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--- polyphen-software [2017/03/09 12:28] – created joguya
+++ polyphen-software [2017/04/01 15:56] (current) – aorth
@@ Line 20: / Line 20: @@
 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
-$ cpanm DBD::SQLite
+$ sudo chown -R aorth:aorth /export/apps/perl/5.22.3
-$ sudo mkdir -p /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 clean
 $ make
 $ 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.