adding iqtree2 version 2.3.4 (#977)

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) <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/ |
 | [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></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><li>[2.3.1](iqtree2/2.3.1/)</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><li>[2.3.1](iqtree2/2.3.1/)</li><li>[2.3.4](iqtree2/2.3.4/)</li></ul> | http://www.iqtree.org/ |
 | [IPA](https://hub.docker.com/r/staphb/pbipa) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbipa)](https://hub.docker.com/r/staphb/pbipa) | <ul><li>[1.8.0](./pbipa/1.8.0/)</li></ul> | https://github.com/PacificBiosciences/pbipa |
 | [IRMA](https://hub.docker.com/r/staphb/irma/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/irma)](https://hub.docker.com/r/staphb/irma) | <ul><li>1.0.2</li><li>1.0.3</li><li>1.1.2</li><li>1.1.3</li><li>[1.1.4](./irma/1.1.4/)</li></ul> | https://wonder.cdc.gov/amd/flu/irma/|
 | [isPcr](https://users.soe.ucsc.edu/~kent/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ispcr)](https://hub.docker.com/r/staphb/ispcr) | <ul><li>[33](ispcr/33/)</li></ul> | https://users.soe.ucsc.edu/~kent/ |

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="${IQTREE2_VER}"
+LABEL description="Efficient software for phylogenomic inference"
+LABEL website="http://www.iqtree.org/"
+LABEL source.code.website="https://github.com/iqtree/iqtree2"
+LABEL license="https://github.com/iqtree/iqtree2/blob/master/LICENSE"
+LABEL maintainer="Jade Wang"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Erin Young"
+LABEL maintainer2.email="[email protected]"
+
+#install dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget ca-certificates procps && \
+    apt-get autoclean && \
+    rm -rf /var/lib/apt/lists/*
+
+# download, uncompress iqtree2 tarball; make /data
+RUN wget -q https://github.com/iqtree/iqtree2/releases/download/v.${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

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
+```