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polyphen-software [2017/03/09 15:28]
joguya created
polyphen-software [2017/04/01 18:56]
aorth
Line 20: Line 20:
 Notes from the sysadmin during installation:​ Notes from the sysadmin during installation:​
  
-<​code>​ +<​code>​$ scl enable devtoolset-3 bash
-$ cd /tmp +
-$ wget -qO- http://​genetics.bwh.harvard.edu/​pph2/​dokuwiki/​_media/​polyphen-2.2.2r405c.tar.gz | tar xzv +
-$ cd polyphen-2.2.2/​ +
-$ scl enable devtoolset-3 bash+
 $ module load perl/5.22.3 $ module load perl/5.22.3
-$ cpanm DBD::​SQLite +$ sudo chown -R aorth:aorth /​export/​apps/​perl/​5.22.3 
-sudo mkdir -/export/apps/​polyphen/​2.2.2 +$ cpanm XML::Simple LWP::​Simple ​DBD::​SQLite 
-$ sudo chown -R joguya:joguya ​/​export/​apps/​polyphen/​2.2.2 +cd /tmp 
-$ ./configure+$ 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 download
 +$ make clean
 $ make $ make
 $ make install $ make install
-cp -r . /export/apps/​polyphen/2.2.2 +cd $PPH 
-$ sudo chown -R root:​root ​/​export/​apps/​polyphen/​2.2.2 +./configure 
-</​code>​+$ 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.
polyphen-software.txt · Last modified: 2017/04/01 18:56 by aorth