Results for "C"
Bio-Scripts
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
...3.0.01.tar.gz from https://wdiceryfd4rjn74bjhhtz2k5di--bioinformatics-psb-ugent-be.translate.goog/.../src/SvgWriter.cpp:1: /usr/include/x86_64-linux-gnu/bits/std...tasetII/ptr_lists_030210_201/scaffold_692.lst -- Installing:...-- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datas...1260 days ago
Command to create conda environment !
# using pip pip install -r requirements.txt # using Conda conda create --name --file requirements.txt #Using yaml conda env create -f environment.yml #Listing env conda env list #Create env with python36 conda create -n myenv python=3.61257 days ago
Steps to install Conda on Linux !
Download the installer: Miniconda installer for Linux. ( https://docs.conda.io/en/latest/miniconda.html#linux-installers ) Anaconda installer for Linux. ( http...020.11-Linux-x86_64.sh $ ./Anaconda3-2020.11-Linux-x86_64.sh...environment named as `envname` conda create --name envname #...1239 days ago
Converting from Windows-style to UNIX-style line endings with dos2unix
...for bioqueen: Reading package lists... Done Building d...tion... Done The following packages were automatically insta...ve them. The following NEW packages will be installed: do...base ... 177704 files and directories currently installed.)...1233 days ago
Install ATOM editor on Elemantory OS / Ubuntu
...for bioqueen: Reading package lists... Done Building dependency tree Reading state i...1 [700 kB] Get:2 http://in.archive.ubuntu.com/ubuntu bionic/...ring to unpack .../gconf-service-backend_3.2.6-4ubuntu1_amd64...-ui to /home/bioqueen/.atom/packages ✓1232 days ago
Parse the NCBI taxonomy database with Perl !
...= Bio::DB::Taxonomy->new(-source => 'flatfile',...=> "taxdump/names.dmp"); #to check #parseTax('homo_sapiens'...$nam->id, "\n"; # 9606 #$abc = $names{$speciesId}; my @...nam); my $lineage = $tree_functions->get_lineage_string($nam...1229 days ago
Perl script to get all the descendent in a tree !
...axonomy; #Rotifera 10190 # Get one from a NCBI taxonomy database my $dbh = Bio::DB::Taxonomy->new(-source => 'flatfile',...-taxonid => 10190); my @taxa = $dbh->get_all_Descendents($taxon); foreach (@ta...1221 days ago
- syntax: $output = open2(\*CHLD_OUT, \*CHLD_IN, 'command arg1 arg2'); It runs a process for both reading and writing and cre...tes a pipe to both STDIN and STDOUT. It can be used in both ways: $o...$in, 'command', 'arg1', 'arg2'); You can read about it more in the d...
1220 days ago
Perl script to run awk inside perl
#!/usr/local/bin/perl eval 'exec /usr/local/bin/perl -S $0 ${1+"$@"}' if $running_under_some_shell; # this emulates #! processing on NIH machines. # (re...GV[0] =~ /^([A-Za-z_0-9]+=)(.*)/ && shift; # process any FOO=bar switches $, =...1220 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtil...led; use LWP::Simple; use Archive::Extract; # # First, check if all t...my @import_modules = ( 'Cwd', 'File::chdir',...end 'for' } # end 'BEGIN' block #Bash script else here...code; my $silva_LSU_ae = Archive::Extract->new( archive =>...1217 days ago
