Staden and MacOSX

darked90
2004-11-24
2013-04-18
  • darked90
    darked90
    2004-11-24

    Hello,

    - what else is needed apart from staden-macosx-1-5-3.tar.gz to have functional Staden installation on MacOSX?

    darked

     
    • James Bonfield
      James Bonfield
      2004-11-25

      In theory, nothing. However there's always the chance that I forgot something when I packaged it up.

      I do not have my own MacOS X machine so I haven't tested it on a "vanilla" machine with no additional tools installed.

      Do you get errors running it?

      James

       
    • darked90
      darked90
      2004-12-06

      Hello,

      I gather that installing Xwindow/xterm is a must -> downloading and unpacking  staden-macosx-1-5-3.tar.gz is not enough (clicking on gap4 opens a text editor).

      Some info on Staden and MacOSX it is here:
      https://dna.biotech.wisc.edu/Staden.html

      but somehow I failed to spot "how to install" on these sites:

      https://sourceforge.net/projects/staden/
      http://staden.sourceforge.net/

      Install info for any unix used to be in $STADENROOT/README but it is not there anymore.

      Also  previous versions on OS X are not compatible with Apple provided X11 targeting the latest MacOSX version.

      Greetings

      darked

       
    • James Bonfield
      James Bonfield
      2004-12-07

      Ah yes you need X11, although I was under the belief that it is now installed by default on MacOS X. I haven't got my own MacOS X box though so I cannot really test things. You do not specifically need "xterm" if it's what I think it is (the X11 terminal program), but xterm is typically supplied with any decent X11 distribution anyway. When I last actually sat at a MacOS X system (10.1 I believe) you could run the programs from a standard terminal (ie bash) window, as long as you'd previously started X11.

      Certainly remotely logging in to a MacOS X system and running Gap4 (etc) with DISPLAY set to a linux box works fine (as that's how I built and tested it). I can't see how this would be incompatible with DISPLAY set to localhost too, unless Apple have done something very strange with their X11 setup.

      As for Staden Package installation notes, realistically there's nothing to do! Just unpack the tar file and run the $STADENROOT/macosx-bin/gap4 program (for example).

      If you wish to directly run the command-line tools (extract_seq, vector_clip, hetins, etc) then you'll need to set the STADENROOT environment variable and source the staden.login (csh users) or staden.profile (sh users). Eg:

      STADENROOT=/some/path
      export STADENROOT
      . $STADENROOT/staden.profile

      You do NOT need to manually set the PATH as described in the url you listed. The staden.profile will do this for you. This is also NOT necessary if all you want to run are the GUI tools (gap4, pregap4, spin and trev).

       
    • any solution to removing this from my opening terminal shell, which by the way has killed my fink!

      tcsh: /usr/ebiotools/staden/staden.login: No such file or directory.

      until i find an answer to this annoying problem i cannot recommend anyone installing the staden package on panther. if you uninstall it messes up things.

       
    • Dear James Bonfield

      2004-12-07 you wrote:

      **I haven't got my own MacOS X box though so I cannot really test things.**

      so WHY did you release a Mac OSX package that has just messed up not only my last two days but is completely annoying when I read that you release your package in such a cavalier way, in disregard to the damage you cause Mac OSX users.

      can you solve for me the problem that now my needed 'fink' is not working!! and every Terminal Window opens with a missing file message:

      <font color="green">tcsh: /usr/ebiotools/staden/staden.login: No such file or directory.</green>

      the cause of which is buried somewhere in what is untested and released code!

      what to do??

      prof. p

       
    • James Bonfield
      James Bonfield
      2004-12-13

      You need to check your facts before launching on a rant, incase you end up looking silly!

      In this case, note that ebiotools is NOTHING to do with me or with the Staden Package. They happen to have bundled (a now out of date) copy of the Staden Packge in their system, but this was done without any consultation or even knowledge from me.

      The Staden Package installation available from this site is nothing other than a gzipped tar file. It is not ebiotools, it is not fink, it is not an apple bundle, it IS just a bunch of files in an archive. It will NOT wreck your terminal window!

      Now I know I *should* do it all the correct apple way, but to be honest I do not have the equipment or time to do this. Perhaps you wish to purchase me my own apple iBook so I can better support MacOS X?

      Like I explained above, if you just want to do what 99% of people do (ie pregap4, gap4, spin, trev) then you do not need to do anything at all except start up X11 before running the appropriate program.

      James