I am trying to setup PSIPRED to run a secondary structure prediction but the README.md file is not detailed enough for a beginner like me to setup and run PSIPRED. I am trying to use it with BLAST+.
I am on a Linux Ubuntu 17.04 operating system, and the following are the steps I take to try and setup PSIPRED. There seems to be missing programs that I am not sure how to install or find where they are as well as missing commands:
sudo apt install ncbi-blast+ #OK: Install BLAST+
wget http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/psipred.4.01.tar.gz #OK: Get the latest PSIPRED
tar xzvf psipred.4.01.tar.gz #OK: Extract the latest PSIPRED
rm psipred.4.01.tar.gz #OK: Remove the the latest PSIPRED .tar.gz download
cd psipred/src #OK: Go to source code directory
make #OK: Compile PSIPRED binaries
make install #OK: Compile PSIPRED binaries
cd .. #OK: Go back to PSIPRED top level directory
wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz #OK: Download the latest uniref90 database
gunzip -v uniref90.fasta.gz #OK: Uncompress the latest uniref90 database
bin/pfilt uniref90.fasta > uniref90filt #ERROR HERE: pfilt not found. Cannot find where the pfilt program is and cannot find from where to install it from
formatdb -t uniref90filt -i uniref90filt #ERROR HERE: formatdb not found. Cannot find where the formatdb program is and cannot find from where to install it from
makeblastdb -dbtype prot -in uniref90filt -out uniref90filt #OK: Not sure what this does but it works fine
./BLAST+/runpsipredplus example/example.fasta #ERROR HERE: /usr/local/bin/psiblast: Command not found. FATAL: Error whilst running blastpgp - script terminated!How can I get PSIPRED to work? what I am doing wrong? Where can I get all the necessary external program to make PSIPRED work? What am I missing?