Log in

No account? Create an account

Previous Entry | Next Entry

Staden Package is a piece of bioinforamtics software mostly written in C.

It is primarily used for tasks such as gene sequencing and single nucelotide polymorphism finding, but the various programs in it can be used for many things. version 1.6.0 is capable of reading 454 Life Sciences pyrophosphate sequencing data (pyrosequencing) from current file formats (will be upgraded when this changes). It also comes with extensive documentation.

It's opensource and it's free (as in beer).

To install it on linux, you need to know how to handle your package management system, and how to set shell variables. A good guide is SAMS publishing Teach yourself fedora in 24 hours.

On the other hand, you could do what I want to do when I get enough cash and buy a mac, where a one click installer will do all this crap for you.

Staden is also available for windowsxp.

well, for the linux install:

  1. Edited To Add: Activate the wheel group! it will come in handy later.
  2. go to the menu Desktop, system settings, security level, and disable selinux completely.
  3. reboot your computer.
  4. if you are using atrpms, disable the repository by finding the [atrpms] entry in your yum.conf or atrpms.repo file and adding the flag enabled=0 at the bottom. - this will avoid having your totem-devel package complain later. while you're there, disable any non-bioinformatics 3rd party repository.
  5. as root, type yum -y update
  6. go to the staden home page at sourceforge and get the io_lib source code release (io_lib-1.9.0.tar.gz in my case) and the linux staden package binary release (staden-linux-1-6-0.tar.gz)
  7. go to the directory where you've put the io_lib-1.9.0.tar.gz file and tar zvxf io_lib-1.9.0.tar.gz
  8. cd io_lib-1.9.0
  9. ./configure
  10. now I fell asleep in the lecture when they tell you why linux has a /usr/local directory. Does anybody know? Anyway, I found that I have to run grep -r \/local | tee io_lib_local.txt and read through the resulting io_lib_local.txt file. where ever I see an instance of /usr/local or such, i change it back to /usr (eg /usr/local/lib becomes /usr/lib). This is especially important in the make file as it will be looking for libraries and include files which are in /usr/lib in /usr/local/lib otherwise.
  11. make
  12. make install
  13. Edited to add: You may have to copy the contents of /usr/local/bin to /usr/bin if that's where some executibles get installed.
  14. now change directory back to where you put the staden-linux-1-6-0.tar.gz and tar xzf staden-linux-1-6-0.tar.gz
  15. cd staden-linux-1-6-0

  16. less README.build
    in the staden README.build readme file, there will be some dependencies. use rpm -q <packagename> to determine if you don't have them. if you don't use yum -y install <packagename> to install them

    After using yum, my package versions were

    * tcl tcl-8.4.9-3
    * tk tk-8.4.9-3
    * itcl itcl-3.3-0.3.RC1.fc4
    * iwidgets iwidgets-4.0.1-3.fc4
    * zlib zlib-
    * libpng libpng-1.2.8-2

    Edited to add: You will also have to install compat-libf2c-32
    * compat-libf2c-32 compat-libf2c-32-3.2.3-47.fc4

  17. believe it or not, you're almost done. cd ..

  18. you may have to sudo or become root to move the staden-linux directory to someplace where you'd expect to find programs that are part of your system.
    I chose to
    mv staden-linux-1.6.0 /bin/staden

  19. now staden-linux will have a few references to /usr/local. some of these are compiled into binaries.
    At this point I caved in and decided to make a few symbolic links

    ln -s /usr/bin/wish /usr/local/bin/wish4.0
    ln -s /usr/bin/wish /usr/local/bin/wish

  20. now you have to tell your computer where to find the staden programs.
    add the following lines to your /etc/profile

    ##For Staden
    export STADENROOT='/bin/staden/staden-linux-1-6-0';
    . /bin/staden/staden-linux-1-6-0/staden.profile


  21. reboot your machine

That's it. Now you don't have to buy sequencher.

Edited to add: If ever you get into trouble running a command, type
export STADEN_DEBUG=1 at the commandline and then type the command again.

If you're missing libraries then you can add them with yum.


Latest Month

May 2019
Powered by LiveJournal.com
Designed by Naoto Kishi