diff --git a/Program_Licenses.md b/Program_Licenses.md
index 0344b1fba..b564c8f39 100644
--- a/Program_Licenses.md
+++ b/Program_Licenses.md
@@ -71,6 +71,7 @@ The licenses of the open-source software that is contained in these Docker image
| NanoPlot | GNU GPLv3 | https://github.com/wdecoster/NanoPlot/blob/master/LICENSE |
| NCBI AMRFinderPlus | Public Domain | https://github.com/ncbi/amr/blob/master/LICENSE |
| ngmaster | GNU GPLv3 | https://github.com/MDU-PHL/ngmaster/blob/master/LICENSE |
+| nullarbor | GNU GPLv2 | https://github.com/tseemann/nullarbor/blob/master/LICENSE |
| OrthoFinder | GNU GPLv3 | https://github.com/davidemms/OrthoFinder/blob/master/License.md |
| Panaroo | MIT | https://github.com/gtonkinhill/panaroo/blob/master/LICENSE |
| Pangolin | GNU GPLv3 | https://github.com/cov-lineages/pangolin/blob/master/LICENSE.txt |
diff --git a/README.md b/README.md
index 3286bcddb..3346825a4 100644
--- a/README.md
+++ b/README.md
@@ -100,6 +100,7 @@ To learn more about the docker pull rate limits and the open source software pro
| [NanoPlot](https://hub.docker.com/r/staphb/nanoplot)
[![docker pulls](https://badgen.net/docker/pulls/staphb/nanoplot)](https://hub.docker.com/r/staphb/nanoplot) |
- 1.27.0
- 1.29.0
- 1.30.1
- 1.32.0
- 1.33.0
| https://github.com/wdecoster/NanoPlot |
| [ngmaster](https://hub.docker.com/r/staphb/ngmaster)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ngmaster)](https://hub.docker.com/r/staphb/ngmaster) | | https://github.com/MDU-PHL/ngmaster |
| [NCBI AMRFinderPlus](https://hub.docker.com/r/staphb/ncbi-amrfinderplus)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-amrfinderplus)](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) | - 3.1.1b
- 3.8.4
- 3.8.28
- 3.9.3
- 3.9.8
- 3.10.1
- 3.10.5
- 3.10.16
- 3.10.20
- 3.10.24
- 3.10.30
| [https://github.com/ncbi/amr](https://github.com/ncbi/amr) |
+| [nullarbor](https://hub.docker.com/r/staphb/nullarbor)
[![docker pulls](https://badgen.net/docker/pulls/staphb/nullarbor)](https://hub.docker.com/r/staphb/nullarbor) | | https://github.com/tseemann/nullarbor |
| [OrthoFinder](https://hub.docker.com/r/staphb/OrthoFinder)
[![docker pulls](https://badgen.net/docker/pulls/staphb/orthofinder)](https://hub.docker.com/r/staphb/orthofinder) | | https://github.com/davidemms/OrthoFinder |
| [Panaroo](https://hub.docker.com/r/staphb/panaroo)
[![docker pulls](https://badgen.net/docker/pulls/staphb/panaroo)](https://hub.docker.com/r/staphb/panaroo) | | https://github.com/gtonkinhill/panaroo |
| [Pangolin](https://hub.docker.com/r/staphb/pangolin)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pangolin)](https://hub.docker.com/r/staphb/pangolin) | Click to see Pangolin v3 and older versions!
**Pangolin version & pangoLEARN data release date** - 1.1.14
- 2.0.4 & 2020-07-20
- 2.0.5 & 2020-07-20
- 2.1.1 & 2020-12-17
- 2.1.3 & 2020-12-17
- 2.1.6 & 2021-01-06
- 2.1.7 & 2021-01-11
- 2.1.7 & 2021-01-20
- 2.1.8 & 2021-01-22
- 2.1.10 & 2021-02-01
- 2.1.11 & 2021-02-01
- 2.1.11 & 2021-02-05
- 2.2.1 & 2021-02-06
- 2.2.2 & 2021-02-06
- 2.2.2 & 2021-02-11
- 2.2.2 & 2021-02-12
- 2.3.0 & 2021-02-12
- 2.3.0 & 2021-02-18
- 2.3.0 & 2021-02-21
- 2.3.2 & 2021-02-21
- 2.3.3 & 2021-03-16
- 2.3.4 & 2021-03-16
- 2.3.5 & 2021-03-16
- 2.3.6 & 2021-03-16
- 2.3.6 & 2021-03-29
- 2.3.8 & 2021-04-01
- 2.3.8 & 2021-04-14
- 2.3.8 & 2021-04-21
- 2.3.8 & 2021-04-23
- 2.4 & 2021-04-28
- 2.4.1 & 2021-04-28
- 2.4.2 & 2021-04-28
- 2.4.2 & 2021-05-10
- 2.4.2 & 2021-05-11
- 2.4.2 & 2021-05-19
- 3.0.5 & 2021-06-05
- 3.1.3 & 2021-06-15
- 3.1.5 & 2021-06-15
- 3.1.5 & 2021-07-07-2
- 3.1.7 & 2021-07-09
- 3.1.8 & 2021-07-28
- 3.1.10 & 2021-07-28
- 3.1.11 & 2021-08-09
- 3.1.11 & 2021-08-24
- 3.1.11 & 2021-09-17
- 3.1.14 & 2021-09-28
- 3.1.14 & 2021-10-13
- 3.1.16 & 2021-10-18
- 3.1.16 & 2021-11-04
- 3.1.16 & 2021-11-09
- 3.1.16 & 2021-11-18
- 3.1.16 & 2021-11-25
- 3.1.17 & 2021-11-25
- 3.1.17 & 2021-12-06
- 3.1.17 & 2022-01-05
- 3.1.18 & 2022-01-20
- 3.1.19 & 2022-01-20
- 3.1.20 & 2022-02-02
- 3.1.20 & 2022-02-28
**Pangolin version & pangolin-data version** - 4.0 & 1.2.133
- 4.0.1 & 1.2.133
- 4.0.2 & 1.2.133
- 4.0.3 & 1.2.133
- 4.0.4 & 1.2.133
- 4.0.5 & 1.3
- 4.0.6 & 1.6
- 4.0.6 & 1.8
- 4.0.6 & 1.9
| https://github.com/cov-lineages/pangolin
https://github.com/cov-lineages/pangoLEARN
https://github.com/cov-lineages/pango-designation
https://github.com/cov-lineages/scorpio
https://github.com/cov-lineages/constellations
https://github.com/cov-lineages/lineages (archived)
https://github.com/hCoV-2019/pangolin (archived) |
diff --git a/nullarbor/2.0.20191013/Dockerfile b/nullarbor/2.0.20191013/Dockerfile
new file mode 100644
index 000000000..72b405f75
--- /dev/null
+++ b/nullarbor/2.0.20191013/Dockerfile
@@ -0,0 +1,399 @@
+FROM ubuntu:focal as app
+
+# pulling a lot of these from the required versions here:
+# https://github.com/tseemann/nullarbor/blob/041ded1748be0c650fb13f6685e205f0f2eef18d/bin/nullarbor.pl#L488
+ARG NULLARBOR_VER="2.0.20191013"
+ARG SHOVILL_VER="1.1.0"
+ARG MEGAHIT_VER="1.2.9"
+ARG SKESA_VER="2.4.0"
+ARG SNIPPY_VER="4.4.3"
+ARG PROKKA_VER="1.14.6"
+ARG QUICKTREE_VER="2.5"
+ARG IQTREE_VER="2.2"
+# roary installed via apt
+#ARG ROARY_VER="3.0"
+ARG MLST_VER="2.22.0"
+ARG ABRICATE_VER="1.0.1"
+ARG SNP_DISTS_VER="0.8.2"
+ARG TRIMMOMATIC_VER="0.39"
+ARG SPADES_VER="3.15.4"
+ARG KRAKEN_VER="1.1.1"
+# might add kraken2 later?
+ARG MASH_VER="2.3"
+ARG CENTRIFUGE_VER="1.0.4"
+ARG IQTREE_VER="1.6.7"
+ARG KRAKEN2_VER="2.1.2"
+
+
+LABEL base.image="ubuntu:focal"
+LABEL dockerfile.version="1"
+LABEL software="Nullarbor"
+LABEL software.version="v2.0.20191013"
+LABEL description="Reads to report for public health and clinical microbiology"
+LABEL website="https://github.com/tseemann/nullarbor"
+LABEL lisence="https://github.com/tseemann/nullarbor/blob/master/LICENSE"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="kapsakcj@gmail.com"
+LABEL maintainer2="Frank Ambrosio"
+LABEL maintainer2.email="frank.ambrosio@theiagen.com"
+
+# to prevent apt from asking for a timezone for locale settings
+ARG DEBIAN_FRONTEND="noninteractive"
+
+# install dependencies, cleanup apt garbage
+# roary via ubuntu:focal apt is 3.13.0
+RUN apt-get update && apt-get install -y --no-install-recommends \
+ git \
+ python \
+ wget \
+ pigz \
+ zlib1g-dev \
+ make \
+ gcc \
+ g++ \
+ libpthread-stubs0-dev \
+ openjdk-11-jre \
+ unzip \
+ bzip2 \
+ libncurses5-dev \
+ libbz2-dev \
+ liblzma-dev \
+ libcurl4-gnutls-dev \
+ libssl-dev \
+ libfindbin-libs-perl \
+ libyaml-tiny-perl \
+ libautobox-list-util-perl \
+ bzip2 \
+ gzip \
+ libdatetime-perl \
+ libxml-simple-perl \
+ libdigest-md5-perl \
+ bioperl \
+ hmmer \
+ libpath-tiny-perl \
+ libmoo-perl \
+ libfile-which-perl \
+ libsvg-perl \
+ libtext-csv-perl \
+ liblist-moreutils-perl \
+ libio-file-withpath-perl \
+ roary=3.13.0+dfsg-1 \
+ libmoo-perl \
+ liblist-moreutils-perl \
+ libjson-perl \
+ file \
+ ncbi-blast+=2.9.0-2 \
+ autoconf \
+ automake \
+ libtool \
+ flex \
+ bison && \
+ apt-get clean && apt-get autoclean && \
+ rm -rf /var/lib/apt/lists/*
+
+# SPAdes
+RUN wget https://github.com/ablab/spades/releases/download/v${SPADES_VER}/SPAdes-${SPADES_VER}-Linux.tar.gz && \
+ tar -xzf SPAdes-${SPADES_VER}-Linux.tar.gz && \
+ rm SPAdes-${SPADES_VER}-Linux.tar.gz
+
+# Seqtk 1.3
+RUN wget https://github.com/lh3/seqtk/archive/v1.3.tar.gz && \
+ tar -zxf v1.3.tar.gz && \
+ rm v1.3.tar.gz && \
+ cd seqtk-1.3/ && \
+ make && \
+ make install
+
+# kmc
+RUN mkdir kmc && \
+ cd kmc && \
+ wget https://github.com/refresh-bio/KMC/releases/download/v3.1.1/KMC3.1.1.linux.tar.gz && \
+ tar -xzf KMC3.1.1.linux.tar.gz && \
+ rm KMC3.1.1.linux.tar.gz
+
+# lighter 1.1.1
+RUN wget https://github.com/mourisl/Lighter/archive/v1.1.1.tar.gz && \
+ tar -zxf v1.1.1.tar.gz && \
+ rm -rf v1.1.1.tar.gz && \
+ cd Lighter-1.1.1 && \
+ make
+
+# trimmomatic
+RUN wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-${TRIMMOMATIC_VER}.zip && \
+ unzip Trimmomatic-${TRIMMOMATIC_VER}.zip && \
+ rm -rf Trimmomatic-${TRIMMOMATIC_VER}.zip && \
+ chmod +x Trimmomatic-${TRIMMOMATIC_VER}/trimmomatic-${TRIMMOMATIC_VER}.jar && \
+ echo "#!/bin/bash" >> trimmomatic && \
+ echo "exec java -jar /Trimmomatic-${TRIMMOMATIC_VER}/trimmomatic-${TRIMMOMATIC_VER}.jar """"$""@"""" " >> trimmomatic && \
+ chmod +x trimmomatic && \
+ mv -v trimmomatic /usr/local/bin
+
+# bwa (mem) 0.7.17
+RUN wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2 && \
+ tar -xjf bwa-0.7.17.tar.bz2 && \
+ rm bwa-0.7.17.tar.bz2 && \
+ cd bwa-0.7.17 && \
+ make
+
+# samtools 1.10
+RUN mkdir samtools && \
+ cd samtools && \
+ wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 && \
+ tar -xjf samtools-1.10.tar.bz2 && \
+ rm samtools-1.10.tar.bz2 && \
+ cd samtools-1.10 && \
+ ./configure && \
+ make && \
+ make install
+
+# skesa
+RUN mkdir skesa && \
+ cd skesa && \
+ wget https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/skesa.centos.7.7 && \
+ mv skesa.centos.7.7 skesa && \
+ chmod +x skesa
+
+# might have to change this version
+RUN mkdir megahit && \
+ cd megahit && \
+ wget https://github.com/voutcn/megahit/releases/download/v${MEGAHIT_VER}/MEGAHIT-${MEGAHIT_VER}-Linux-x86_64-static.tar.gz && \
+ tar -xzf MEGAHIT-${MEGAHIT_VER}-Linux-x86_64-static.tar.gz && \
+ rm -v MEGAHIT-${MEGAHIT_VER}-Linux-x86_64-static.tar.gz
+
+# Velvet 1.2.10
+RUN mkdir velvet && \
+ cd velvet && \
+ wget https://github.com/dzerbino/velvet/archive/v1.2.10.tar.gz && \
+ tar -xzf v1.2.10.tar.gz && \
+ rm -rf v1.2.10.tar.gz && \
+ cd velvet-1.2.10 && \
+ make
+
+# Flash 1.2.11
+RUN mkdir flash && \
+ cd flash && \
+ wget https://sourceforge.net/projects/flashpage/files/FLASH-1.2.11.tar.gz && \
+ tar -zxf FLASH-1.2.11.tar.gz && \
+ rm -rf FLASH-1.2.11.tar.gz && \
+ cd FLASH-1.2.11 && \
+ make
+
+# pilon 1.22
+RUN mkdir pilon && \
+ cd pilon && \
+ wget https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar && \
+ chmod +x pilon-1.22.jar && \
+ echo "#!/bin/bash" >> pilon && \
+ echo "exec java -jar /pilon/pilon-1.22.jar """"$""@"""" " >> pilon && \
+ chmod +x pilon
+
+# Samclip
+RUN mkdir samclip && \
+ cd samclip && \
+ wget https://raw.githubusercontent.com/tseemann/samclip/master/samclip && \
+ chmod +x samclip
+
+# shovill
+# extra perl module I had to install via apt-get: libfindbin-libs-perl
+# create /data for working directory
+RUN wget https://github.com/tseemann/shovill/archive/v${SHOVILL_VER}.tar.gz && \
+ tar -xzf v${SHOVILL_VER}.tar.gz && \
+ rm -v v${SHOVILL_VER}.tar.gz && \
+ mkdir /data
+
+# snippy
+RUN wget https://github.com/tseemann/snippy/archive/v${SNIPPY_VER}.tar.gz && \
+ tar -zxf v${SNIPPY_VER}.tar.gz && \
+ rm v${SNIPPY_VER}.tar.gz
+
+## PROKKA ##
+# bedtools (required by prokka)
+RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.29.0/bedtools-2.29.0.tar.gz && \
+ tar -zxf bedtools-2.29.0.tar.gz && \
+ rm bedtools-2.29.0.tar.gz && \
+ cd bedtools2 && \
+ make
+
+# so that barnnap tests pass
+ENV PATH="${PATH}:/bedtools2/bin"
+
+# install barrnap
+RUN wget https://github.com/tseemann/barrnap/archive/0.9.tar.gz && \
+ tar -zxf 0.9.tar.gz && \
+ rm 0.9.tar.gz && \
+ cd barrnap-0.9 && \
+ make test
+
+# install tbl2asn manually since the one included with prokka is expired.
+# Probably will have to do again in Dec 2021 unless Torsten removes it from prokka
+RUN wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz -O linux64.tbl2asn.gz && \
+ gunzip linux64.tbl2asn.gz && \
+ mv -v linux64.tbl2asn /usr/bin/tbl2asn && \
+ chmod 755 /usr/bin/tbl2asn
+
+# prokka
+# perl modules installed via apt: libautobox-list-util-perl
+RUN wget https://github.com/tseemann/prokka/archive/v${PROKKA_VER}.tar.gz && \
+ tar -xzf v${PROKKA_VER}.tar.gz && \
+ rm -rf v${PROKKA_VER}.tar.gz && \
+ /prokka-${PROKKA_VER}/bin/prokka --setupdb && /prokka-${PROKKA_VER}/bin/prokka --listdb
+
+## END PROKKA ##
+
+## ROARY ##
+# DL Jellyfish, unpack, and install
+RUN wget https://github.com/gmarcais/Jellyfish/releases/download/v1.1.12/jellyfish-1.1.12.tar.gz && \
+ tar -zxf jellyfish-1.1.12.tar.gz && \
+ rm -rf jellyfish-1.1.12.tar.gz && \
+ cd jellyfish-1.1.12 && \
+ ./configure --prefix=/opt/ && \
+ make -j 4 && \
+ make install
+
+# DL Kraken1, unpack, and install
+RUN wget https://github.com/DerrickWood/kraken/archive/v${KRAKEN_VER}.tar.gz && \
+ tar -xzf v${KRAKEN_VER}.tar.gz && \
+ rm -rf v${KRAKEN_VER}.tar.gz && \
+ cd kraken-${KRAKEN_VER} && \
+ mkdir /opt/kraken && \
+ ./install_kraken.sh /opt/kraken/
+
+# roary itself installed via apt
+## END ROARY ##
+
+## MLST ##
+# any2fasta
+RUN cd /usr/local/bin && \
+ wget https://raw.githubusercontent.com/tseemann/any2fasta/master/any2fasta && \
+ chmod +x any2fasta
+
+# get mlst
+RUN wget https://github.com/tseemann/mlst/archive/v${MLST_VER}.tar.gz &&\
+ tar -xzf v${MLST_VER}.tar.gz &&\
+ rm v${MLST_VER}.tar.gz && \
+ /mlst-${MLST_VER}/bin/mlst --check && /mlst-${MLST_VER}/bin/mlst --list
+
+## END MLST ##
+
+# abricate
+RUN wget https://github.com/tseemann/abricate/archive/v${ABRICATE_VER}.tar.gz && \
+ tar -zxvf v${ABRICATE_VER}.tar.gz && \
+ rm -rf v${ABRICATE_VER}.tar.gz && \
+ /abricate-${ABRICATE_VER}/bin/abricate --check && \
+ /abricate-${ABRICATE_VER}/bin/abricate --setupdb
+
+
+# snp-dists
+RUN wget https://github.com/tseemann/snp-dists/archive/v${SNP_DISTS_VER}.tar.gz && \
+ tar -xzf v${SNP_DISTS_VER}.tar.gz && \
+ rm v${SNP_DISTS_VER}.tar.gz && \
+ cd /snp-dists-${SNP_DISTS_VER} && \
+ make && \
+ make PREFIX=/usr/local install
+
+# download mash binary
+RUN wget https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar && \
+ tar -xvf mash-Linux64-v${MASH_VER}.tar && \
+ rm -rf mash-Linux64-v${MASH_VER}.tar
+
+# centrifuge
+# this does not include building an index AKA database
+RUN wget https://github.com/DaehwanKimLab/centrifuge/archive/refs/tags/v${CENTRIFUGE_VER}.tar.gz && \
+ tar -xzf v${CENTRIFUGE_VER}.tar.gz && \
+ rm -v v${CENTRIFUGE_VER}.tar.gz && \
+ cd centrifuge-${CENTRIFUGE_VER} && \
+ make && \
+ make install prefix=/usr/local && \
+ mkdir -v /centrifuge-db
+
+# iqtree
+RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v${IQTREE_VER}/iqtree-${IQTREE_VER}-Linux.tar.gz && \
+ tar -xzf iqtree-${IQTREE_VER}-Linux.tar.gz && \
+ rm iqtree-${IQTREE_VER}-Linux.tar.gz
+
+# FastTree binary download; as of 2022-06-01 downloads version 2.1.11
+RUN mkdir -v /FastTree && \
+ wget http://www.microbesonline.org/fasttree/FastTree -P /FastTree && \
+ chmod +x /FastTree/FastTree
+
+# quicktree
+RUN wget https://github.com/khowe/quicktree/archive/refs/tags/v${QUICKTREE_VER}.tar.gz && \
+ tar -xzf v${QUICKTREE_VER}.tar.gz && \
+ rm -v v${QUICKTREE_VER}.tar.gz && \
+ cd /quicktree-${QUICKTREE_VER} && \
+ make
+
+# newick_utils
+# no releases or tags, so manually setting to latest commit (da12115) to master branch
+RUN git clone https://github.com/tjunier/newick_utils.git && \
+ cd newick_utils && \
+ git reset --hard da12115 && \
+ autoreconf -fi && \
+ ./configure && \
+ make && \
+ make check && \
+ make install
+
+# DL Kraken2, unpack, and install
+RUN wget https://github.com/DerrickWood/kraken2/archive/v${KRAKEN2_VER}.tar.gz && \
+ tar -xzf v${KRAKEN2_VER}.tar.gz && \
+ rm -rf v${KRAKEN2_VER}.tar.gz && \
+ cd kraken2-${KRAKEN2_VER} && \
+ ./install_kraken2.sh . && \
+ mkdir -v /kraken2-db /kraken-db
+
+# nullarbor
+RUN wget https://github.com/tseemann/nullarbor/archive/refs/tags/v${NULLARBOR_VER}.tar.gz && \
+ tar -xzf v${NULLARBOR_VER}.tar.gz && \
+ rm v${NULLARBOR_VER}.tar.gz
+
+# set /data as working directory
+WORKDIR /data
+
+# set $PATH's
+ENV PATH="${PATH}:\
+/SPAdes-${SPADES_VER}-Linux/bin:\
+/kmc:\
+/Lighter-1.1.1:\
+/Trimmomatic-${TRIMMOMATIC_VER}:\
+/bwa-0.7.17:\
+/skesa:\
+/megahit/MEGAHIT-${MEGAHIT_VER}-Linux-x86_64-static/bin/:\
+/velvet/velvet-1.2.10:\
+/flash/FLASH-1.2.11:\
+/shovill-${SHOVILL_VER}/bin:\
+/pilon:\
+/samclip:\
+/nullarbor-${NULLARBOR_VER}/bin:\
+/bedtools2/bin:\
+/barrnap-0.9/bin:\
+/prokka-${PROKKA_VER}/bin:\
+/prokka-${PROKKA_VER}/binaries/common:\
+/snippy-${SNIPPY_VER}/bin:\
+/snippy-${SNIPPY_VER}/binaries/linux:\
+/snippy-${SNIPPY_VER}/binaries/noarch:\
+/mlst-${MLST_VER}/bin:\
+/abricate-${ABRICATE_VER}/bin:\
+/mash-Linux64-v${MASH_VER}:\
+/iqtree-${IQTREE_VER}-Linux/bin/:\
+/FastTree:\
+/quicktree-${QUICKTREE_VER}:\
+/opt/kraken:\
+/kraken2-${KRAKEN2_VER}"\
+ LC_ALL=C\
+ KRAKEN_DEFAULT_DB="/kraken-db"\
+ KRAKEN2_DEFAULT_DB="/kraken2-db"\
+ CENTRIFUGE_DEFAULT_DB="/centrifuge-db"
+
+# test layer; may add more later once everything is installed
+FROM app as test
+
+# print version and check dependencies
+RUN nullarbor.pl --version
+
+# make fake files to trick nullarbor dependency check
+RUN touch ${KRAKEN_DEFAULT_DB}/database.idx ${KRAKEN_DEFAULT_DB}/database.kdb && \
+ touch ${CENTRIFUGE_DEFAULT_DB}.1.cf ${CENTRIFUGE_DEFAULT_DB}.2.cf ${CENTRIFUGE_DEFAULT_DB}.3.cf
+
+# uncomment for final checks
+RUN nullarbor.pl --check
\ No newline at end of file
diff --git a/nullarbor/2.0.20191013/README.md b/nullarbor/2.0.20191013/README.md
new file mode 100644
index 000000000..835f0d192
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+# Nullarbor Container
+
+Main tool : [Nullarbor](https://github.com/tseemann/nullarbor#readme)
+
+Full documentation: https://github.com/tseemann/nullarbor#readme
+
+Nullarbor is a pipeline to generate complete public health microbiology reports from sequenced isolates.
+
+Original tool developed by Torsten Seeman.
+
+## Example Usage
+
+```bash
+nullarbor.pl --name "Run_Name" --ref ./path/to/reference/genome/ref.fasta --input ./path/to/tsv/of/fasq/file/paths/fastq_file_paths.tsv --outdir ./path/to/target/outdir/nullarbor_outdir/ --treebuilder iqtree_slow --taxoner kraken2 --mode all --run
+```