Commit 1c096611 authored by peguerin's avatar peguerin
Browse files

installation blast and blastdb

parent ea058571
## anvage
pip3 install anvage
## ncbi blast local
tar zxvpf ncbi-blast-2.11.0+-x64-linux.tar.gz
mv ncbi-* $HOME/src
export PATH=$PATH:/$HOME/src/ncbi-blast-2.10.1+/bin
mkdir $HOME/src/blastdb
export BLASTDB=$HOME/src/blastdb
perl $HOME/src/ncbi-blast-2.10.1+/bin/ --help
## show all ncbi preformated database
perl ${HOME}/src/ncbi-blast-2.11.0+/bin/ --showall
## download swissprot database
perl ${HOME}/src/ncbi-blast-2.11.0+/bin/ --decompress swissprot
mv * $HOME/src/blastdb
cd $HOME/src/blastdb
zcat uniprotkb_swissprot.gz | awk '{if (/^>/) { print ">" $2} else { print $_}}' > swissprot.fasta
makeblastdb -in swissprot.fasta -dbtype prot -input_type fasta -parse_seqids -out swissprot_prot -title swissprot_prot
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