Ruby :: Kappa :: Installation

Information regarding Kappa
http://psilambda.com/

Installation on Ubuntu 10.10
- Download Jockey from https://launchpad.net/jockey
- To build it you need python-distutils-extra at https://launchpad.net/python-distutils-extra
$ cd  python-distutils-extra-2.22
$ ./setup.py build
$ sudo ./setup.py install


In Jockey the ../setup.py is giving errors
$ sudo apt-get install python-encutils

Tryptophan biosynthesis pathway

Enzymes present in Tryptophan biosynthesis pathway.

1. Anthranilate synthase
2. Anthranilate PR-transferase
3. PR-anthranilate isomerase
4. Indole-3-glyserol phosphate synthase
5. Trp synthase
6. Tryptophan aminotransferase

Tryptophan synthase beta chain
Tryptophan synthase alpha chain
Tryptophanase
COG0134 Indole-3-glycerol phosphate synthase
COG0133 Tryptophan synthase beta chain
COG0159 Tryptophan synthase alpha chain
COG3033 Tryptophanase

Library check

TO check for libraries needed for the package

$ ldd rmblastn 
    linux-vdso.so.1 =>  (0x00007fff5b9e4000)
    libz.so.1 => /lib/libz.so.1 (0x00007f7e7c416000)
    libdl.so.2 => /lib/libdl.so.2 (0x00007f7e7c212000)
    libpcre.so.0 => not found
    libnsl.so.1 => /lib/libnsl.so.1 (0x00007f7e7bff7000)
    libpthread.so.0 => /lib/libpthread.so.0 (0x00007f7e7bdda000)
    libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f7e7bac5000)
    libm.so.6 => /lib/libm.so.6 (0x00007f7e7b842000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f7e7b62b000)
    libc.so.6 => /lib/libc.so.6 (0x00007f7e7b2a7000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f7e7c63c000)

This tells you that libpcre.so.0 library is missing.

MEGAN :: Install :: Execute

URL: http://www-ab.informatik.uni-tuebingen.de/software/megan
The MEGAN package can be downloaded from (http://www-ab.informatik.uni-tuebingen.de/data/software/megan/download/welcome.html)

$ wget http://www-ab.informatik.uni-tuebingen.de/data/software/megan/download/V3_9/MEGAN_unix_3_9.sh

Mac :: MySQL

URL: http://dev.mysql.com/downloads/
> MySQL Community Server
> Select Platform: Mac OS X
> Download Mac OS X ver. 10.6 (x86, 64-bit), DMG Archive


Double-click on dmg
- enter password whenever required
- double-click on mysql-5.1.50-osx10.6-x86_64.pkg, MySQLStartupItem.pkg, MySQL.prefPane
- open ~/.bash_login, and enter the information.

export PATH="/usr/local/mysql/bin/:$PATH"

- Now check for MySQL installation.

$ mysql --version

Pre :: parameters

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Mac :: Ruby :: Gem :: Rails

To install Ruby

curl -O ftp://ftp.ruby-lang.org/pub/ruby/1.8/ruby-1.8.7-p72.tar.gz
tar xzvf ruby-1.8.7-p72.tar.gz
cd ruby-1.8.7-p72
./configure --enable-shared --enable-pthread CFLAGS=-D_XOPEN_SOURCE=1
make
sudo make install
cd ..

To install Gem

curl -O http://production.cf.rubygems.org/rubygems/rubygems-1.3.7.tgz
tar zxvf rubygems-1.3.7.tgz
cd rubygems-1.3.7
sudo ruby setup.rb