Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
seaconnect
annotationVariant
Commits
1c096611
Commit
1c096611
authored
Feb 15, 2021
by
peguerin
Browse files
installation blast and blastdb
parent
ea058571
Changes
1
Hide whitespace changes
Inline
Side-by-side
INSTALL.sh
0 → 100644
View file @
1c096611
## anvage
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
## show all ncbi preformated database
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
#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
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment