Install Staden in UBUNTU 9.0

  • Nobody/Anonymous

    Hi, I am new in linux world and I would like to know if anyone has any guide to install the Staden package 1-7-0 in UBUNTU 9.0.
    Thanks a lot

    • James Bonfield

      James Bonfield - 2009-07-31

      I'm working on improving the build environment to make it far easier to compile from scratch on newer machines.

      However easiest is just to try the linux binaries and see if they work. They may, or may not, depending on packages you have installed. Likely you'll need the g2c (g77?) package to get some bits working.

      • Istvan Nagy

        Istvan Nagy - 2009-08-05

        I would like to apply some repeat masking in pregap4.
        (Staden Package 1.7 on Linux)
        I downloaded RepeatMasker and the repeat libraries. etc.
        However, to install and run RepeatMasker properly, one needs
        either WU-Blast, Cross_match or DeCypher.
        None of them are promptly available. I should probably try to obtain a
        licence for Phred/Phrap/Consed in order to install Cross_match, but until
        now I was happy with Gap4.
        The "Tag_repeats" module of Pregap4 would be probably a suitable alternative,
        as I would like to mask just one or two types of repeats.
        The "Tag_repeats" module is described in several places in different Staden Package documentations (e.g. in the Staden Mini Manual), but this module is not installable in the newer Pregap4 versions.
        I checked some older Staden distributions as well, but none of them contained a "tag_repeats.p4m"  file.
        Is there any way to install this module ?

    • Nobody/Anonymous

      Thank you

      I wonder if you can send me what are the packages / libraries that I need to properly work of the Staden Package. With regard to the library you mention (G2C), that is in my linux. Apart from a small guide, as discussed in the previous message, how can I install the Staden Package.
      I also want to know what is the cost to acquire the license of the Staden Package to work with it in a company. There is a possibility that next year I start work in a biotech and if I gain experience with Staden, the company will implements it in my daily duties.
      I am very grateful and hope to hear from you soon

      Best regards
      Eitel Peltzer Meschini

      PD: would appreciate if we could stay in touch by e-mail. My personal e-mail is

      • James Bonfield

        James Bonfield - 2009-08-06

        The Staden Package is now free to all - so no need to acquire a licence.

        I'm not sure what you miss to get the binaries working for you. Setting STADEN_DEBUG environment variable (to anything should work, but I normally use 1) will give some diagnostics of libraries it's attempting to load. Perhaps it will become obvious.

        I've been trying to tackle this from a different direction though as I've been working a lot recently on making the package more integrated with the typical linux distribution, meaning that I no longer need to include a dedicated version of the tcl, tk, itcl, itk, iwidgets, png, etc libraries. Instead it uses the system ones.

        What this means is two fold - firstly it should be FAR easier to compile from source and for linux vendors to package up the programs for a specific linux distribution release; secondly however it may be trickier to provide generic binaries that work on many systems (but let's face it - they've been error prone for years).

        Ubuntu 9 is infact one of the systems I've been testing it with. I started on a server based virtual machine and started installing bits that were needed to compile. It's not worth listing them here until I package up a new source release, but that should be coming soon, hopefully with binaries to follow.

    • Nobody/Anonymous

      this is good. I keep trying to see how it can operate. If you need someone to proof your beta, I would be happy to try

    • Nobody/Anonymous

      The first beta test of the 2.0 source distribution is available for download now. There's still lots of things lacking (eg proper documentation for gap5), but I mainly wanted to make it available as a test of the new build system and installed directory layout.


    • Nobody/Anonymous

      OK, I´ll download it and try. But now I have an other problem with the Windows version: After selecting the files and modules of interest and starting with the analysis, at the end of the prosses  arrogates the following message:
      - Report from 'Enter assembly (into Gap4)' --
      ERR: Failed to change directory to C: / Documents and Settings / epeltzer / My Documents / GATS / ErGPAT / Run Folder-8-6-09-5-44-PM/ErGPAT.assembly.
      ERR: "could not change working directory to" C: / Documents and Settings / epeltzer / My Documents / GATS / ErGPAT / Run Folder-8-6-09-5-44-PM/ErGPAT.assembly ": no such file or directory "
      ERR: Aborting enter assembly.
      The ERGPAT is a personal file in the Run caperta ...
      What is the problem and how I fix it?
      Thank you very much again

    • Istvan Nagy

      Istvan Nagy - 2009-08-14


      I just realized that I am with my question on repeat masking at a wrong place here.
      (This is probably the reason that I did not get answer ...)

      Anyway, when being here, I would like to react to the original question of this topic:
      (I just managed to install Staden package for a collegaues Macbook with Linux Mint 7 (basically the same as Ubuntu 9)).

      Some hints, if  the Staden programs will not start after  install:
      1. There are some libraries that have newer versions in the current Linux distribution and the Staden programs look for older versions.
      Making the following symbolic link will help:

      /usr/lib/    =>   /usr/lib/
      /usr/lib/ =>   /usr/lib/
      /usr/lib/ =>/usr/lib/
      (From the command line: < ln -s /usr/lib/  /usr/lib/ >, etc.)

      2. After making these, most probably trev, spin and pregap4 will start, but gap4 not. In this case, the  reason is that a file is missing. You need to install the libg2c0 package.
      (In Debian based systems:  < apt-get install libg2c0 >

    • Nobody/Anonymous

      Thanks for your advice, I´ll try it!!!

    • Nobody/Anonymous

      Here I'm again with informatic problems, but this time from another point of view. While this is not the right forum, but I hope you can help in any way. I wonder if there are any script, in perl or another language, that allows me to compare two nucleotide databases and give me back as a result what is not in common between them, that is, the new sequences that may be in a database  and not  in the other. I hope you have understood and can help me.
      Thank you very much

    • ben

      ben - 2009-09-06


      I'd like to add to the advice from Istvan.

      I agree with the symlinking idea, but I would think that linking to the versionless libraries would make it work further into the future:

      /usr/lib/ => /usr/lib/
      /usr/lib/ => /usr/lib/
      /usr/lib/ =>/usr/lib/

      I also had to install the iwidgets4 Ubuntu package, and then manually remove the bad symlink that is included with the 1.7.0 distribution:

      staden-linux-x86-1-7-0/lib$ rm iwidgets
      staden-linux-x86-1-7-0/lib$ ln -s /usr/share/tcltk/iwidgets4.0.1 iwidgets

      Also, I had to install the libstdc++5 package. I was then able to run gap4.

      I noticed in the debug file that something wasn't right, however:
      load => couldn't load file "": cannot open shared object file: No such file or directory

      This didn't seem to stop it starting up, but I don't like errors.


      • James Bonfield

        James Bonfield - 2009-09-07

        The binary distributions are badly aging and showing signs of version dependency hell, as many of you are seeing!

        However feel free to give the beta release a try, from source. I tested this on a 32-bit ubuntu 9 server and put the list of packages I had to install in the news posting. See for more details.

        While not ideal for everyone, it's a start down a different road with the dependencies being explicitly listed as package requirements to be installed on the system itself by the sysadmin rather than bundled in a tarball with the source/binaries. This may make it trickier to install as non-root (as it'll need someone to install the dependencies), but it is far more maintainable and my hope is if it becomes easy enough then the community can easily support prebuilt binaries on a variety of platforms. (I can perhaps do a few myself via vmplayer images.)

        Anyway, I'm seeking feedback on the source compilation route so will be happy to answer queries or assist where possible.

    • James Bonfield

      James Bonfield - 2009-09-07

      Oh a quick PS - the "couldn't load file "": cannot open shared object file: No such file or directory" error is bogus, and one reason why the STADEN_DEBUG=1 environment isn't on by default.

      When loading packages into Tcl I always attempt to add both tcl source paths and also to load a compiled dynamic library into memory. Some packages simply don't have the latter (eg iwidgets) as they're pure tcl packages. It's not bright enough to realise this and just reports an error, which is normally glossed over unless STADEN_DEBUG is set.


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