Installation

Clone the package

git clone https://github.com/hurraygong/SCpre-seq.git
cd SCpre-seq

Install dependencies

1. Install Anaconda3

Download Anaconda and install. If your computer has alread installed, pass this step.

2. Install HHsuite

Using conda install hhsuite. It is also can be installed by other methods shown on official website, If you have installed, pass this step.

conda install -c conda-forge -c bioconda hhsuite

Install HHsuite database.

mkdir HHsuitDB
cd HHsuitDB
wget http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz
mkdir -p UniRef30_2020_06
tar xfz UniRef30_2020_06_hhsuite.tar.gz -C ./UniRef30_2020_06
rm UniRef30_2020_06_hhsuite.tar.gz

3. Install DSSP

Using conda install DSSP programe. (https://anaconda.org/salilab/dssp)

conda install -c salilab dssp

Then to find the execute programe mkdssp. You can change the mkdssp to dssp using cp command by yourself.

whereis mkdssp

4.Install BLAST++

We also recommend to install BLAST++ using conda. To install this package with conda run one of the following:

conda install -c bioconda blast
conda install -c bioconda/label/cf201901 blast

Install BLAST++ database.

mkdir PsiblastDB/
cd PsiblastDB
wget https://ftp.ncbi.nlm.nih.gov/blast/db/swissprot.tar.gz
wget https://ftp.ncbi.nlm.nih.gov/blast/db/swissprot.tar.gz.md5
tar -zxvf swissprot.tar.gz
rm swissprot.tar.gz
rm swissprot.tar.gz.md5

Then you can proceed to the next step.