VALET is a tool for validating metagenomic assemblies. These instructions assume your cluster has the following software modules already installed and loaded:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
follow the instructuctions, and re-open the shell when finished. to make sure miniconda3 is installed in the right path:
which python
if it shows the yourpath/miniconda/bin, means you made the right move. Then add bioconda:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda install -c bioconda bowtie2
conda install cmake
conda install -c bioconda perl-app-cpanminus
for successful use of REAPR:
cpanm File::Basename File::Copy File::Spec File::Spec::Link Getopt::Long List::Util
git clone https://github.com/Fu-Yilei/VALET.git
export VALET=`pwd`/src/py/
python $VALET/pipeline.py -a test/carsonella_asm.fna -c test/carsonella_asm.cvg -q \
-1 test/lib1.1.fastq -2 test/lib1.2.fastq -o test_validate