I'm in trouble of converting with tg_index

  • Koji

    Koji - 2013-02-08


    I couldn't make a gap5 db file from .bam file with using tg_index.

    First, I installed .msi windows package to XP machine. finished without problem. The .msi file is staden-windows-2.0.0b9.msi.

    I could just find tg_index.bin file, not executable on windows, so I renamed the file into tg_index.bin.exe because the tg_index.bin.exe file can be found in the former version package, 2.0.0b8.

    Then I ran the tg_index.bin.exe with -b option.

    After that, at any trial, I only receive a message telling "libmisc.dll was not found".

    Do you have any suggestion to me?


  • Anonymous - 2013-03-19

    Dear all,

    I also have the same problems regard to tg_index:

    $ ./tg_index
    ./tg_index: error while loading shared libraries: libgap5.so: cannot open shared object file: No such file or directory

    However, I could find libgap5.so in /home/jingjing/software/staden-2.0.0b9-src/build.myhost/lib.

    Can anyone give me some suggestion about how to fix this problem?



  • James Bonfield

    James Bonfield - 2013-03-20

    This looks like you've compiled from source, but not done a "make install".  Do a make install (possibly after reconfiguring using a -prefix option) and then run from the install directory.

    Regarding the windows one, it looks like the tg_index program is missing a wrapper to make it work properly unless you have bash installed. Ie it was shipped with the unix wrapper instead of the windows one. We're fixing the interface in the next release so you don't need to be in DOS to launch tg_index (which the current version you did, even with the working wrapper). My apologies for this error.

  • James Bonfield

    James Bonfield - 2013-03-20

    I forgot to mention, the easy workaround for the lack of the wrapper is to copy all the .dll files from <install_root>/lib/staden/*.dll to the bin directory (or append the lb/staden to your PATH environment variable). Tg_index.bin.exe will then launch, but it still needs DOS.


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