/augur/27.0.0/)</li><li>[27.0.0](./build-files/augur/28.0.1/)</li></ul> | https://github.com/nextstrain/augur |
 | [Auspice](https://hub.docker.com/r/staphb/auspice) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/auspice)](https://hub.docker.com/r/staphb/auspice) | <ul><li>2.12.0</li></ul> | https://github.com/nextstrain/auspice |
+| [Autocycler](https://hub.docker.com/r/staphb/autocycler) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/autocycler)](https://hub.docker.com/r/staphb/autocycler) | <ul><li>[0.2.1](./build-files/autocycler/0.2.1/)</li><li>[0.2.1-tutorial](./build-files/autocycler/0.2.1-tutorial/)</li></ul> | https://github.com/rrwick/Autocycler/ |
 | [bakta](https://hub.docker.com/r/staphb/bakta) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | <ul><li>[1.9.2](./build-files/bakta/1.9.2/)</li><li>[1.9.2-light](./build-files/bakta/1.9.2-5.1-light/)</li><li>[1.9.3](./build-files/bakta/1.9.3/)</li><li>[1.9.3-light](./build-files/bakta/1.9.3-5.1-light/)</li><li>[1.9.4](./build-files/bakta/1.9.4/)</li><li>[1.9.4-5.1-light](./build-files/bakta/1.9.4-5.1-light/)</li><li>[1.10.3](./build-files/bakta/1.10.3/)</li><li>[1.10.3-light](./build-files/bakta/1.10.3-5.1-light/)</li><li>[1.10.4](./build-files/bakta/1.10.4/)</li><li>[1.10.4-5.1-light](./build-files/bakta/1.10.4-5.1-light/)</li></ul> | https://github.com/oschwengers/bakta |
 | [bandage](https://hub.docker.com/r/staphb/bandage) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bandage)](https://hub.docker.com/r/staphb/bandage) | <ul><li>[0.8.1](./bandage/0.8.1/)</li></ul> | https://rrwick.github.io/Bandage/ |
 | [BBTools](https://hub.docker.com/r/staphb/bbtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bbtools)](https://hub.docker.com/r/staphb/bbtools) | <ul><li>[38.76](./build-files/bbtools/38.76/)</li><li>[38.86](./build-files/bbtools/38.86/)</li><li>[38.95](./build-files/bbtools/38.95/)</li><li>[38.96](./build-files/bbtools/38.96/)</li><li>[38.97](./build-files/bbtools/38.97/)</li><li>[38.98](./build-files/bbtools/38.98/)</li><li>[38.99](./build-files/bbtools/38.99/)</li><li>[39.00](./build-files/bbtools/39.00/)</li><li>[39.01](./build-files/bbtools/39.01/)</li><li>[39.06](./build-files/bbtools/39.06/)</li><li>[39.10](./build-files/bbtools/39.10/)</li><li>[39.13](./build-files/bbtools/39.13/)</li><li>[39.16](./build-files/bbtools/39.16/)<li/></ul> | https://jgi.doe.gov/data-and-tools/bbtools/ |

build-files/autocycler/0.2.1-tutorial/Dockerfile

@@ -0,0 +1,64 @@
+FROM mambaorg/micromamba:2.0.5-ubuntu22.04 AS app
+
+ARG AUTOCYCLER_VER="0.2.1"
+
+USER root
+WORKDIR /
+
+LABEL base.image="mambaorg/micromamba:2.0.5-ubuntu22.04"
+LABEL dockerfile.version="1"
+LABEL software="Autocycler"
+LABEL software.version="${AUTOCYCLER_VER}"
+LABEL description="generating consensus long-read assemblies for bacterial genomes"
+LABEL website="https://github.com/rrwick/Autocycler"
+LABEL license="https://github.com/rrwick/Autocycler/blob/main/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# get conda environment file for extra tools
+RUN wget -q https://github.com/rrwick/Autocycler/archive/refs/tags/v${AUTOCYCLER_VER}.tar.gz && \
+    tar -xvf v${AUTOCYCLER_VER}.tar.gz && \
+    rm v${AUTOCYCLER_VER}.tar.gz && \
+    micromamba env create --file /Autocycler-${AUTOCYCLER_VER}/scripts/environment.yml --name autocycler && \
+    micromamba clean -a -f -y && \
+    rm -rf /Autocycler-${AUTOCYCLER_VER} && \
+    mkdir /data
+
+# install autocycler and helper scripts
+WORKDIR /usr/local/bin
+
+RUN wget https://github.com/rrwick/Autocycler/releases/download/v${AUTOCYCLER_VER}/autocycler-linux-x86_64-musl-v${AUTOCYCLER_VER}.tar.gz && \
+    tar -vxf autocycler-linux-x86_64-musl-v${AUTOCYCLER_VER}.tar.gz && \
+    rm autocycler-linux-x86_64-musl-v${AUTOCYCLER_VER}.tar.gz && \
+    wget https://github.com/rrwick/Autocycler/releases/download/v${AUTOCYCLER_VER}/autocycler-helper-scripts-v${AUTOCYCLER_VER}.tar.gz && \
+    tar -vxf autocycler-helper-scripts-v${AUTOCYCLER_VER}.tar.gz && \
+    rm autocycler-helper-scripts-v${AUTOCYCLER_VER}.tar.gz
+
+ENV PATH="/opt/conda/envs/autocycler/bin/:/opt/conda/bin/:${PATH}" \
+    LC_ALL=C.UTF-8
+
+CMD [ "autocycler", "--help" ]
+
+WORKDIR /data
+
+FROM app AS test
+
+WORKDIR /test
+
+RUN autocycler --help && \
+    autocycler --version
+
+COPY test.sh .
+
+RUN wget https://github.com/rrwick/Autocycler/releases/download/v0.1.0/autocycler-demo-dataset.tar && \
+    tar -vxf autocycler-demo-dataset.tar && \
+    bash test.sh && \
+    head autocycler_out/consensus_assembly.fasta
+
+RUN micromamba list -n autocycler