Command line to download blast database / protein
...tein database as a single file #Database location - NCBI where all databases are ava...//ftp.ncbi.nlm.nih.gov/blast/db/ https://ftp.ncbi.nlm.nih.gov/blast/db/ #...#First run this to download wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.t...1004 days ago
Download desire version of Blast software !
#Create a directory and wget it wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64...ux.tar.gz #unpacking blast tar -zxvf ncbi-blast-2.6.0+-x64-linux.tar....des=1 #SBATCH --ntasks-per-node=32 #SBATCH --time=1:00:00 #SBATCH --jo...1003 days ago
1003 days ago
Downloading mmseqs databases !
...- UniRef90 Aminoacid yes https://www.unipr...- UniProtKB Aminoacid yes https://www.unipr...- PDB Aminoacid - https://www.rcsb....ath/swissprot tmp #In this case, since Swiss-Prot has a va...1003 days ago
989 days ago
Onliner to convert multi line fasta to single line fasta !
#Oneliner to convert awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa > fileres.fa #Then delete the first empty line tail -n +2 fileres.fa > fileout.fa989 days ago
Perl onliner to check the ids in two files !
perl -lane 'BEGIN{open(A,"ids2.txt"); while(){chomp; $k{$_}++}} if (defined($k{$F[0]})) {print "$_\t$F[0]\t1"} else {print "$_\tNA\t0"}; ' ids1.txt > aaa.xls988 days ago
Installing Covid19 Environment !
...-320-15ISK:~/vinodLab/Genepi$ conda env create -f covid19-environment.y...#################### | 100% cairo-1.16.0 | 1.5 MB...############# | 100% liblapack-3.9.0 | 12 KB | ###...#################### | 100% ca-certificates-2021 | 139 KB...984 days ago
980 days ago
Install Php on Ubuntu / Apache server !
#Installing PHP 7.2 with Apache #If you are using Apache as your web server to install PHP and Apache PHP module run the following command: sudo apt install php libapache2-mod-php #Once the packages are installed restart the Apache service: sudo systemctl restart apache2980 days ago