adding metaphlan version 4.1.1 (#996)

* adding metaphlan version 4.1.1

* Update Dockerfile

micromamba clean -afy

---------

Co-authored-by: Kutluhan Incekara <[email protected]>

README.md

@@ -198,7 +198,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [mashtree](https://hub.docker.com/r/staphb/mashtree) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mashtree)](https://hub.docker.com/r/staphb/mashtree) | <ul><li>[0.52.0](./mashtree/0.52.0/)</li><li>[0.57.0](./mashtree/0.57.0/)</li><li>[1.0.4](./mashtree/1.0.4/)</li><li>[1.2.0](./mashtree/1.2.0/)</li><li>[1.4.6](./mashtree/1.4.6/)</li></ul> | https://github.com/lskatz/mashtree |
 | [MaSuRCA](https://hub.docker.com/r/staphb/masurca) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/masurca)](https://hub.docker.com/r/staphb/masurca) | <ul><li>4.0.8</li><li>4.0.9</li><li>4.1.0</li></ul> | https://github.com/alekseyzimin/masurca |
 | [medaka](https://hub.docker.com/r/staphb/medaka) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/medaka)](https://hub.docker.com/r/staphb/medaka) | <ul><li>0.8.1</li><li>1.0.1</li><li>1.2.0</li></ul> | https://github.com/nanoporetech/medaka |
-| [metaphlan](https://hub.docker.com/r/staphb/metaphlan) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/metaphlan)](https://hub.docker.com/r/staphb/metaphlan) | <ul><li>3.0.3-no-db (no database)</li><li> 3.0.3 (~3GB db)</li><li>[4.1.0](./metaphlan/4.1.0/) (no database)</li></ul> | https://github.com/biobakery/MetaPhlAn |
+| [metaphlan](https://hub.docker.com/r/staphb/metaphlan) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/metaphlan)](https://hub.docker.com/r/staphb/metaphlan) | <ul><li>[3.0.3-no-db (no database)](./metaphlan/3.0.3-no-db/)</li><li> [3.0.3 (~3GB db)](./metaphlan/3.0.3/)</li><li>[4.1.0](./metaphlan/4.1.0/) (no database)</li><li>[4.1.1](./metaphlan/4.1.1/) (no database)</li></ul> | https://github.com/biobakery/MetaPhlAn |
 | [MIDAS](https://hub.docker.com/r/staphb/midas) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/midas)](https://hub.docker.com/r/staphb/midas) | <ul><li>1.3.2 (no database)</li> | https://github.com/snayfach/MIDAS |
 | [minimap2](https://hub.docker.com/r/staphb/minimap2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minimap2)](https://hub.docker.com/r/staphb/minimap2) | <ul><li>2.17</li><li>2.18</li><li>2.21</li><li>2.22</li><li>2.23</li><li>2.24</li><li>2.25</li><li>[2.26](./minimap2/2.26)</li><li>[2.27](./minimap2/2.27/)</li>li>[2.28](./minimap2/2.28/)</li></ul> | https://github.com/lh3/minimap2 |
 | [minipolish](https://hub.docker.com/r/staphb/minipolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minipolish)](https://hub.docker.com/r/staphb/minipolish) | <ul><li>0.1.3</li></ul> | https://github.com/rrwick/Minipolish |

metaphlan/4.1.1/Dockerfile

@@ -0,0 +1,44 @@
+FROM mambaorg/micromamba:1.5.8 as app
+
+ARG METAPHLAN_VER="4.1.1"
+
+USER root
+
+WORKDIR /
+
+LABEL base.image="mambaorg/micromamba:1.5.8"
+LABEL dockerfile.version="1"
+LABEL software="MetaPhlAn"
+LABEL software.version="${METAPHLAN_VER}"
+LABEL description="MetaPhlAn is a computational tool for species-level microbial profiling from metagenomic shotgun sequencing data"
+LABEL website="https://github.com/biobakery/MetaPhlAn"
+LABEL license="https://github.com/biobakery/MetaPhlAn/blob/master/license.txt"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    procps &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN micromamba install --name base -c conda-forge -c bioconda metaphlan=${METAPHLAN_VER} &&\
+    micromamba clean -afy
+
+ENV PATH="/opt/conda/bin/:${PATH}" \
+    LC_ALL=C.UTF-8
+
+CMD [ "metaphlan", "--help" ]
+
+WORKDIR /data
+
+## Test ##
+FROM app as test
+
+RUN metaphlan --help
+
+# get test sample
+RUN wget https://github.com/biobakery/MetaPhlAn/releases/download/4.1.0/SRS014476-Supragingival_plaque.fasta.gz
+# download toy db
+RUN metaphlan --install --index mpa_vJan21_TOY_CHOCOPhlAnSGB_202103 --bowtie2db /toy
+# metaphlan test
+RUN metaphlan SRS014476-Supragingival_plaque.fasta.gz --input_type fasta --bowtie2db /toy --index mpa_vJan21_TOY_CHOCOPhlAnSGB_202103 > test.txt &&\
+    cat test.txt

metaphlan/4.1.1/README.md

@@ -0,0 +1,26 @@
+# MetaPhlAn container
+
+Main tool: [MetaPhlAn](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4.1)
+
+Code repository: https://github.com/biobakery/MetaPhlAn
+
+Basic information on how to use this tool:
+- executable: metaphlan
+- help: -h
+- version: -v
+- description: MetaPhlAn is a computational tool for species-level microbial profiling (bacteria, archaea, eukaryotes, and viruses) from metagenomic shotgun sequencing data. StrainPhlAn (available within MetaPhlAn) allows strain-level microbial population genomics.
+
+Additional information:
+
+The MetaPhlAn 4 database has been substantially increased (~21GB) in comparison with the previous 3.1 version. Thus, for running MetaPhlAn 4, a minimum of 25GB or memory is needed.
+The database can be downloaded from [Segatalab FTP](http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/) or via metaphlan with the following command:
+
+```metaphlan --install```
+
+Full documentation: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4.1
+
+## Example Usage
+
+```bash
+metaphlan metagenome.fastq --input_type fastq -o profiled_metagenome.txt
+```