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  • #16
    Thanks for your mails. Here come a post of en email send by Michael Thon from the AMOS help-list which solved our common problem:

    To compile AMOS on 64 bit Ubuntu linux, I first had to install gcc-4.1 and then set these two environment variables:

    export CC=gcc-4.1
    export CXX=g++-4.1

    Unfortunatly have still have a problem, despite the compilation seems to be OK. I can't execute executables, as example bank-transact, I receive a command not found. AMOS makes me crazyyyyyy

    Comment


    • #17
      I put some specific instructions for how to install AMOS on the wiki.
      For Ubuntu: http://sourceforge.net/apps/mediawik...u_installation
      For Fedora: http://sourceforge.net/apps/mediawik...a_installation

      That should solve your problem agroster.

      Also, some of the issues mentioned in this topic have been resolved in the development (CVS) version of AMOS. So, I suggest installing the development version. Again, check the links I provided above for specific instructions.

      Comment


      • #18
        I'm working on Ubuntu 10.04 x64. I had difficulties with compiling AMOS as well. Now all works. Things I did:

        1. Installed gcc-4.1 and g++-4.1 as Mathgon advised and then set the env.vars:

        Code:
        sudo apt-get install gcc-4.1 g++-4.1
        export CC=gcc-4.1
        export CXX=g++-4.1
        2. Followed tutorial of F-flow - downloaded CVS instead of stable version, and compiled is as in the tutorial.

        Everthing went smoothly
        Cheers

        Comment


        • #19
          I'm having some issues with AMOS compilation.
          When I do make:
          Code:
          g++ -DHAVE_CONFIG_H -I. -I../..  -I../../src/Common -I../../src/AMOS
          -I../../src/GNU -I../../src/GNU   -g -O2 -MT shotgunSim.o -MD -MP -MF
          .deps/shotgunSim.Tpo -c -o shotgunSim.o shotgunSim.cc
          shotgunSim.cc:24:25: error: gsl/gsl_rng.h: No existe el fichero o el
          directorio 
          shotgunSim.cc:25:29: error: gsl/gsl_randist.h: No existe el fichero o el
          directorio
          shotgunSim.cc: In function ‘int main(int, char**)’:
          shotgunSim.cc:354: error: ‘gsl_rng’ no se declaró en este ámbito
          shotgunSim.cc:354: error: ‘rng’ no se declaró en este ámbito
          shotgunSim.cc:354: error: ‘gsl_rng_mt19937’ no se declaró en este ámbito
          shotgunSim.cc:354: error: ‘gsl_rng_alloc’ no se declaró en este ámbito
          shotgunSim.cc:384: error: ‘gsl_rng_uniform_int’ no se declaró en este ámbito
          shotgunSim.cc:384: error: ‘gsl_ran_gaussian’ no se declaró en este ámbito
          shotgunSim.cc:393: error: ‘gsl_rng_uniform_int’ no se declaró en este ámbito
          shotgunSim.cc:395: error: ‘gsl_ran_gaussian’ no se declaró en este ámbito
          shotgunSim.cc:440: error: ‘gsl_ran_gaussian’ no se declaró en este ámbito
          shotgunSim.cc:518: error: ‘gsl_rng_uniform’ no se declaró en este ámbito
          make[3]: *** [shotgunSim.o] Error 1
          make[3]: se sale del directorio `/opt/AMOS/src/Sim'
          make[2]: *** [all-recursive] Error 1
          make[2]: se sale del directorio `/opt/AMOS/src'
          make[1]: *** [all-recursive] Error 1
          make[1]: se sale del directorio `/opt/AMOS'
          make: *** [all] Error 2
          The sentence "no se declaró en este ámbito" means "was not declared in this scope" and "No existe el fichero o el directorio " is the usual "No such file or directory" or "File not found".

          Help!!!

          Comment


          • #20
            Hello,

            I just installed AMOS on a computer after not doing so for months. I just wanted to point out that instead of doing it the way Eskeww proposed, it's quite easy to do it as lechu502 posted.

            In my case as the department blocks several ports, I couldn't do the cvs checkout but I was able to download all the code from: http://amos.cvs.sourceforge.net/viewvc/amos/ Just click on "download GNU tarball". Then it's just a matter of following the instructions that lechu502 linked to: http://sourceforge.net/apps/mediawik...u_installation

            Greetings,
            Leonardo
            L. Collado Torres, Ph.D. student in Biostatistics.

            Comment


            • #21
              Hey guys,

              I have installed amos cvs on my ubuntu 10.04 64. I followed the tutorial of F-flow. The only problem is that when I try to lunch hawkeye from the console it says that the program does not exist/command not found. I guess the link was not made.
              If I look in the /usr/local/bin folder the hawkeye, or any other tool from amos, has an X on it and says it was not found in the path ./bin.
              If I run it directly from the amos folder the program opens. But every time I try to import an ace file it says it could not find toAmos. Even tho if I run toAmos alone it runs...

              I think it all has to do with the linking process. How should I repair this?

              Comment


              • #22
                Hawkeye install on Ubuntu 12

                If anyone is around that may know the answer to this please let me know. My compile ends with this error everytime and I am not sure who to fix it:

                /usr/bin/ld: cannot find -lexpat
                collect2: ld returned 1 exit status
                make[3]: *** [toAmos_new] Error 1
                make[3]: Leaving directory `/home/brandon/amos-3.1.0/src/Converters'
                make[2]: *** [all-recursive] Error 1
                make[2]: Leaving directory `/home/brandon/amos-3.1.0/src'
                make[1]: *** [all-recursive] Error 1
                make[1]: Leaving directory `/home/brandon/amos-3.1.0'
                make: *** [all] Error 2

                I'm on a 64bit Ubuntu 12 build with QT4...

                Comment


                • #23
                  I had a similar error and I downloaded and installed expat first

                  Download Expat XML Parser for free. Fast XML parser library in C. PLEASE NOTE that we are in the process of moving to GitHub: https://github.com/libexpat/libexpat This is James Clark's Expat XML parser library in C. It is a stream oriented parser that requires setting handlers to deal with the structure that the parser discovers in the document.


                  And it went away. I had to use a --prefix during the expat configure statement.

                  But now that I'm trying to write a script to install this, I'm having problems. I'm wondering if I forgot another step, so let me know if you figure it out.

                  Comment


                  • #24
                    Hello,

                    I was wondering if anyone has installed AMOS3.1 (on a 64-bit Linux system) and is still running into issues with the installation. I think I have installed Qt5 correctly, but do you think I should install Qt4 instead? I am not sure how you decide which version of Qt I should choose?
                    I have been trying to install AMOS for more than a week and have absolutely no success. If anyone has had some success, could you run through the commands. Any suggestions would be greatly appreciated.

                    Thanks,
                    Akshaya

                    Comment


                    • #25
                      Originally posted by akshaya.ramesh View Post
                      Hello,

                      I was wondering if anyone has installed AMOS3.1 (on a 64-bit Linux system) and is still running into issues with the installation. I think I have installed Qt5 correctly, but do you think I should install Qt4 instead? I am not sure how you decide which version of Qt I should choose?
                      I have been trying to install AMOS for more than a week and have absolutely no success. If anyone has had some success, could you run through the commands. Any suggestions would be greatly appreciated.

                      Thanks,
                      Akshaya
                      This page is indicating that there is support for Qt4 so you should perhaps install that.

                      What exact errors are you getting?

                      Comment


                      • #26
                        Originally posted by GenoMax View Post
                        This page is indicating that there is support for Qt4 so you should perhaps install that.

                        What exact errors are you getting?
                        I just got it to work.

                        I had to add #include <getopt.h> in the src/Align/find-tandem.cc file (http://seqanswers.com/forums/showthr...highlight=AMOS) and
                        install expat. That did the trick.
                        Last edited by akshaya.ramesh; 05-10-2013, 05:53 PM.

                        Comment


                        • #27
                          Hi folks - not sure if this has already been addressed, but there is a known issue with AMOS 3.1.0 release and celera assembler 7.0 release. As someone mentioned this is fixed in the development branch.

                          Another solution to get AMOS 3.1.0 running with CA 7.0 is provided by Sergey Koren here and fixed my issues building AMOS.

                          Comment


                          • #28
                            Hi guys,

                            I have installed AMOS-3.1.0 in Ubuntu 12.04, it was ok, but when I tried to run goBambus2 it did not work. There were some mistakes that I have to change on the script (according to http://amos.git.sourceforge.net/git/...7bcd40;hb=HEAD
                            ). I continued editing the file until no error warning appeared on the command prompt.
                            Now, I am trying to check if Bambus runs ok, so I am using some example files from: http://www.ncbi.nlm.nih.gov/pubmed/21400694 and http://sourceforge.net/projects/amos/files/sample_data/, using KVP40 data. And now it says "mate pair info not present". So I do not know what I am doing wrong.

                            I would appreciate any help

                            Nadia

                            Comment

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