Commit ad0813a9 authored by peguerin's avatar peguerin
Browse files

build container

parent 1c096611
......@@ -2,24 +2,25 @@
pip3 install anvage
## ncbi blast local
wget https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.11.0+-x64-linux.tar.gz
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/update_blastdb.pl --help
#perl $HOME/src/ncbi-blast-2.10.1+/bin/update_blastdb.pl --help
## show all ncbi preformated database
perl ${HOME}/src/ncbi-blast-2.11.0+/bin/update_blastdb.pl --showall
#perl ${HOME}/src/ncbi-blast-2.11.0+/bin/update_blastdb.pl --showall
## download swissprot database
perl ${HOME}/src/ncbi-blast-2.11.0+/bin/update_blastdb.pl --decompress swissprot
mv * $HOME/src/blastdb
#perl ${HOME}/src/ncbi-blast-2.11.0+/bin/update_blastdb.pl --decompress swissprot
#mv * $HOME/src/blastdb
#swissprot
#refseq_protein
cd $HOME/src/blastdb
wget ftp://ftp.ebi.ac.uk/pub/databases/fastafiles/uniprot/uniprotkb_swissprot.gz
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
## build container
sudo singularity build -s snpsdata_analysis.simg Singularity.snpsdata_analysis
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