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.