====== PolyPhen-2 ======

PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.

===== Information =====

  * Latest version: 2.2.2
  * Added: March, 2017
  * Link: http://genetics.bwh.harvard.edu/pph2/dokuwiki/start

===== Usage =====

See versions of polyphen which are available:
<code>$ module avail polyphen</code>

Load polyphen:
<code>$ module load polyphen</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ scl enable devtoolset-3 bash
$ module load perl/5.22.3
$ sudo chown -R aorth:aorth /export/apps/perl/5.22.3
$ cpanm XML::Simple LWP::Simple DBD::SQLite
$ cd /tmp
$ wget http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-2.2.2r405c.tar.gz
$ tar xf polyphen-2.2.2r405c.tar.gz
$ wget ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2
$ wget ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2
$ wget ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2
$ tar xf polyphen-2.2.2-databases-2011_12.tar.bz2
$ tar xf polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2
$ tar xf polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2
$ cd polyphen-2.2.2
$ wget ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-linux.tar.gz
$ tar xf ncbi-blast-2.2.31+-x64-linux.tar.gz
$ mv ncbi-blast-2.2.31+/* blast
$ rm -rf ncbi-blast-2.2.31+*
$ wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat -O bin/blat
$ wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa -O bin/twoBitToFa
$ chmod +x bin/blat bin/twoBitToFa
$ cd nrdb
$ wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/uniref/uniref100/uniref100.fasta.gz
$ gunzip uniref100.fasta.gz
$ ../update/format_defline.pl uniref100.fasta >uniref100-formatted.fasta
$ ../blast/bin/makeblastdb -in uniref100-formatted.fasta -dbtype prot -out uniref100 -parse_seqids
$ rm -f uniref100.fasta uniref100-formatted.fasta
$ cd ..
$ rsync -rltv --delete-after --port=33444 rsync.wwpdb.org::ftp/data/structures/divided/pdb/ wwpdb/divided/pdb/
$ rsync -rltv --delete-after --port=33444 rsync.wwpdb.org::ftp/data/structures/all/pdb/ wwpdb/all/pdb/
$ sleep 8h && rsync -rltvz --delete-after rsync://rsync.cmbi.ru.nl/dssp/ dssp/
$ cd ..
$ sudo mkdir /export/apps/polyphen
$ sudo chown aorth:aorth /export/apps/polyphen
$ cp -r polyphen-2.2.2 /export/apps/polyphen/2.2.2
$ export PPH=/export/apps/polyphen/2.2.2
$ cd $PPH/src
$ make download
$ make clean
$ make
$ make install
$ cd $PPH
$ ./configure
$ find $PPH/scratch -type d -exec chmod 777 {} \;
$ find $PPH/scratch -type d -exec chmod +t {} \;
$ sudo chown -R root:root $PPH</code>

Note that this can take nearly 200GB of space and many hours to download, expand, and process all the data files.