diff --git a/README.md b/README.md index 166f6783c..75e4994ea 100644 --- a/README.md +++ b/README.md @@ -172,7 +172,7 @@ To learn more about the docker pull rate limits and the open source software pro | [homopolish](https://hub.docker.com/r/staphb/homopolish)
[![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | | https://github.com/ythuang0522/homopolish/ | | [htslib](https://hub.docker.com/r/staphb/htslib)
[![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | | https://www.htslib.org/ | | [iqtree](https://hub.docker.com/r/staphb/iqtree/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | | http://www.iqtree.org/ | -| [iqtree2](https://hub.docker.com/r/staphb/iqtree2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | | http://www.iqtree.org/ | +| [iqtree2](https://hub.docker.com/r/staphb/iqtree2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | | http://www.iqtree.org/ | | [IPA](https://hub.docker.com/r/staphb/pbipa)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbipa)](https://hub.docker.com/r/staphb/pbipa) | | https://github.com/PacificBiosciences/pbipa | | [IRMA](https://hub.docker.com/r/staphb/irma/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/irma)](https://hub.docker.com/r/staphb/irma) | | https://wonder.cdc.gov/amd/flu/irma/| | [isPcr](https://users.soe.ucsc.edu/~kent/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ispcr)](https://hub.docker.com/r/staphb/ispcr) | | https://users.soe.ucsc.edu/~kent/ | diff --git a/iqtree2/2.3.4/Dockerfile b/iqtree2/2.3.4/Dockerfile new file mode 100644 index 000000000..352dcc28e --- /dev/null +++ b/iqtree2/2.3.4/Dockerfile @@ -0,0 +1,52 @@ +ARG IQTREE2_VER="2.3.4" + +FROM ubuntu:jammy as app + +# for easy upgrade later. ARG variables only persist during build time. +ARG IQTREE2_VER + +# metadata +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="IQ-Tree2" +LABEL software.version="${IQTREE2_VER}" +LABEL description="Efficient software for phylogenomic inference" +LABEL website="http://www.iqtree.org/" +LABEL source.code.website="https://github.com/iqtree/iqtree2" +LABEL license="https://github.com/iqtree/iqtree2/blob/master/LICENSE" +LABEL maintainer="Jade Wang" +LABEL maintainer.email="jwang7@health.nyc.gov" +LABEL maintainer2="Erin Young" +LABEL maintainer2.email="eriny@utah.gov" + +#install dependencies +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget ca-certificates procps && \ + apt-get autoclean && \ + rm -rf /var/lib/apt/lists/* + +# download, uncompress iqtree2 tarball; make /data +RUN wget -q https://github.com/iqtree/iqtree2/releases/download/v.${IQTREE2_VER}/iqtree-${IQTREE2_VER}-Linux-intel.tar.gz && \ + tar -xvf iqtree-${IQTREE2_VER}-Linux-intel.tar.gz && \ + rm -v iqtree-${IQTREE2_VER}-Linux-intel.tar.gz && \ + mkdir /data + +# set PATH and locale settings for singularity compatibility +ENV PATH="/iqtree-${IQTREE2_VER}-Linux-intel/bin:${PATH}"\ + LC_ALL=C + +# final working directory is /data +WORKDIR /data + +# default command is to pull up help options +CMD [ "iqtree2", "--help" ] + +FROM app as test + +ARG IQTREE2_VER + +# print version and help +RUN iqtree2 --version && iqtree2 --help + +###TEST TREE TOPOLOGY +RUN iqtree2 -s /iqtree-${IQTREE2_VER}-Linux-intel/example.phy --rate diff --git a/iqtree2/2.3.4/README.md b/iqtree2/2.3.4/README.md new file mode 100644 index 000000000..4c53969e5 --- /dev/null +++ b/iqtree2/2.3.4/README.md @@ -0,0 +1,28 @@ +# IQ-TREE2 container + +Main tool : [iqtree2](https://github.com/iqtree/iqtree2) + +Full documentation: [https://github.com/rrwick/Polypolish/wiki](http://www.iqtree.org/doc/) + +| Efficient and versatile phylogenomic software by maximum likelihood + +## Example Usage + +An example phylip file (IQ-TREE2 also supports other file formats such as FASTA, NEXUS, CLUSTALW) + +``` +7 28 +Frog AAATTTGGTCCTGTGATTCAGCAGTGAT +Turtle CTTCCACACCCCAGGACTCAGCAGTGAT +Bird CTACCACACCCCAGGACTCAGCAGTAAT +Human CTACCACACCCCAGGAAACAGCAGTGAT +Cow CTACCACACCCCAGGAAACAGCAGTGAC +Whale CTACCACGCCCCAGGACACAGCAGTGAT +Mouse CTACCACACCCCAGGACTCAGCAGTGAT +``` + +Can be aligned with the following command: + +```bash +iqtree2 -s example.phy --redo +```