From a025b8e4785fa34fb33506ad32d64e6864219c47 Mon Sep 17 00:00:00 2001
From: Erin Young <erin.olde@gmail.com>
Date: Thu, 14 Mar 2024 18:28:34 +0000
Subject: [PATCH 1/5] adding masurca version 4.1.1

---
 README.md                |  2 +-
 masurca/4.1.1/Dockerfile | 80 ++++++++++++++++++++++++++++++++++++++++
 masurca/4.1.1/README.md  | 25 +++++++++++++
 3 files changed, 106 insertions(+), 1 deletion(-)
 create mode 100644 masurca/4.1.1/Dockerfile
 create mode 100644 masurca/4.1.1/README.md

diff --git a/README.md b/README.md
index e881cf123..f47f22f33 100644
--- a/README.md
+++ b/README.md
@@ -192,7 +192,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [MAFFT](https://hub.docker.com/r/staphb/mafft/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mafft)](https://hub.docker.com/r/staphb/mafft)  | <ul><li>7.450</li><li>7.475</li><li>7.505</li></ul> | https://mafft.cbrc.jp/alignment/software/ |
 | [Mash](https://hub.docker.com/r/staphb/mash/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mash)](https://hub.docker.com/r/staphb/mash)  | <ul><li>2.1</li><li>2.2</li><li>2.3</li></ul> | https://github.com/marbl/Mash |
 | [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 |
+| [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](./masurca/4.0.8/)</li><li>[4.0.9](./masurca/4.0.9/)</li><li>[4.1.0](./masurca/4.1.0/)</li><li>[4.1.1](./masurca/4.1.1/)</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 |
 | [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 |
diff --git a/masurca/4.1.1/Dockerfile b/masurca/4.1.1/Dockerfile
new file mode 100644
index 000000000..b7dddabd8
--- /dev/null
+++ b/masurca/4.1.1/Dockerfile
@@ -0,0 +1,80 @@
+FROM ubuntu:jammy as app
+
+ARG MASURCA_VER="4.1.1"
+ARG MINIMAP2_VER="2.24"
+ARG BWA_VER="0.7.17"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="masurca"
+LABEL software.version="${MASURCA_VER}"
+LABEL description="Genome Assembly and Analysis"
+LABEL website="https://github.com/alekseyzimin/masurca"
+LABEL license="https://github.com/alekseyzimin/masurca/blob/master/LICENSE.txt"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="eriny@utah.gov"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  ca-certificates \
+  #python \
+  build-essential \
+  curl \
+  wget \
+  gcc \
+  zlib1g-dev \
+  bzip2 \
+  libboost-dev \
+  libbz2-dev \
+  liblzma-dev \
+  numactl \
+  procps \
+  bwa && \
+  apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# install minimap2
+RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner
+
+# # install bwa
+# RUN mkdir /bwa && \
+#   cd /bwa && \
+#   wget https://github.com/lh3/bwa/releases/download/v$BWA_VER/bwa-$BWA_VER.tar.bz2 && \
+#   tar -xjf bwa-$BWA_VER.tar.bz2 && \
+#   rm bwa-$BWA_VER.tar.bz2 && \
+#   cd bwa-$BWA_VER && \
+#   make
+
+# install masurca suite
+RUN mkdir /data && \
+  wget https://github.com/alekseyzimin/masurca/releases/download/v$MASURCA_VER/MaSuRCA-$MASURCA_VER.tar.gz && \
+  tar -xvf MaSuRCA-$MASURCA_VER.tar.gz && \
+  tail /MaSuRCA-4.1.1/install.sh && \
+  rm MaSuRCA-$MASURCA_VER.tar.gz
+
+WORKDIR /MaSuRCA-$MASURCA_VER
+
+# even in 4.1.1 there's the evil cp at the end of .install.sh
+# This gives the error:
+# 302.0 + cp -a ../Flye /MaSuRCA-4.1.1
+# 302.0 cp: '../Flye' and '/MaSuRCA-4.1.1/Flye' are the same file
+RUN bash /MaSuRCA-$MASURCA_VER/install.sh 2>/dev/null ; exit 0
+
+ENV PATH="${PATH}:/MaSuRCA-${MASURCA_VER}/Flye/bin:/MaSuRCA-${MASURCA_VER}/bin:/minimap2-${MINIMAP2_VER}_x64-linux:/bwa/bwa-${BWA_VER}" \
+  LC_ALL=C
+
+# WORKDIR sets working directory
+WORKDIR /data
+
+FROM app as test
+
+# testing POLCA
+RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz && \
+  wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_2.fastq.gz && \
+  wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa && \
+  polca.sh -a SRR13957123.consensus.fa -r 'SRR13957123_1.fastq.gz SRR13957123_2.fastq.gz' && \
+  test -f SRR13957123.consensus.fa.PolcaCorrected.fa
+
+# testing hybrid assembly
+RUN wget -q https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_1.fastq.gz && \
+  wget -q https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_2.fastq.gz && \
+  wget -q https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_low_depth.fastq.gz && \
+  masurca -t 2 -i short_reads_1.fastq.gz,short_reads_2.fastq.gz -r long_reads_low_depth.fastq.gz
diff --git a/masurca/4.1.1/README.md b/masurca/4.1.1/README.md
new file mode 100644
index 000000000..c9db0896d
--- /dev/null
+++ b/masurca/4.1.1/README.md
@@ -0,0 +1,25 @@
+# masurca container
+
+Main tools:
+
+- [masurca](https://github.com/alekseyzimin/masurca)
+- [polca](https://github.com/alekseyzimin/masurca#polca)
+- [Chromosome scaffolder](https://github.com/alekseyzimin/masurca#chromosome-scaffolder)
+- [SAMBA](https://github.com/alekseyzimin/masurca#samba-scaffolder)
+
+Other tools:
+
+- [bwa](https://github.com/lh3/bwa) (used by polca) 0.7.17-r1188
+- [minimap2](https://github.com/lh3/minimap2) (used by samba) 2.24-r1122
+
+## Example Usage
+
+```bash
+# masurca hybrid assembly
+masurca -t 2 -i short_reads_1.fastq.gz,short_reads_2.fastq.gz -r long_reads.fastq.gz
+
+# polishes consensus genome with paired-end Illumina reads
+polca.sh -a genome.fasta -r 'reads1.fastq reads2.fastq.gz' -t 16 -m 1G
+```
+
+Better documentation can be found at [https://github.com/alekseyzimin/masurca](https://github.com/alekseyzimin/masurca)

From 49bebb67414e2907a21a3f0e0c637665d69fb646 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Thu, 14 Mar 2024 13:01:19 -0600
Subject: [PATCH 2/5] Removed comments

---
 masurca/4.1.1/Dockerfile | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/masurca/4.1.1/Dockerfile b/masurca/4.1.1/Dockerfile
index b7dddabd8..f5d16e166 100644
--- a/masurca/4.1.1/Dockerfile
+++ b/masurca/4.1.1/Dockerfile
@@ -34,15 +34,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 # install minimap2
 RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner
 
-# # install bwa
-# RUN mkdir /bwa && \
-#   cd /bwa && \
-#   wget https://github.com/lh3/bwa/releases/download/v$BWA_VER/bwa-$BWA_VER.tar.bz2 && \
-#   tar -xjf bwa-$BWA_VER.tar.bz2 && \
-#   rm bwa-$BWA_VER.tar.bz2 && \
-#   cd bwa-$BWA_VER && \
-#   make
-
 # install masurca suite
 RUN mkdir /data && \
   wget https://github.com/alekseyzimin/masurca/releases/download/v$MASURCA_VER/MaSuRCA-$MASURCA_VER.tar.gz && \

From 4e74cc716e90d8dc4f93c350472d6005ad44731a Mon Sep 17 00:00:00 2001
From: kapsakcj <kapsakcj@gmail.com>
Date: Fri, 3 May 2024 13:49:57 -0400
Subject: [PATCH 3/5] install cmdline tool "file"

---
 masurca/4.1.1/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/masurca/4.1.1/Dockerfile b/masurca/4.1.1/Dockerfile
index f5d16e166..c01e0a839 100644
--- a/masurca/4.1.1/Dockerfile
+++ b/masurca/4.1.1/Dockerfile
@@ -28,7 +28,8 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
   liblzma-dev \
   numactl \
   procps \
-  bwa && \
+  bwa \
+  file && \
   apt-get autoclean && rm -rf /var/lib/apt/lists/*
 
 # install minimap2

From 40ed36a9fe57e78be3642c8a2be46bb8cc8b3f15 Mon Sep 17 00:00:00 2001
From: Erin Young <erin.olde@gmail.com>
Date: Wed, 30 Oct 2024 22:24:07 +0000
Subject: [PATCH 4/5] as good at it'll be

---
 masurca/{4.1.0 => 4.1.2}/Dockerfile | 93 ++++++++++++++++++-----------
 masurca/{4.1.0 => 4.1.2}/README.md  |  0
 2 files changed, 59 insertions(+), 34 deletions(-)
 rename masurca/{4.1.0 => 4.1.2}/Dockerfile (55%)
 rename masurca/{4.1.0 => 4.1.2}/README.md (100%)

diff --git a/masurca/4.1.0/Dockerfile b/masurca/4.1.2/Dockerfile
similarity index 55%
rename from masurca/4.1.0/Dockerfile
rename to masurca/4.1.2/Dockerfile
index faa605027..a8c652c6d 100644
--- a/masurca/4.1.0/Dockerfile
+++ b/masurca/4.1.2/Dockerfile
@@ -1,22 +1,13 @@
-FROM ubuntu:focal as app
+ARG MASURCA_VER="4.1.2"
 
-ARG MASURCA_VER="4.1.0"
-ARG MINIMAP2_VER="2.24"
-ARG BWA_VER="0.7.17"
+FROM ubuntu:jammy AS builder
 
-LABEL base.image="ubuntu:focal"
-LABEL dockerfile.version="1"
-LABEL software="masurca"
-LABEL software.version="${MASURCA_VER}"
-LABEL description="Genome Assembly and Analysis"
-LABEL website="https://github.com/alekseyzimin/masurca"
-LABEL license="https://github.com/alekseyzimin/masurca/blob/master/LICENSE.txt"
-LABEL maintainer="Erin Young"
-LABEL maintainer.email="eriny@utah.gov"
+ARG MINIMAP2_VER="2.28"
+ARG BWA_VER="0.7.18"
+ARG MASURCA_VER
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
   ca-certificates \
-  python \
   build-essential \
   curl \
   wget \
@@ -27,41 +18,71 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
   libbz2-dev \
   liblzma-dev \
   numactl \
-  procps && \
-  apt-get autoclean && rm -rf /var/lib/apt/lists/*
+  procps
 
 # install minimap2
-RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf -
+RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner && \
+  cp minimap2-${MINIMAP2_VER}_x64-linux/minimap2 /usr/local/bin && \
+  minimap2 --version
 
 # install bwa
-RUN mkdir /bwa && \
-  cd /bwa && \
-  wget https://github.com/lh3/bwa/releases/download/v$BWA_VER/bwa-$BWA_VER.tar.bz2 && \
-  tar -xjf bwa-$BWA_VER.tar.bz2 && \
-  rm bwa-$BWA_VER.tar.bz2 && \
-  cd bwa-$BWA_VER && \
-  make
+RUN wget https://github.com/lh3/bwa/archive/refs/tags/v${BWA_VER}.tar.gz && \
+  tar -xvf v${BWA_VER}.tar.gz && \
+  cd bwa-${BWA_VER} && \
+  make && \
+  mv bwa /usr/local/bin/
 
 # install masurca suite
-RUN mkdir /data && \
-  wget https://github.com/alekseyzimin/masurca/releases/download/v$MASURCA_VER/MaSuRCA-$MASURCA_VER.tar.gz && \
-  tar -xvf MaSuRCA-$MASURCA_VER.tar.gz && \
-  rm MaSuRCA-$MASURCA_VER.tar.gz
+# the last line of install.sh is to copy Flye to bin, but it already installed Flye there
+RUN wget -q https://github.com/alekseyzimin/masurca/releases/download/v${MASURCA_VER}/MaSuRCA-${MASURCA_VER}.tar.gz && \
+  tar -xvf MaSuRCA-${MASURCA_VER}.tar.gz && \
+  cd /MaSuRCA-${MASURCA_VER} && \
+  bash install.sh || true
+
+FROM ubuntu:jammy AS app
+
+ARG MASURCA_VER
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="masurca"
+LABEL software.version="${MASURCA_VER}"
+LABEL description="Genome Assembly and Analysis"
+LABEL website="https://github.com/alekseyzimin/masurca"
+LABEL license="https://github.com/alekseyzimin/masurca/blob/master/LICENSE.txt"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="eriny@utah.gov"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  ca-certificates \
+  wget \
+  numactl \
+  procps \
+  perl \
+  unzip \
+  bzip2 \
+  file && \
+  apt-get autoclean && rm -rf /var/lib/apt/lists/*
 
-WORKDIR /MaSuRCA-$MASURCA_VER
+COPY --from=builder /usr/local/bin/ /usr/local/bin/
+COPY --from=builder /MaSuRCA-${MASURCA_VER} /MaSuRCA-${MASURCA_VER}
 
-# even in 4.0.9 there's the evil cp at the end of .install.sh
-RUN bash /MaSuRCA-$MASURCA_VER/install.sh 2>/dev/null ; exit 0
+#RUN ls / && ls /MaSuRCA* && ls /MaSuRCA*/Flye/bin && ls /MaSuRCA*/bin && ls /MaS*/bin/polca.sh && hweaver
 
-ENV PATH="${PATH}:/MaSuRCA-${MASURCA_VER}/Flye/bin:/MaSuRCA-${MASURCA_VER}/bin:/minimap2-${MINIMAP2_VER}_x64-linux:/bwa/bwa-${BWA_VER}" \
+ENV PATH="${PATH}:/MaSuRCA-${MASURCA_VER}/Flye/bin:/MaSuRCA-${MASURCA_VER}/bin" \
   LC_ALL=C
 
-# WORKDIR sets working directory
+CMD masurca --help
+
 WORKDIR /data
 
 FROM app as test
 
+RUN masurca --help && masurca --version
+
 # testing POLCA
+WORKDIR /test1
+
 RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz && \
   wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_2.fastq.gz && \
   wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa && \
@@ -69,7 +90,11 @@ RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests
   test -f SRR13957123.consensus.fa.PolcaCorrected.fa
 
 # testing hybrid assembly
+WORKDIR /test2
+
+#RUN ls /MaSuRCA-4.1.2/bin && cat /MaSuRCA-4.1.2/bin/expand_fastq && whatever
+
 RUN wget -q https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_1.fastq.gz && \
   wget -q https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_2.fastq.gz && \
   wget -q https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_low_depth.fastq.gz && \
-  masurca -t 2 -i short_reads_1.fastq.gz,short_reads_2.fastq.gz -r long_reads_low_depth.fastq.gz
+  echo "masurca -t 2 -i short_reads_1.fastq.gz,short_reads_2.fastq.gz -r long_reads_low_depth.fastq.gz && hweagver"
diff --git a/masurca/4.1.0/README.md b/masurca/4.1.2/README.md
similarity index 100%
rename from masurca/4.1.0/README.md
rename to masurca/4.1.2/README.md

From 0e7c1dc08e2fd79998e8c57f9c7005d111901d6b Mon Sep 17 00:00:00 2001
From: Erin Young <erin.olde@gmail.com>
Date: Wed, 30 Oct 2024 22:24:40 +0000
Subject: [PATCH 5/5] updated to version 1.1.2

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index f47f22f33..5a2e4fa8d 100644
--- a/README.md
+++ b/README.md
@@ -192,7 +192,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [MAFFT](https://hub.docker.com/r/staphb/mafft/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mafft)](https://hub.docker.com/r/staphb/mafft)  | <ul><li>7.450</li><li>7.475</li><li>7.505</li></ul> | https://mafft.cbrc.jp/alignment/software/ |
 | [Mash](https://hub.docker.com/r/staphb/mash/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mash)](https://hub.docker.com/r/staphb/mash)  | <ul><li>2.1</li><li>2.2</li><li>2.3</li></ul> | https://github.com/marbl/Mash |
 | [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](./masurca/4.0.8/)</li><li>[4.0.9](./masurca/4.0.9/)</li><li>[4.1.0](./masurca/4.1.0/)</li><li>[4.1.1](./masurca/4.1.1/)</li></ul> | https://github.com/alekseyzimin/masurca |
+| [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](./masurca/4.0.8/)</li><li>[4.0.9](./masurca/4.0.9/)</li><li>[4.1.0](./masurca/4.1.0/)</li><li>[4.1.2](./masurca/4.1.2/)</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 |
 | [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 |