Results for "Command Line"
Bio-Scripts
Set up WGD environment using conda !
...zsh: correct 'wgd' to 'gd' [nyae]? n Usage: wgd [OPTIONS] COMMAND [ARGS]... Welcome to the wgd command line interface!.... pre Check and optionally rename CDS files. syn Co-linearity analyses. viz Plot h...1231 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
...lt [-Wunused-result] system(command.append(outputPath).c_str());...lt [-Wunused-result] system(command.append(outputPath).c_str());...da3/envs/wgd/./post_processing/collinearityViz.pl -- Installing: /h...nda3/envs/wgd/./post_processing/colinear_portions.pl -- Installing:...1231 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=3.61228 days ago
- syntax: $output = open2(\*CHLD_OUT, \*CHLD_IN, 'command arg1 arg2'); It runs a process for both readi...both ways: $output = open2(my $out, my $in, 'command arg1 arg2'); OR without us...g the shell $output = open2(my $out, my $in, 'comm...
1191 days ago
Perl script to run awk inside perl
#!/usr/local/bin/perl eval 'exec /usr/local/bin/perl -S $0 ${1+"$@"}' if $running_under_some_shell; # this emulates #! processing on NIH machines. # (remove #! line above if indigestible) eva...1191 days ago
Conda command to install checkV
(mENV) [jnarayan@hn1 Monkey_Pox]$ conda install -c conda-forge -c bioconda checkv Collecting package metadata (current_repodata.json): done Solving environment: done...663 days ago
- #use strict; use warnings; use ExtUtils::Installed; use LWP::Simple; use Archive::Extract; # # First, check if all the required modules have been installed in th...
1186 days ago
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa1024 days ago
- ...*** This is BWISE - High order De Bruijn graph assembler *** The command line was: /home/urbe/anaconda3/env...se --help` and/or check the logs files of the various steps of the pipeline (logs/logBloo coo, lo...
1018 days ago
Run multiple bash command in screen !
#login to screen screen -r 123 #bash.sh srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh #Run and check the status in screen contol +A +D990 days ago
