Installing on linux

  • Nobody/Anonymous

    Can you please tell me how to install this on linux  system

    • Nobody/Anonymous


      installing Staden Package on Linux (redhat Fedora Core 4)
      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 is a replacement for sequencher, and it is free.

      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. go to the menu Desktop, system settings, security level, and disable selinux completely.
         2. reboot your computer.
         3. 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 library.
         4. as root, type yum -y update
         5. 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)
         6. 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
         7. cd io_lib-1.9.0
         8. ./configure
         9. 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.
        10. make
        11. make install

        12. 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
        13. cd staden-linux-1-6-0

        14. less
            in the staden 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

            the packages I had to check if i had were:

            * tcl (tested with 8.4.6)
            * tk (tested with 8.4.6)
            * itcl (tested with 3.2.1)
            * iwidgets (tested with 4.0.1)
            * zlib (tested with 1.2.2)
            * libpng (tested with 1.2.7)

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

        16. 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

        17. 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

        18. 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


        19. reboot your machine

      That's it. you have saved the cost of sequencher.

  • Nobody/Anonymous


  • James Bonfield

    James Bonfield - 2011-03-02

    There are prebuilt binaries in 2.0.0b8 for linux, which should work on most systems.

    However if you want to compile from sources then the instructions above are a reasonable start, albeit now a bit out of date. With the latest source tarball there is no longer a requirement to use itcl/itk/iwidgets which makes a huge difference in the ease of compilation. All 2.x versions using gnu autoconf too so you can use ./configure for both io_lib and staden now. 1.6.0 was indeed a royal PITA to build.

    Your step 10 about /usr/local is misleading too. Just do "./configure -prefix=/some/path" and it'll install into /some/path instead. It's entirely up to you where you wish to place things.

    Finally, you should never have to reboot! Just install it and run.  You may need to bring up new terminal windows if you want changes to your login files to take affect, but that's about it. (Or logout / login again.)


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