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The "DebianMed/PredictProtein" page has been changed by LaszloKajan: http://wiki.debian.org/DebianMed/PredictProtein?action=diff&rev1=1&rev2=2 Comment: conf added === Databases === PredictProtein needs databases to function. The easiest and most convenient is to download these as a compressed archive from the [[http://rostlab.org/services/ppmi/|PredictProtein web site]]. All of the databases in the archive are available publicly, the archive is provided for convenience only. The link to the database archive download is hidden until you click 'Click here to download a Debian based image'. Read `man predictprotein` if you want to choose your databases. {{{ - # You will need up to 30GB free space in ${YOUR_DATA_ROOT}/rost_db + # You will need up to 30GB free space in ${YOUR_DATA_ROOT}/rostlab-data $ wget 'http://www.rostlab.org/services/ppmi/download_file?format=gzip&file_to_download=db' --continue -O /tmp/rostlab-data.txz - $ mkdir -p ${YOUR_DATA_ROOT}/rost_db && tar -xvJf /tmp/rostlab-data.txz -C ${YOUR_DATA_ROOT}/rost_db + $ mkdir -p ${YOUR_DATA_ROOT}/rostlab-data && tar -xvJf /tmp/rostlab-data.txz -C ${YOUR_DATA_ROOT}/rostlab-data }}} == Configuration == + Default configuration is in `/usr/share/predictprotein/predictproteinrc.default`. + + Create `/etc/predictproteinrc` with these values (replace `${YOUR_DATA_ROOT}` with the actual value): + {{{ + # Override default predictprotein configuration in /usr/share/predictprotein/predictproteinrc.default with these values: + bigblastdb=${YOUR_DATA_ROOT}/rostlab-data/data/big/big + big80blastdb=${YOUR_DATA_ROOT}/rostlab-data/data/big/big_80 + prositedat=${YOUR_DATA_ROOT}/rostlab-data/data/prosite/prosite.dat + prositeconvdat=${YOUR_DATA_ROOT}/rostlab-data/data/prosite/prosite_convert.dat + swissblastdb=${YOUR_DATA_ROOT}/rostlab-data/data/swissprot/uniprot_sprot + pfam2db=${YOUR_DATA_ROOT}/rostlab-data/data/pfam_legacy/Pfam_ls + pfam3db=${YOUR_DATA_ROOT}/rostlab-data/data/pfam/Pfam-A.hmm + spkeyidx=${YOUR_DATA_ROOT}/rostlab-data/data/swissprot/keyindex_loctree.txt + }}} == Test run == _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
