Update singularity definitions

minos/etc/Singularity.busco.def

@@ -1,28 +1,14 @@
-Bootstrap: docker
-From: conda/miniconda3-centos7
-Include: yum which wget
-
+From: continuumio/miniconda3
 
+%test
+	export PATH="/usr/local/bin:$PATH:/usr/local/conda/bin/"
+	python --version
 %environment
-	export BUSCO_CONFIG_FILE=/opt/software/busco/config/container_config.ini
-
+	export PYTHONDONTWRITEBYTECODE=true
 %post
 
-	yum makecache fast && yum update -y
-	yum -y install git bzip2 wget which sudo vi
-	yum -y group install "Development Tools"
-
-	conda update -y conda
-	conda remove -y asn1crypto
-	conda install -c conda-forge -c bioconda -y asn1crypto busco=4.0.6
-	conda remove -y busco
-	mkdir /opt/software
-	cd /opt/software
-	git clone https://gitlab.com/ezlab/busco.git
-	cd busco
-	git checkout 4.0.6
-	python3 setup.py install
-	python3 scripts/busco_configurator.py config/config.ini config/container_config.ini
-	cat config/container_config.ini
+	conda update conda -n base -y
+	conda install -c conda-forge mamba
+	mamba install -c conda-forge -c bioconda busco
 
-	conda clean --all --yes
+	busco --help

minos/etc/Singularity.mikado.def

@@ -0,0 +1,101 @@
+Bootstrap: docker
+From: ubuntu:20.04
+
+%test
+    python3 --version
+    python3 -c "import numpy"
+    mikado --help
+
+%environment
+    export PYTHONDONTWRITEBYTECODE=true
+
+%post
+
+    ### Install your packages ###
+
+    export PYTHONDONTWRITEBYTECODE=true
+
+    mkdir /opt/software
+    cd /opt/software/
+
+    apt update
+    apt install -y software-properties-common
+    add-apt-repository universe
+    add-apt-repository multiverse
+    add-apt-repository restricted
+    apt update
+    apt install -y zlib1g-dev libboost-dev '^libboost-.*71-dev' build-essential automake autoconf curl libbz2-dev libncurses-dev lzma-dev python3 python3-numpy python3-dev python3-scipy python3-pandas python3-pip libtool liblzma-dev git pip wget libcurl4-openssl-dev  pkg-config
+    apt -y install software-properties-common build-essential zlib1g-dev libbz2-dev libncurses5-dev libgdbm-dev libnss3-dev libssl-dev gzip unzip
+
+    pip --no-cache-dir   install numpy
+    pip --no-cache-dir  install sortedcontainers
+    pip --no-cache-dir  install pandas
+    pip --no-cache-dir  install Cython
+
+    # Mikado
+    pip3 --no-cache-dir install wheel
+    pip3 --no-cache-dir install python-rapidjson
+    pip3 install "Mikado>=2.0"
+
+    # Samtools
+    wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
+    tar xaf samtools-1.11.tar.bz2
+    mv samtools-1.11 samtools  # Necessary for augustus
+    cd samtools  # and similarly for bcftools and htslib
+    ./configure --enable-libcurl --enable-plugins --enable-s3
+    make -j 20
+    make install
+    samtools --help 2>&1 | head
+    cd ../
+    rm samtools-1.11.tar.bz2
+
+    # Portcullis
+    git clone https://github.com/EI-CoreBioinformatics/portcullis.git
+    cd portcullis
+    ./autogen.sh
+    ./configure
+    make -j 8
+    make install
+    cd /opt/software
+
+    # Diamond
+    git clone https://github.com/bbuchfink/diamond.git
+    cd diamond
+    mkdir build
+    cd build
+    cmake ../
+    make
+    make install
+    cd ../../
+    rm -rf diamond
+    diamond --help
+
+    # Prodigal
+    wget https://github.com/hyattpd/Prodigal/releases/download/v2.6.3/prodigal.linux
+    chmod +x prodigal.linux
+    mv prodigal.linux /usr/local/bin/prodigal
+    prodigal -h
+
+    # Create global folder
+    mkdir -p /global && cd /global
+
+%apprun snakemake
+    snakemake "@"
+
+%apprun mikado
+    mikado "@"
+
+%apprun daijin
+    daijin "@"
+
+%apprun prodigal
+    prodigal "@"
+
+%apprun samtools
+    samtools "@"
+
+%apprun diamond
+    diamond "@"
+
+%apprun portcullis
+    portcullis "@"

minos/etc/Singularity.tools.def

@@ -1,27 +1,22 @@
 Bootstrap: docker
-From: conda/miniconda3-centos7
-Include: yum which wget
-
+From: continuumio/miniconda3
 
+%test
+	export PATH="/usr/local/bin:$PATH:/usr/local/conda/bin/"
+	python --version
 %environment
-	alias python=python3
-
+	export PYTHONDONTWRITEBYTECODE=true
 %post
 
-	yum makecache fast && yum update -y
-	yum -y install git bzip2 wget which sudo vi
-	yum -y group install "Development Tools"
-
-	conda update -y conda
-	conda remove -y asn1crypto
-	conda install -c conda-forge -c bioconda -y asn1crypto kallisto=0.44.0 diamond=0.9.34 bedtools=2.29.2 blast=2.9.0 biopython prinseq numpy genometools-genometools=1.5.10 gffread=0.11.6 seqkit=2.1.0
+	conda update conda -n base -y && conda install -c conda-forge -n base -y mamba pip git gcc gxx wget bzip2 gzip tar make
+	mamba install -c conda-forge -c bioconda -y asn1crypto kallisto=0.44.0 diamond=0.9.34 bedtools=2.29.2 blast=2.9.0 biopython prinseq numpy genometools-genometools gffread=0.11.6 seqkit=2.1.0
 
 	mkdir -p /opt/software
 	cd /opt/software
-	git clone --depth=1 https://github.com/EI-CoreBioinformatics/CPC2
+
+	git clone https://github.com/EI-CoreBioinformatics/CPC2 CPC2
 	cd CPC2
 	python3 setup.py bdist_wheel && pip3 install dist/*whl
+        CPC2 -h
 
-	CPC2 --help
-
-	conda clean --all --yes
+	mamba clean --all --yes

minos/etc/minos_config.yaml

@@ -1,5 +1,5 @@
 paths:
-  augustus_config_data: "/usr/local/config"
+  augustus_config_data: "/opt/conda/config"
 params:
   mikado:
     prepare: "--minimum-cdna-length 100"