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How to get Staden running on Mac OS X 10.3.9

2006-08-30
2013-04-18
  • Hi folks,

    i have Mac OS X 10.3.9 running with X11 installed. I downloaded the Staden 1.6.0 package and put it in the Applications folder. But if i try to start gap4, pregap4, trev or spin form the macosx-bin folder nothing happens. What do i have to do get those programms working?

    Greets.

     
    • This instruction requires that you have admin authorities to your mac.

      ###Put Staden dirctory in /Applications
      ###Open the terminal. Print the following and Press return.

      sudo mv staden-macosx-1-6-0 /Applications

      ###Start a text editor and edit the .bashrc file as follows. Return after each of the three lines.

      nano -w .bashrc
      STADENROOT=/Applications/staden-macosx-1-6-0; export STADENROOT
      . $STADENROOT/staden.profile

      ###save changes to .bashrc by printing ctrl-o and close nano by printin ctrl-x

      ###Now, Staden is installed.

      ###Open the xterm (X11 window)
      ###Preferrably, cd 'yourself' to the directory where your sequence files are.
      ###In the xterm, type pregap4 or gap4 or whatever Staden application you want to start.
      ###Note, that Phred and Phrap are not part of the Staden package.

       
    • 4 steps to make sure Staden will run on your Mac OS 10.4

      1. bash shell
      This manual assumes that bash is your default shell, which is easy to check and change.

      (Applications/Utilities/NetInfo Manager -> click on users, then find you account. In the lower pane is "shell". If necessary edit it to /bin/bash. Exit and Restart your computor.
      (THANKS to www.askdavetaylor.com)

      2. X11
      Make sure you have X11 installed. You find it in the Applications/Utilities.

      I have had difficulties when installing X11 on different machines. The successful way turned out to be:

      "Insert your MacOS Install DVD (Xcode tools Install disk 1, not the OS X Install Disk 1) into the drive and when the window pops up, SCROLL DOWN and select "Optional Installs". Click a couple of 'Continue' until you reach 'Custom Install' . Click on the 'Applications' arrow, check X11, and install it.

      (THANKS Peter!)

      3. Installing Staden.
      The following Staden install manual requires that you have admin rights for your account.

      a) Download and unpack Staden.
      b) Put it in the Applications folder
      c) Start/Open your Terminal
      d) Edit the .bashrc file by opening it in a texteditor, e.g.  nano, like this
      nano -w .bashrc
      e) When you have started nano and opened the .bashrc file, print the following two lines:
      STADENROOT=/Applications/staden-macosx-1-6-0; export STADENROOT
      . $STADENROOT/staden.profile
      f) exit (ctrl-x) nano (and save on your way out). (Check that your changes were saved by re-opening the file in nano (nano .bashrc).

      g)Exit the Terminal

      4) Running Staden

      a) Open the xterm (by clicking on X11)
      (a-2) If you don't have bash as your shell (see step 1 above), type bash first (and strike return))
      b) run the Staden application you like  by printing its command, e.g.:
      pregap4
      c) Don't forget to check how your mouse's right-click works in X11

       
    • Additional comment to the entry above (2006-09-15 15.12)

      It assumes that the Staden files are put in a directory named "staden-macosx-1-6-0" in /Applications