Results for "DB"
Bio-Scripts
(JitMetaENV) ➜ JitMeta conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1233 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen...
1231 days ago
Download minikraken database !
...://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken2_v2_8GB_20190...z (JitMetaENV) ➜ day3 mkdir krakenDB (JitMetaENV) ➜ day3 cd krak...krakenDB ls (JitMetaENV) ➜ krakenDB mv ../minikraken2_v2_8GB_2019...#kraken2 --use-names --threads 4 --db minikraken2_v2_8GB_201904_UPD...1230 days ago
- (JitMetaENV) ➜ day3 conda install -c bioconda maxbin2 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen sol...
1230 days ago
Set up WGD environment using conda !
...3689200 sha256=7daa115fd1b052d429abb6c7082cbbb96defc81716da99ce873760cedf0dbe6f Stored in directory: /h...YAML-5.3.1-cp37-cp37m-linux_x86_64.whl size=44620 sha256=89175438317c730e5db0088255ca2f5a9745368487ed0fd0c...1219 days ago
Converting from Windows-style to UNIX-style line endings with dos2unix
...aring to unpack .../dos2unix_7.3.4-3_amd64.deb ... Unpacking dos2unix (7.3.4-3) ... Setting up dos2unix (7.3.4-3) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ...1193 days ago
Parse the NCBI taxonomy database with Perl !
use Bio::DB::Taxonomy; use warnings; m...a NCBI taxonomy database my $dbh = Bio::DB::Taxonomy->new(-so...etazoa'); #exit; #my $nam = $dbh->get_taxon(-name => $sps);...es{$speciesId}; my @taxa = $dbh->each_Descendent($nam); #...Tree::Tree->new(); my $nam = $dbh->get_taxon(-taxonid => $line...1188 days ago
Perl script to get all the descendent in a tree !
use warnings; use Bio::DB::Taxonomy; #Rotifera 10190 # Get one from a NCBI taxonomy database my $dbh = Bio::DB::Taxonomy->new(-so...namesfile=> "taxdump/names.dmp"); my $taxon = $dbh->get_taxon(-taxonid => 10190...1180 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...ename', 'Bio::SeqIO', 'FindBin', 'File::Remove',...und', 'File::Find', 'Bio::DB::Taxonomy', 'Pod::Usage'...= $ae->extract( to => 'third_party_DB/taxdump' ); #Install sil..._party_DB/' ); #Install diamondDB __END__ # BlastDB dow...1176 days ago
- ..., 'Data::Dumper', 'File::Basename', 'Bio::SeqIO', 'FindBin', 'File::Remove',..., 'Statistics::R', 'Math::Round', 'File::Find', 'Bio::DB::Taxonomy', 'Pod::Usage'...
1174 days ago
