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running staden 1.6 under amd64 debian linux

2007-08-29
2013-04-18
  • Hi Developers, Hi James

    (Greetings from Heidelberg)

    Shortly to the 1.7 linux binary version:
    when trying to run pregap4 the following error occurs:
    load libpregap4.so => couldn't load file "libpregap4.so": libpregap4.so: cannot open shared object file: No such ...
    This seems to be unsolvable by me.

    Now to the 1.6 linux binary:

    After some hard work and problems with our amd64 debian linux I finally ended up with a running staden 1.6.
    The main problem is that there are not enough 32bit compatibility packages available for the 32 bit staden which is provided on sourceforge. This is what I have done to get it running:
    First you need the ia32-libs package  (apt-get install ia32-libs) for general compatibility of 32bit apps in the 64bit environment.
    The following 32bit packages are installed on my system, but I can not say if they are needed by staden:
      ia32-libs lib32asound2 lib32gcc1 lib32ncurses5 lib32stdc++6 lib32z1 libc6-i386
    From a i386 system where libg2c0-dev (fortran runtime) is installed copy /usr/lib/libg2c.so into staden-linux-1-6-0/lib/linux-binaries and create a symbolic link named libg2c.so.0 to it:
      cd staden-linux-1-6-0/lib/linux-binaries
      ln -s libg2c.so libg2c.so.0
    In staden-linux-1-6-0/lib create a symbolic link named tcl8.4 or tcl8.3 (depending on your tcl version):
      cd staden-linux-1-6-0/lib
      ln -s tcl tcl8.4
    The following applications fom the staden-linux-1-6-0/linux-bin directory needed to be patched because they set the MACHINE variable wrong:
      copy_reads gap4 pregap4 staden_help trev
    Comment out the lines with MACHINE= and set MACHINE to 'linux':
      #MACHINE=`uname -srm | s...
      MACHINE='linux'
    Do the same in
      staden-linux-1-6-0/staden.login
      staden-linux-1-6-0/staden.profile
    if you need them.
    (Another solution maybe use of the linux32 command, I did not try)
    The library libiwidgets.so is still missing but gap4 runs without it.

    Thats it (if I did not forget something).

    A very important information to solve problems is to set the STADEN_DEBUG environment variable, e.g. (csh):
      setenv STADEN_DEBUG 1
    or (bash:)
      export STADEN_DEBUG=1
    This gives the needed error messages to get the information of missing libraries.
    If you think that the library where staden says "libxxx.so file not found" is there, it is propably the 64bit library which can not be loaded into a 32bit application.

    In the 1.7 version there are a lot more missing 32bit libraries:
      libcurl.so libidn.so libssl.so libcrypto.so libgssapi_krb5.so libkrb5.so
      libk5crypto.so libcom_err.so libkrb5support
    copying them from a i386 machine did help until the libpregap4.so problem occured.

    Building staden from source made a lot of trouble (with 1.5 and 1.6) so I did not tried with the 1.7 version. Maybe I try later and describe solutions again here. But for now I am satisfied with the running 1.6 32bit binaries.

    I hope I can help other peoples with my report.

    With best regards to James, Roger and the other volunteers working hard the the staden package,

    Oli

    /////////////////////////////////
    Oliver Heil

    DKFZ - Deutsches Krebsforschungszentrum
    Im Neuenheimer Feld 515
    69120 Heidelberg

    Tel    (+49 6221) / 42 4708

    Email  o one_dot heil an_at dkfz a_dot de
    WWW    www.dkfz.de
    /////////////////////////////////

     
    • sghignone
      sghignone
      2007-08-31

      Hi all,
      thanks Olivier for the nice summary.
      I would like to add some notes from my experience on setting up the package (1.7) on my ubuntu freisty amd64.

      >The following applications fom the staden-linux-1-6-0/linux-bin directory needed to be patched because they set the MACHINE variable >wrong:
      >copy_reads gap4 pregap4 staden_help trev

      I solved this issue just renaming the directories ./linux-bin and ./lib/linux-binaries in linux-x86_64-bin and linux-x86_64-binaries, respectively.

      >The library libiwidgets.so is still missing but gap4 runs without it.
      Right, but also don't forget to modify the ./lib/iwidgets links that comes with the package, to point to the iwidgets folder uon your machine.

      >in the 1.7 version there are a lot more missing 32bit libraries:
      >libcurl.so libidn.so libssl.so libcrypto.so libgssapi_krb5.so libkrb5.so 
      >libk5crypto.so libcom_err.so libkrb5support
      >copying them from a i386 machine did help until the libpregap4.so problem occured.

      If a i386 machine is not available, those libraries could be retrieved using the getlibs script I found in the ubuntu forum; you can find more details here

      http://ubuntuforums.org/showthread.php?t=474790

      (you don't have to spread links in your system...;-)

      Hope this could help too.

      Cheers from turin, Italy

      Stefano Ghignone
      Istituto per la Protezione delle Piante, Sez. Torino - CNR
      c/o Dpt. Plant Biology, University of Turin
      V.le P.A. Mattioli, 25
      I-10125 Turin
      Italy
      Phone:    +39 011 6705951
      Fax:      +39 011 6705962
      e-mail:   stefano.ghignone_at_unito.it

      http://www.bioveg.unito.it
      http://www.sppadbase.com
      - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

       
    • Hi,

      I just want to thank you for the help. I have been able to install staden 1.6 in a ubuntu feisty amd64. Thank you very much for giving a detailed explanation on how to do it.

      Jose Blanca