diff --git a/kubernetes/Dockerfile b/kubernetes/Dockerfile
index 846f1645feca6601ac2f11adbc842950f9cfb858..0a3e1a95be118cb5a5b90f0f7d0ad6124bb00b9c 100644
--- a/kubernetes/Dockerfile
+++ b/kubernetes/Dockerfile
@@ -23,10 +23,10 @@ ENV DEBIAN_FRONTEND=noninteractive LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LANGUAGE=en_U
# Fix issue with scipy no lapack/blas resources found and other compilation problems
# Install ubuntu modules and the workflow application # --no-install-recommends
-RUN apt-get update && apt-get install --yes build-essential cpanminus curl git gnupg htop libfontconfig1 locales nano nodejs pigz python3-dev python3-distutils python3.8 raptor2-utils raptor2-utils sshpass unzip wget zip libblas-dev liblapack-dev zlib1g-dev pkg-config libhdf5-100 libhdf5-dev gfortran libblas-dev liblapack-dev zlib1g-dev pkg-config libhdf5-100 libhdf5-dev gfortran libbz2-dev python-setuptools libidn11
+RUN apt-get update && apt-get install --yes build-essential cpanminus curl git gnupg htop libfontconfig1 locales nano nodejs pigz python3-dev python3-distutils python3.8 raptor2-utils raptor2-utils sshpass unzip wget zip libblas-dev liblapack-dev zlib1g-dev pkg-config libhdf5-100 libhdf5-dev gfortran libblas-dev liblapack-dev zlib1g-dev pkg-config libhdf5-100 libhdf5-dev gfortran libbz2-dev python-setuptools libidn11 rsync
RUN curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3.8 get-pip.py && \
- python3.8 -m pip install cwltool==3.1.20211004060744 &&\
+ python3.8 -m pip install cwltool==3.1.20220224085855 &&\
cwltool --version && python3.8 -m pip install html5lib
# Enable icommands
diff --git a/kubernetes/scripts/setup.sh b/kubernetes/scripts/setup.sh
deleted file mode 100644
index 496b1dbdb26630360103411ec7a6c8a9aa5be65f..0000000000000000000000000000000000000000
--- a/kubernetes/scripts/setup.sh
+++ /dev/null
@@ -1,119 +0,0 @@
-# Installs packages on the computational nodes
-
-R_location=/unlock/infrastructure/R/library
-conda_location=/unlock/infrastructure/conda
-python_location=/unlock/infrastructure/python_venv
-
-# Ensures that R can use the library folder
-mkdir --parents $R_location
-
-################################################################
-# Conda environments
-################################################################
-
-# Update conda
-source /root/miniconda/bin/activate
-conda update -y -n base -c defaults conda
-
-# New attempt for picrust
-if [[ ! -d "$conda_location/picrust2_v2.4.2" ]]
-then
- mamba create --yes --prefix $conda_location/picrust2_v2.4.2 -c bioconda -c conda-forge picrust2=2.4.2
-fi
-
-# Krona and install taxonomy
-if [[ ! -d "$conda_location/krona_v2.8.1" ]]
-then
- mamba create --yes --prefix $conda_location/krona_v2.8.1 -c bioconda krona krona=2.8.1
- conda activate $conda_location/krona_v2.8.1
- ktUpdateTaxonomy.sh
-fi
-
-# Medaka
-if [[ ! -d "$conda_location/medaka_v1.5.0" ]]
-then
- mamba create --yes --prefix $conda_location/medaka_v1.5.0 -c bioconda -c conda-forge medaka=1.5.0
-fi
-
-# pycoQC
-if [[ ! -d "$conda_location/pycoqc_v2.5.2" ]]
-then
- mamba create --yes --prefix $conda_location/pycoqc_v2.5.2 -c conda-forge -c bioconda pycoqc=2.5.2
-fi
-# LongQC
-# ?
-
-# NanoQC
-if [[ ! -d "$conda_location/nanoqc_v0.9.4" ]]
-then
- mamba create --yes --prefix $conda_location/nanoqc_v0.9.4 -c conda-forge -c bioconda nanoqc=0.9.4
-fi
-
-# Busco
-if [[ ! -d "$conda_location/busco_v5.2.2" ]]
-then
- mamba create --yes --prefix $conda_location/busco_v5.2.2 -c conda-forge -c bioconda busco=5.2.2
-fi
-
-# GTDB-Tk
-if [[ ! -d "$conda_location/gtdbtk_v1.7.0" ]]
-then
- mamba create --yes --prefix $conda_location/gtdbtk_v1.7.0 -c conda-forge -c bioconda gtdbtk=1.7.0
- echo "export GTDBTK_DATA_PATH=/unlock/references/databases/GTDBTK/release202/" > $conda_location/gtdbtk_v1.7.0/etc/conda/activate.d/gtdbtk.sh
-fi
-
-# CheckM
-if [[ ! -d "$conda_location/checkm_v1.1.3" ]]
-then
- mamba create --yes --prefix $conda_location/checkm_v1.1.3 -c conda-forge -c bioconda checkm-genome=1.1.3
- conda activate $conda_location/checkm_v1.1.3
- checkm data setRoot /unlock/references/databases/CheckM/
- conda deactivate
-fi
-
-# HUMAnN 3
-if [[ ! -d "$conda_location/humann_v3.0.1" ]]
-then
- mamba create --yes --prefix $conda_location/humann_v3.0.1 -c biobakery -c bioconda -c conda-forge humann=3.0.1
- conda activate /unlock/infrastructure/conda/humann_v3.0.1
- humann_config --update database_folders nucleotide /unlock/references/databases/HUMAnN/chocophlan
- humann_config --update database_folders utility_mapping /unlock/references/databases/HUMAnN/utility_mapping
- humann_config --update database_folders protein /unlock/references/databases/HUMAnN/uniref
- conda deactivate
-fi
-
-# KEGG - kofamscan
-if [[ ! -d "$conda_location/kofamscan_v1.3.0" ]]
-then
- mamba create --yes --prefix $conda_location/kofamscan_v1.3.0 -c conda-forge -c bioconda kofamscan=1.3.0
-fi
-
-################################################################
-# Pip environments
-################################################################
-
-# Python virtual environment
-python3 -m venv /unlock/infrastructure/venv
-# Activate venv
-source /unlock/infrastructure/venv/bin/activate
-# Upgrade because we can
-/unlock/infrastructure/venv/bin/python3 -m pip install --upgrade pip
-
-## Pip dependencies
-python3 -m pip install wheel biom-format pysam numpy matplotlib checkm-genome gtdbtk rdflib python-irodsclient html5lib
-
-python3 -m pip install cwltool==3.1.20211004060744
-cwltool --version && python3 -m pip install html5lib
-
-## Pip quast rc1 for 3.9 support
-wget https://github.com/ablab/quast/releases/download/quast_5.1.0rc1/quast-5.1.0rc1.tar.gz
-pip install quast-5.1.0rc1.tar.gz
-
-deactivate
-
-################################################################
-# R Packages
-################################################################
-
-R -e "install.packages('docopt',dependencies=TRUE, repos='https://packagemanager.rstudio.com/all/__linux__/bionic/latest')"
-Rscript /scripts/install2.R -n 10 -s -l $R_location -r https://packagemanager.rstudio.com/all/__linux__/bionic/latest data.table futile.logger ggplot2 optparse plyr readr reshape2 scales viridis yaml parallel castor
\ No newline at end of file