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

Keep Your Important SSH Session Running when You Disconnect from Server !!!

Jitendra Narayan — Sat, 15 Mar 2014 21:39:17 -0500

As a Bioinformatician/ Computational biologist we swim in the ocean of genomic/proteomics data, and play with them with an ease. In our day to day simulation, analysis, comparative study we do need to run exhaustive programs, which might take more than a week. In such cases we do need to disconnect from sever in a way that our program/session should not get terminated. To do so there are lots of software, tools such as tmux ( http://tmux.sourceforge.net/, nohup (http://ss64.com/bash/nohup.html) , byobu (https://help.ubuntu.com/10.04/serverguide/byobu.html) and other commands (disown -a && exit), but following are the ones I use the most.

Screen is like a window manager for your console. It will allow you to keep multiple terminal sessions running and easily switch between them. It also protects you from disconnection, because the screen session doesn’t end when you get disconnected.

You’ll need to make sure that screen is installed on the server you are connecting to. If that server is Ubuntu or Debian, just use this command:

sudo apt-get install screen

Now you can start a new screen session by just typing screen at the command line. You’ll be shown some information about screen. Hit enter, and you’ll be at a normal prompt.

To disconnect (but leave the session running)

Hit Ctrl + A and then Ctrl + D in immediate succession. You will see the message [detached]

To reconnect to an already running session

screen -r

To reconnect to an existing session, or create a new one if none exists

screen -D -r

To create a new window inside of a running screen session

Hit Ctrl + A and then C in immediate succession. You will see a new prompt.

To switch from one screen window to another

Hit Ctrl + A and then Ctrl + A in immediate succession.

To list open screen windows

Hit Ctrl + A and then W in immediate succession

Monitor running jobs on Linux server

Jitendra Narayan — Fri, 06 Jun 2014 16:18:43 -0500

You as a bioinformatican run lots of program on your servers. Sometime the shared server is also used by your colleague. If server is busy you sometime need to check the running programs and want to monitor the running programs as well. The "top" command will come in handy when you need to find out if things are still running, how long they’ve been running, or how much memory is being used.

‘top’ is very simple to run: type

%% top

You’ll get a screen that looks like this, and is updated regularly:

Simple, right? Heh.

First! Note that you can use ‘q’ or ‘CTRL-C’ to exit from ‘top’.

Now let’s read and understand at each line independently.

The first line:

top - 23:00:48 up 39 days, 2 user, load average: 0.00, 0.00, 0.00

The first line tells you the current time, how long the machine has been up, how many users are logged in, and the short/medium/long-term compute load on the machine. If you run something for a long time, you’ll see these numbers go up. Right now, the machine is basically just sitting there, so these are all close to 0.

The second line:

Tasks: 239 total,   1 running, 238 sleeping,   0 stopped,   0 zombie

This line tells you how many processes are running. If you are using laptops machines it’s not so interesting because you really are the only one using this machine.

Cpu(s): 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st

This line contains the CPU load. The first two numbers are how busy the system is doing computation (“us” stands for “user”) and how busy the system is doing system-y things like accessing disks or network (“sy” stands for “system”). We’ll talk more about this later.

Mem:   49457320k total,    3492174k used, 14535596k free,    1435148k buffers

This should be easy to understand – how much memory you’re using!

Swap:   539356k total,   28332k used,   836562k free,    29862014k cached

Swap is just on-disk memory that can be used to “swap” out programs from main memory. Again, we’ll talk about this later.:

PID USER      PR NI VIRT RES SHR S %CPU %MEM    TIME+ COMMAND
1 root      39 19 0 0 0 S 0.0 0.0   246:57.22 kipmi0
2 root      RT   0     0    0    0 S 0.0 0.0   0:00.00 migration/0

And... finally! What’s actually running! The two most important numbers are the %CPU and %MEM towards the right, as well as the COMMAND. This tells you how compute- and memory-intensive your program is. Right now, nothing’s running so the numbers aren’t very interesting, but just wait until we run something...

BioLinux Ubuntu Desktop folder and files disappeared !!

Jit — Tue, 16 Feb 2016 08:40:41 -0600

Restarted my BioLinux ubuntu computer after an update, and when I logged back in, I noticed that all of my files went missing. Instead of Desktop folder, icons of all of my home folder are showed on desktop.

Then I thaught it migh be a problem of graphical display and I opened the terminal out of curiosity, and I found out that there is no ~/Desktop folder at all. What happened? What do I need to do?

Then I google the problem and found this is a very common problem after updates. To fix this problem, follow these steps:

You need to edit the ~/.config/user-dirs.dirs file, and make sure the contents of the file are like the following:

XDG_DESKTOP_DIR="$HOME/Desktop"
XDG_DOWNLOAD_DIR="$HOME/Downloads"
XDG_TEMPLATES_DIR="$HOME/"
XDG_PUBLICSHARE_DIR="$HOME/Share"
XDG_DOCUMENTS_DIR="$HOME/Documents"
XDG_MUSIC_DIR="$HOME/Music"
XDG_PICTURES_DIR="$HOME/Pictures"
XDG_VIDEOS_DIR="$HOME/Videos"

Then restart nautilus:

killall nautilus

or

nautilus -q

Then, open nautilus via Unity menu (press the Super key) or using the run command (Alt+F2)

Creating conda environment for python2.7

Jit — Mon, 07 May 2018 08:56:52 -0500

TIP: By default, environments are installed into the envs directory in your conda directory. Run conda create --help for information on specifying a different path.

Use the Terminal or an Anaconda Prompt for the following steps.

To create an environment:
```
conda create --name myenv
```
NOTE: Replace myenv with the environment name.
When conda asks you to proceed, type y:
```
proceed ([y]/n)?
```

This creates the myenv environment in /envs/. This environment uses the same version of Python that you are currently using, because you did not specify a version.

To create an environment with a specific version of Python:

conda create -n myenv python=3.4

To create an environment with a specific package:

conda create -n myenv scipy

OR:

conda create -n myenv python
conda install -n myenv scipy

To create an environment with a specific version of a package:

conda create -n myenv scipy=0.15.0

OR:

conda create -n myenv python
conda install -n myenv scipy=0.15.0

To create an environment with a specific version of Python and multiple packages:

conda create -n myenv python=3.4 scipy=0.15.0 astroid babel

TIP: Install all the programs that you want in this environment at the same time. Installing 1 program at a time can lead to dependency conflicts.

To automatically install pip or another program every time a new environment is created, add the default programs to the create_default_packages section of your .condarc configuration file. The default packages are installed every time you create a new environment. If you do not want the default packages installed in a particular environment, use the --no-default-packages flag:

conda create --no-default-packages -n myenv python

TIP: You can add much more to the conda create command. For details, run conda create --help.

➜ redundans git:(master) ✗ conda create --name py27 python=2.7
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.5.0
latest version: 4.5.2

Please update conda by running

$ conda update -n base conda

## Package Plan ##

environment location: /home/urbe/anaconda3/envs/py27

added / updated specs:
- python=2.7

The following packages will be downloaded:

package | build
---------------------------|-----------------
wheel-0.31.0 | py27_0 61 KB
python-2.7.15 | h1571d57_0 12.1 MB
certifi-2018.4.16 | py27_0 142 KB
sqlite-3.23.1 | he433501_0 1.5 MB
setuptools-39.1.0 | py27_0 582 KB
openssl-1.0.2o | h20670df_0 3.4 MB
pip-10.0.1 | py27_0 1.7 MB
ca-certificates-2018.03.07 | 0 124 KB
------------------------------------------------------------
Total: 19.6 MB

The following NEW packages will be INSTALLED:

ca-certificates: 2018.03.07-0
certifi: 2018.4.16-py27_0
libedit: 3.1-heed3624_0
libffi: 3.2.1-hd88cf55_4
libgcc-ng: 7.2.0-hdf63c60_3
libstdcxx-ng: 7.2.0-hdf63c60_3
ncurses: 6.0-h9df7e31_2
openssl: 1.0.2o-h20670df_0
pip: 10.0.1-py27_0
python: 2.7.15-h1571d57_0
readline: 7.0-ha6073c6_4
setuptools: 39.1.0-py27_0
sqlite: 3.23.1-he433501_0
tk: 8.6.7-hc745277_3
wheel: 0.31.0-py27_0
zlib: 1.2.11-ha838bed_2

Proceed ([y]/n)? y

Downloading and Extracting Packages
wheel 0.31.0: #################################################################################################################################################################################################### | 100%
python 2.7.15: ################################################################################################################################################################################################### | 100%
certifi 2018.4.16: ############################################################################################################################################################################################### | 100%
sqlite 3.23.1: ################################################################################################################################################################################################### | 100%
setuptools 39.1.0: ############################################################################################################################################################################################### | 100%
openssl 1.0.2o: ################################################################################################################################################################################################## | 100%
pip 10.0.1: ###################################################################################################################################################################################################### | 100%
ca-certificates 2018.03.07: ###################################################################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > source activate py27
#
# To deactivate an active environment, use:
# > source deactivate
#

➜ redundans git:(master) ✗ source activate py27

Subprocess pkg

Rahul Agarwal — Sun, 17 Aug 2014 07:59:32 -0500

Subprocess is one of simplest way of running linux command from within python code

Example:

if you want to run fastqc for QC of fastq file:

from subprocess import Popen,PIPE,call

p=Popen(["fastqc","-f","fastq","-o", "/home/name/result/","/dev/stdin"],stdin=fopen("read.fastq","r") ,stdout=PIPE,stderr=PIPE)

print p.stderr

p.stdout.close()

http://pymotw.com/2/subprocess/

Installing ELGG on Ubuntu !

Neel — Wed, 25 May 2022 02:26:05 -0500

Elgg is an open-source and highly customizable framework used for building an online social environment. It provides a simple and powerful user interface that helps to manage and build your content through a web browser. Elgg offers a rich set of features including messaging, microblogging, file-sharing, RSS support, access control, groups, and many more.

In this tutorial, we will show you how to install and configure Elgg social networking platform on Ubuntu 20.04.

Prerequisites

• A fresh Ubuntu 20.04 VPS on the Atlantic.net Cloud Platform
• A valid domain name pointed to your server IP
• A root password configured on your server

Step 1 – Create Atlantic.Net Cloud Server

First, log in to your Atlantic.Net Cloud Server. Create a new server, choosing Ubuntu 20.04 as the operating system with at least 2GB RAM. Connect to your Cloud Server via SSH and log in using the credentials highlighted at the top of the page.

Once you are logged in to your Ubuntu 20.04 server, run the following command to update your base system with the latest available packages.

apt-get update -y

Step 2 – Install Apache, MariaDB and PHP

Elgg runs on Apache web server, is written in PHP, and uses MySQL/MariaDB as a database backend, so you will need to install the Apache, MariaDB, PHP and other required PHP extensions to your server. You can install all of them with the following command:

apt-get install apache2 mariadb-server php libapache2-mod-php php-common php-sqlite3 php-curl 
php-intl php-mbstring php-xmlrpc php-mysql php-gd php-xml php-cli php-zip unzip wget -y

After installing all the packages, edit the php.ini file and change some recommended settings.

nano /etc/php/7.4/apache2/php.ini

Change the following values:

max_execution_time = 300
memory_limit = 512M
upload_max_filesize = 100M
date.timezone = Asia/Kolkata

Save and close the file, then restart the Apache service to apply the configuration changes.

systemctl restart apache2

Step 3 – Create a Database for Elgg

Next, you will need to create a database and user for Elgg. First, log in to MySQL shell with the following command:

mysql

Once logged in, create a database and user with the following command:

CREATE DATABASE elgg;
CREATE USER 'elgg'@'localhost' IDENTIFIED BY 'secure-password';

Next, grant all the privileges to the elgg database with the following command:

GRANT ALL ON elgg.* TO 'elgg'@'localhost' IDENTIFIED BY 'secure-password' WITH GRANT 
OPTION;

Next, flush the privileges and exit from the MariaDB shell with the following command:

FLUSH PRIVILEGES;
EXIT;

At this point, the MariaDB database is created for Elgg.

Step 4 – Install Elgg

First, download the latest version of Elgg from its official website using the following command:

wget https://elgg.org/download/elgg-3.3.13.zip

Once the download is completed, unzip the downloaded file with the following command:

unzip elgg-3.3.13.zip

Next, move the extracted directory to the Apache root directory:

mv elgg-3.3.13 /var/www/html/elgg

Next, create a data directory and set proper ownership and permissions to the Elgg directory:

mkdir /var/www/html/data
chown -R www-data:www-data /var/www/html/elgg
chown -R www-data:www-data /var/www/html/data
chmod -R 755 /var/www/html/elgg

Once you are finished, you can proceed to the next step.

Step 5 – Configure Apache for Elgg

Next, you will need to configure Apache to serve Elgg. You can configure it by creating a new Apache virtual host configuration file:

nano /etc/apache2/sites-available/elgg.conf

Add the following lines:


ServerAdmin admin@example.com
DocumentRoot /var/www/html/elgg/
ServerName elgg.example.com
Options FollowSymLinks
AllowOverride All
ErrorLog /var/log/apache2/elgg-error_log
CustomLog /var/log/apache2/elgg-access_log common

Save and close the file, then enable the virtual host and Apache rewrite module with the following command:

a2ensite elgg.conf
a2enmod rewrite

Finally, restart the Apache service to apply the changes:

systemctl restart apache2

Step 6 – Access Elgg Web Interface

Now, open your web browser and access the Elgg web interface using the URL http://elgg.example.com. You should see the Elgg welcome screen:

Fancy Oneliner for Bioinformatics !!

Poonam Mahapatra — Thu, 07 Jul 2016 12:05:50 -0500

This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder structures as we have. We are sharing these codes with the intention that if they are useful and help you in your analyses, then we will be appropriately credited as considerable effort has been put into devising them.

Address of the bookmark: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html

How to install Perl modules manually, using CPAN command, and other quick ways

Jit — Fri, 12 Jul 2013 07:20:24 -0500

As a bioinformatics programmer, and crunchy data analyser you need to install several perl modules and dependencies. Installing Perl modules manually by resolving all the dependencies is tedious and annoying process. Some of the packages like GD is the real pain.

However, Installing Perl modules using CPAN is a better solution, as it resolves all the dependencies automatically. In this article, let us review how to install Perl modules on Linux ( which is prefereced amonst bioinformatician) using both manual and CPAN method.

When a Perl module is not installed, application will display the following error message. In this example, XML::Parser Perl module is missing.

Can't locate XML/parser.pm in @INC (@INC contains:
/usr/lib/perl5/5.10.0/i386-linux-thread-multi
/usr/lib/perl5/5.10.0
/usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi
/usr/local/lib/perl5/site_perl/5.10.0
/usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl
/usr/lib/perl5/site_perl/5.10.0 .)

Manual Method of Perl Module Installation

Install Perl Modules Manually

This manual method is very useful when your computer or server is not connected to the Internet.

Download Perl module:
Go to CPAN Search website and search for the module that you wish to download. In this example, let us search, download and install XML::Parser Perl module. I have downloaded the XML-Parser-2.36.tar.gz to /home/download

# cd /home/download
# gzip -d XML-Parser-2.36.tar.gz
# tar xvf XML-Parser-2.36.tar
# cd XML-Parser-2.36

Build the perl module:
Build by running Makefile.PL, remember the case sensitivity, make and make test.

# perl Makefile.PL
Checking if your kit is complete...
Looks good
Writing Makefile for XML::Parser::Expat
Writing Makefile for XML::Parser
# make
# make test

Install the perl module:
Now your package is ready to install.

# make install

As a newbie it looks pretty simple, and one go. But, luckily this is a very simple one module with no dependencies. Typically, Perl modules will be dependent on several other modules. Just imagine chasing all these dependencies one-by-one, thinking ... oh ye I got it. That will be very painful and annoying task. I recommend the CPAN method of installation as shown below.

Install Perl Modules using CPAN automatically

Logically, you should must have the CPAN perl module installed in your server or computer before you can install any other Perl modules using CPAN. I know you are laughing, "to install a perl module you need another perl module" ;)

Lets verify whether CPAN is already installed:

To install Perl modules using CPAN, make sure the cpan command is working. Following are the error message when CPAN module is not installed.

# cpan
-bash: cpan: command not found

# perl -MCPAN -e shell
Can't locate CPAN.pm in @INC (@INC contains:
/usr/lib/perl5/5.10.0/i386-linux-thread-multi
/usr/lib/perl5/5.10.0
/usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi
/usr/local/lib/perl5/site_perl/5.10.0
/usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.10.0
/usr/lib/perl5/vendor_perl /usr/lib/perl5/site_perl/5.10.0 .).
BEGIN failed--compilation aborted.

Install the CPAN module using yum:
If CPAN in not installed in your system, you can use "yum" for the rescue. Dont worry biological data cruncher, this is true we are now dependent all these tiny magicians :).

# yum install perl-CPAN

Output of yum install perl-CPAN command:

Loaded plugins: refresh-packagekit
updates-newkey                       | 2.3 kB     00:00
primary.sqlite.bz2                   | 2.4 MB     00:00
Setting up Install Process
Parsing package install arguments

Resolving Dependencies
Transaction Summary
=============================================================================
Install      5 Package(s)
Update       0 Package(s)
Remove       0 Package(s)

Total download size: 1.0 M
Is this ok [y/N]: y
Downloading Packages:
(1/5): perl-ExtUtils-ParseXS-2.18-31.fc9.i386.rpm     | 30 kB     00:00
(2/5): perl-Test-Harness-2.64-31.fc9.i386.rpm         | 70 kB     00:00
(3/5): perl-CPAN-1.9205-31.fc9.i386.rpm               | 217 kB     00:00
(4/5): perl-ExtUtils-MakeMaker-6.36-31.fc9.i386.rpm   | 284 kB     00:00
(5/5): perl-devel-5.10.0-31.fc9.i386.rpm              | 408 kB     00:00

Installing     : perl-ExtUtils-ParseXS                             [1/5]
Installing     : perl-devel                                        [2/5]
Installing     : perl-Test-Harness                                 [3/5]
Installing     : perl-ExtUtils-MakeMaker                           [4/5]
Installing     : perl-CPAN                                         [5/5]

Installed: perl-CPAN.i386 0:1.9205-31.fc9
Dependency Installed:
perl-ExtUtils-MakeMaker.i386 0:6.36-31.fc9
perl-ExtUtils-ParseXS.i386 1:2.18-31.fc9
perl-Test-Harness.i386 0:2.64-31.fc9
perl-devel.i386 4:5.10.0-31.fc9
Complete!

Configure cpan the first time:
Once the CPAN is installed, you need to configure it by executing cpan, you should set some configuration parameters as shown below. I have shown only the important configuration parameters below. Accept all the default values by pressing enter.

Note: Make sure to execute “o conf commit” in the cpan prompt after the configuration to save the settings.

# cpan

Sorry, we have to rerun the configuration dialog for CPAN.pm due
to some missing parameters...

CPAN build and cache directory? [/root/.cpan]
Download target directory? [/root/.cpan/sources]
Directory where the build process takes place? [/root/.cpan/build]

Always commit changes to config variables to disk? [no]
Cache size for build directory (in MB)? [100]
Let the index expire after how many days? [1]

Perform cache scanning (atstart or never)? [atstart]
Cache metadata (yes/no)? [yes]
Policy on building prerequisites (follow, ask or ignore)? [ask]

Parameters for the 'perl Makefile.PL' command? []
Parameters for the 'perl Build.PL' command? []

Your ftp_proxy? []
Your http_proxy? []
Your no_proxy? []
Is it OK to try to connect to the Internet? [yes]

First, pick a nearby continent and country by typing in the number(s)
(1) Africa
(2) Asia
(3) Central America
(4) Europe
(5) North America
(6) Oceania
(7) South America
Select your continent (or several nearby continents) [] 5

(1) Bahamas
(2) Canada
(3) Mexico
(4) United States
Select your country (or several nearby countries) [] 4

(2) ftp://carroll.cac.psu.edu/pub/CPAN/
(3) ftp://cpan-du.viaverio.com/pub/CPAN/
(4) ftp://cpan-sj.viaverio.com/pub/CPAN/
(5) ftp://cpan.calvin.edu/pub/CPAN
(6) ftp://cpan.cs.utah.edu/pub/CPAN/
e.g. '1 4 5' or '7 1-4 8' [] 2-16

cpan[1]> o conf commit
commit: wrote '/usr/lib/perl5/5.10.0/CPAN/Config.pm'

cpan[2]> quit
No history written (no histfile specified).
Lockfile removed.

Install Perl Modules using CPAN

Hey smile please, now you are ready with CPAN and can download modules in one line command.

You can use one of the following method to install a Perl module using cpan:

# perl -MCPAN -e 'install Bundle::BioPerl'

(or)

# cpan
cpan shell -- CPAN exploration and modules installation (v1.9205)
ReadLine support available (maybe install Bundle::CPAN or Bundle::CPANxxl?)

cpan[1]> install "Bundle::BioPerl"

In the example above, CPAN will check for Bundle::BioPerl dependencies and automatically resolves and installs Bundle::BioPerl with all the dependent Perl modules.

Quick Ways

Oh, look at your face.. smily hmm :). This is what your are looking for, a quick and best way to install Perl modules, Bioperl. Following are the the steps to download BioPerl in your server/computer.

# sudo apt-cache search perl BioPerl

Output will be like as follows:

bioperl - Perl tools for computational molecular biology
bioperl-run - BioPerl wrappers: scripts
libbio-perl-perl - BioPerl core perl modules
libbio-perl-run-perl - BioPerl wrappers: modules
libbio-samtools-perl - Perl interface to SamTools library for DNA sequencing
libbiojava-java - Java API to biological data and applications (default version)
libbiojava3-java - Java API to biological data and applications (default version)
python-biopython-sql - Biopython support for the BioSQL database schema
libbtlib-perl - library for basic sequence manipulation

# sudo apt-get install bioperl

If it is installed then flash the following message:

Reading package lists... Done
Building dependency tree
Reading state information... Done
bioperl is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.

In it is found not installed in your server or system them install all with dependencies.

You can use the same approach to install all the modules, and packages if required.

Thanks for reading. Best of luck for your research.

Perl in a day !!

Jitendra Narayan — Sat, 10 Aug 2013 21:14:03 -0500

This pdf based tutorial in good resource to understand the basic of Perl in a day

http://ritg.med.harvard.edu/training/perl/RC_Perl_Intro.pdf