Recette Tombo

Singularity/tombo.def

+Bootstrap: library
+From: ubuntu:22.04
+
+%environment
+    export PATH="/usr/local/bin:$PATH"
+    
+%help 
+
+This container launches TOMBO-ont software used for the identification of modified nucleotides from nanopore sequencing data.
+
+======================================================================================
+
+
+	usage (help)	: singularity run tombo.sif
+	usage (basic)	: 1 st step : conda activate tombo 
+			  2 nd step : tombo [option] 
+	
+	building container : singularity build tombo.sif tombo.def 
+
+
+======================================================================================
+
+
+%post
+    # ================================
+    # PREPARE the system
+    # ================================
+    export DEBIAN_FRONTEND=noninteractive
+    apt-get update
+    apt-get install -y software-properties-common
+    apt-add-repository universe
+    apt-get update
+    export LC_ALL=C.UTF-8
+    export LANG=C.UTF-8
+    echo 'export LC_ALL=C.UTF-8' >> "$SINGULARITY_ENVIRONMENT"
+    echo 'export LANG=C.UTF-8' >> "$SINGULARITY_ENVIRONMENT"
+
+    apt-get install -y \
+        wget \
+        build-essential
+
+	apt-get install -y libc6
+	
+	
+    # ================================
+    # INSTALL Conda
+    # ================================
+    
+    
+	wget -c https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh
+	/bin/bash Anaconda3-2020.02-Linux-x86_64.sh -bfp /usr/local
+	
+	#Conda configuration of channels from .condarc file
+	
+	conda config --file /.condarc --add channels defaults
+	conda config --file /.condarc --add channels conda-forge
+	conda update conda
+	apt-get install -y git-all
+	
+	# Conda Environement Creation
+	
+	
+	conda create --name tombo python=3.7
+	. activate tombo
+	pip install numpy==1.19.4
+	git clone https://github.com/nanoporetech/tombo
+	cd tombo
+	pip install -e .
+	
+	
+%labels 	
+	TOMBO-ONT