BOL: Related items

OSDDlinux : Computational resources for drug discovery

Archana Malhotra — Sun, 22 Sep 2013 13:15:58 -0500

Open Source Drug Discovery (OSDD), a mission to provide affordable drugs for poors, is in the process of creating an in silico plateform for designing, discovering and simulating drugs. OSDD have initiate number of projects to support in silico drug discovery, including OSDDlinux and computational resources for drug discovery (CRDD).

The main purpose of OSDDLinux is to provide an in silico platform for computer-aided drug design. This is a collection and compilation of large number of software and web services which will be directly or indirectly useful for researches working in the field of drug design/discovery. Overall objective of OSDDlinux is to promote open source in drug discovery, crowdsourcing and network based collobrations. Following are major features of OSDDlinux ...

Find more @ http://osddlinux.osdd.net/index.php

Linux Sort Commands for Bioinformatics

Rahul Nayak — Sat, 31 May 2014 15:41:16 -0500

Almost all the scripting languages such as Perl, Python etc have built-in sort, but unfortunately none of them are as flexible as sort command. But one when it come to space efficiency GNU sort stands at the top. It can sort a 20Gb file with less than 2Gb memory. It is not trivial to implement so powerful a sort by yourself.

sort a space-delimited file based on its first column, then the second if the first is the same, and so on:
sort input.txt

sort a huge file (GNU sort ONLY):
sort -S 1500M -t $HOME/tmp input.txt > sorted.txt

sort starting from the third column, skipping the first two columns:
sort +2 input.txt

sort the second column as numbers, descending order; if identical, sort the 3rd as strings, ascending order:
sort -k2,2nr -k3,3 input.txt

sort starting from the 4th character at column 2, as numbers:
sort -k2.4n input.txt

More Linxu sort command information

If you have any sort commands you'd like to share, please add them to our comments section below. For more help, you can also type:

man sort

or

sort --help

on your Unix/Linux system.

Cheatsheet for Linux !!

Jit — Wed, 22 Jun 2016 07:55:06 -0500

Linux Commands Cheat Sheet

    File System

    ls — list items in current directory

    ls -l — list items in current directory and show in long format to see perimissions, size, an modification date

    ls -a — list all items in current directory, including hidden files

    ls -F — list all items in current directory and show directories with a slash and executables with a star

    ls dir — list all items in directory dir

    cd dir — change directory to dir

    cd .. — go up one directory

    cd / — go to the root directory

    cd ~ — go to to your home directory

    cd - — go to the last directory you were just in

    pwd — show present working directory

    mkdir dir — make directory dir

    rm file — remove file

    rm -r dir — remove directory dir recursively

    cp file1 file2 — copy file1 to file2

    cp -r dir1 dir2 — copy directory dir1 to dir2 recursively

    mv file1 file2 — move (rename) file1 to file2

    ln -s file link — create symbolic link to file

    touch file — create or update file

    cat file — output the contents of file

    less file — view file with page navigation

    head file — output the first 10 lines of file

    tail file — output the last 10 lines of file

    tail -f file — output the contents of file as it grows, starting with the last 10 lines

    vim file — edit file

    alias name 'command' — create an alias for a command
    System

    shutdown — shut down machine

    reboot — restart machine

    date — show the current date and time

    whoami — who you are logged in as

    finger user — display information about user

    man command — show the manual for command

    df — show disk usage

    du — show directory space usage

    free — show memory and swap usage

    whereis app — show possible locations of app

    which app — show which app will be run by default
    Process Management

    ps — display your currently active processes

    top — display all running processes

    kill pid — kill process id pid

    kill -9 pid — force kill process id pid
    Permissions

    ls -l — list items in current directory and show permissions

    chmod ugo file — change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is everyone else's permissions. The values of u, g, and o can be any number between 0 and 7.

    7 — full permissions

    6 — read and write only

    5 — read and execute only

    4 — read only

    3 — write and execute only

    2 — write only

    1 — execute only

    0 — no permissions

    chmod 600 file — you can read and write - good for files

    chmod 700 file — you can read, write, and execute - good for scripts

    chmod 644 file — you can read and write, and everyone else can only read - good for web pages

    chmod 755 file — you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share
    Networking

    wget file — download a file

    curl file — download a file

    scp user@host:file dir — secure copy a file from remote server to the dir directory on your machine

    scp file user@host:dir — secure copy a file from your machine to the dir directory on a remote server

    scp -r user@host:dir dir — secure copy the directory dir from remote server to the directory dir on your machine

    ssh user@host — connect to host as user

    ssh -p port user@host — connect to host on port as user

    ssh-copy-id user@host — add your key to host for user to enable a keyed or passwordless login

    ping host — ping host and output results

    whois domain — get information for domain

    dig domain — get DNS information for domain

    dig -x host — reverse lookup host

    lsof -i tcp:1337 — list all processes running on port 1337
    Searching

    grep pattern files — search for pattern in files

    grep -r pattern dir — search recursively for pattern in dir

    grep -rn pattern dir — search recursively for pattern in dir and show the line number found

    grep -r pattern dir --include='*.ext — search recursively for pattern in dir and only search in files with .ext extension

    command | grep pattern — search for pattern in the output of command

    find file — find all instances of file in real system

    locate file — find all instances of file using indexed database built from the updatedb command. Much faster than find

    sed -i 's/day/night/g' file — find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions
    Compression

    tar cf file.tar files — create a tar named file.tar containing files

    tar xf file.tar — extract the files from file.tar

    tar czf file.tar.gz files — create a tar with Gzip compression

    tar xzf file.tar.gz — extract a tar using Gzip

    gzip file — compresses file and renames it to file.gz

    gzip -d file.gz — decompresses file.gz back to file
    Shortcuts

    ctrl+a — move cursor to beginning of line

    ctrl+f — move cursor to end of line

    alt+f — move cursor forward 1 word

    alt+b — move cursor backward 1 word

Setting python version as default on Linux

Rahul Nayak — Tue, 04 Sep 2018 10:15:47 -0500

If you have a later version than 2.6 you'll need to set 2.6 as the default Python. Later versions would be 2.7 and 3.1; see what you have by typing

python -V

at the terminal. For purposes of this example we'll assume you have 3.1 installed. You'll next need to execute the following commands:

sudo apt-get install python2.6 idle-python2.6
sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.1 1
sudo update-alternatives --install /usr/bin/python python /usr/bin/python2.6 10
sudo update-alternatives --config python

This last command will allow you to choose which version of python to use by default. If you have done everything above correctly, python2.6 should already be set as the default. If it is not, choose it to be the default. From now on, running python should start version 2.6.

Undoing These Changes

In some cases (e.g., installing or updating certain packages), you'll get an error message if you've run the commands above. To update these packages, you'll have to temporarily undo these changes. Here's how to do that:

sudo update-alternatives --remove-all python
sudo ln -s python3.1 /usr/bin/python

Once you're done updating these packages, execute the commands at the top to set python2.6 as the default again.

Linux advantages

Rahul Agarwal — Thu, 30 Jan 2020 06:27:29 -0600

https://www.forbes.com/sites/jasonevangelho/2018/07/30/ditching-windows-heres-how-ubuntu-updates-your-pc-and-why-its-better/#7aa6fa5f7c23

https://www.forbes.com/sites/jasonevangelho/2018/07/23/5-reasons-you-should-switch-from-windows-to-linux-right-now/#70c74923777b

Ten recommendations for creating usable bioinformatics command line software

RAJESH DETROJA — Sun, 08 Jun 2014 10:06:26 -0500

Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author’s tools to follow, which I believe would greatly improve the uptake and usability of their products, waste less user’s time, and improve the quality of scientific analyses.

Address of the bookmark: http://www.gigasciencejournal.com/content/2/1/15?utm_content=buffer25ee0&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

Google Genomics

Tenzin Paul — Thu, 18 Dec 2014 11:05:42 -0600

Explore genetic variation interactively. Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.
Process big genomic data easily. Run batch analyses like principal component analysis and Hardy-Weinberg equilibrium on as many samples as you like, in minutes or hours, with just a little code.
Use Google's infrastructure and big data expertise. Store one genome or a million using Google Genomics and take advantage of the same infrastructure that powers Search, Maps, YouTube, Gmail and Drive.
Support emerging global standards. Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

Address of the bookmark: https://cloud.google.com/genomics/

Enrichr: a comprehensive gene set enrichment analysis

Jit — Thu, 27 Apr 2017 05:42:09 -0500

Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw377

Address of the bookmark: http://amp.pharm.mssm.edu/Enrichr/

Apache server setting !

Abhi — Fri, 29 Oct 2021 04:29:51 -0500

Apache is an open source web server that’s available for Linux servers free of charge.

In this tutorial we’ll be going through the steps of setting up an Apache server.

What you’ll learn

How to set up Apache
Some basic Apache configuration

Address of the bookmark: https://ubuntu.com/tutorials/install-and-configure-apache#3-creating-your-own-website

Heatmap Draw !

BioStar — Mon, 06 Mar 2023 04:24:57 -0600

Server for heatmap generation !

https://software.broadinstitute.org/morpheus/

Address of the bookmark: https://software.broadinstitute.org/morpheus/