BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics. It is open source and widely used in the bioinformatics community. Bioperl provides software modules for many of the typical tasks of bioinformatics programming. These include:
yum stands for 'Yellowdog Updater Modified'. YellowDog Linux is a rpm based distribution of Linux created for the ppc architecture. Fedora Core took up this package manager as of Fedora Core 1.
Finding files on unix and linux Find is an extremely useful command for finding files. It searches based a specified condition at a specified directory and descends into all subdirectories of the specified directory. You must always specify a directory and a condition. Files offers lots of very powerful options which allow you to precisely define your search criteria. Following are the most useful ones:
This article shows some techniques of manipulating data in an array. To keep it simple, let's start by looking how we can remove quotes from a variable. To remove a character, we can replace it with nothing using str_replace() function.
$a = "'pineapple'"; $b = '"guava"'; print "$a $b\n"; $a = str_replace("'","",$a); $b = str_replace('"','',$b); print "$a $b\n";
This results in:
'pineapple' "guava" pineapple guava
Consider this code
The tar command is used to collate collections of files into one larger file.
Creating archives Suppose we have directory xdir containing many files, we use the following command to archive them into one file.
tar -cvf x.tar xdir
This command would archive the directory xdir and its contents into a file called x.tar. The extension '.tar' is used by convention to indicate tar files.
To create an archive and apply gzip to compress the archive,
My system is configured as follows:
Web root = c:/www Apache version = 2.2.6 Apache installation directory = c:/Apache2.2/
Download ActivePerlDownload windows MSI version from http://www.activestate.com/store/activeperl/download
Install ActivePerlDouble click on the downloaded file to install it. By default it installs at c:/Perl.
Test InstallationTo test whether the installation was successfull, we need to create and run a hello world file.
When using Apache and Perl on Windows, it is common to get Couldn't spawn child process error. The solution is very simple. Verify that you have using the correct directive at the top of your file.
should be changed to
I am assuming that your perl.exe file is located at c:/Perl/bin/perl.exe. If it is at another address, use that address.
Here I describe installation and configuration of Apache. These instructions should be valid for version 2.0.x and above.
SCP allows file to be copied to, from, or between different hosts using ssh for data transfer.
Copy files from remote computer to a local computer:
$ scp firstname.lastname@example.org:~/somefile.txt /home/local/directory
Copy files from local computer to remote computer:
$ scp /home/local/directory/somefile.txt email@example.com:~/
Copy a directory 'dir' from local computer to remote computer
$ scp -r /home/local/dir firstname.lastname@example.org:~/
SCP uses Triple-DES by default. To change cipher, use the following command:
Mathematical formulas can be written in HTML without installing special fonts, MathML, or inserting images. This article shows how this can be done.