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  • #16
    I do that you tell me, but when I wrote ./configure the last line have a error

    Code:
    $ ./configure
    checking build system type... i686-pc-linux-gnu
    checking host system type... i686-pc-linux-gnu
    checking for gcc... gcc
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking how to run the C preprocessor... gcc -E
    checking for g++... g++
    checking whether we are using the GNU C++ compiler... yes
    checking whether g++ accepts -g... yes
    configure: error: you must configure in a separate build directory
    and make

    Code:
    $ make
    Makeconfig:85: sysdeps/../config.make: No such file or directory
    The GNU C library has not been configured.
    Run `configure' to configure it before building.
    Try `configure --help' for more details.
    make: Failed to remake makefile `sysdeps/../config.make'.

    Comment


    • #17
      Originally posted by Daniel Fernandez View Post
      I do that you tell me, but when I wrote ./configure the last line have a error

      Code:
      $ ./configure
      checking build system type... i686-pc-linux-gnu
      checking host system type... i686-pc-linux-gnu
      checking for gcc... gcc
      checking for suffix of object files... o
      checking whether we are using the GNU C compiler... yes
      checking whether gcc accepts -g... yes
      checking for gcc option to accept ISO C89... none needed
      checking how to run the C preprocessor... gcc -E
      checking for g++... g++
      checking whether we are using the GNU C++ compiler... yes
      checking whether g++ accepts -g... yes
      configure: error: you must configure in a separate build directory
      and make

      Code:
      $ make
      Makeconfig:85: sysdeps/../config.make: No such file or directory
      The GNU C library has not been configured.
      Run `configure' to configure it before building.
      Try `configure --help' for more details.
      make: Failed to remake makefile `sysdeps/../config.make'.
      You should find both libraries in your Ubuntu repos; have a look at the links I sent, in which one you wil have to search ...

      If you really want to compile on your own, create an extra build dir:

      mkdir build
      cd build
      ../src/configure --help

      or whatever ...

      Comment


      • #18
        Well, when I run the tgicl, the first cluster have more than 1700 reads (and these are assembled in more than 200 contigs) and the rest have less than 100 reads.

        I only run: tgicl AlpEST.fasta

        I check the tgicl.cfg, may be here is the problem. I thought the tgicl compared with all Gene Index Database from TIGR by default, or I can wrote the database (all mammals for example)

        -----------------------
        # do not perform all-vs-all search, but search DB_FILE against
        # TARGET_DB_FILE instead. Stops after the pairwise hits are generated.
        # TARGET_DB_FILE =
        -----------------------

        Comment


        • #19
          Originally posted by Daniel Fernandez View Post
          Well, when I run the tgicl, the first cluster have more than 1700 reads (and these are assembled in more than 200 contigs) and the rest have less than 100 reads.

          I only run: tgicl AlpEST.fasta

          I check the tgicl.cfg, may be here is the problem. I thought the tgicl compared with all Gene Index Database from TIGR by default, or I can wrote the database (all mammals for example)

          -----------------------
          # do not perform all-vs-all search, but search DB_FILE against
          # TARGET_DB_FILE instead. Stops after the pairwise hits are generated.
          # TARGET_DB_FILE =
          -----------------------
          Not sure what you are trying to accomplish ... if you just want to cluster and assemble your sequences you did it the right way. Maybe you want to alter a few parameters?

          Comment


          • #20
            TGICL installation

            Originally posted by sklages View Post
            1. I thought you have commented out the DB_FILE entry in tgicl.cfg? Then it should work as intented, "tgicl AlpEST.fasta"



            hth,
            Sven
            Hello,

            I have been trying to make TGICL work. I get the same error as Daniel Fernandez, after commented out the DB_FILE entry in tgicl.cfg, when I try

            $ tgicl test.fasta

            Use of :locked is deprecated at .... /perl5/TGI/DBDrv.pm line 36.
            tgicl (test.fasta) finished on machine
            in /test, without a detectable error.

            Seems to work for Daniel Fernandez, but not for me. Any idea? Or any alternative to TGICL? Thanks!

            Comment


            • #21
              Originally posted by Kate.W View Post
              Hello,

              I have been trying to make TGICL work. I get the same error as Daniel Fernandez, after commented out the DB_FILE entry in tgicl.cfg, when I try

              $ tgicl test.fasta

              Use of :locked is deprecated at .... /perl5/TGI/DBDrv.pm line 36.
              tgicl (test.fasta) finished on machine
              in /test, without a detectable error.

              Seems to work for Daniel Fernandez, but not for me. Any idea? Or any alternative to TGICL? Thanks!

              What is not working? What are you expecting? The message about ':locked' is just a (perl) warning, not an error.

              And, alternatives? What kind of data do you have? What do you want to do?

              Sven

              Comment


              • #22
                Hi Sven,

                Thnaks for your reply! Sorry I pasted the wrong message. So I got the "locked" warning message when I manually insert the fasta file in the config file :

                DB_FILE = My.fasta

                So doing this managed to make to program work, with a warning message.

                When I commented the previous line by doing the following :

                # DB_FILE =

                and then, inside the folder where the fasta file is, type :

                $ tgicl My.fasta

                I get the following :
                Use of :locked is deprecated at /usr/share/perl5/TGI/DBDrv.pm line 36.
                Error: cannot find input file ''

                That's what my problem really is. Sorry for the confusion.

                I am merging several RNA-seq assemblies. So I have this huge file with multiple isoforms that I want to cluster...

                Comment


                • #23
                  Originally posted by Kate.W View Post
                  $ tgicl My.fasta

                  Error: cannot find input file ''
                  Is this error message complete? I can only see one ".

                  What does 'ls -l My.fasta' spit out?

                  Sven

                  Comment


                  • #24
                    $ ls -l My.fasta

                    -rw-r--r-- 1 userk userk 287940826 Oct 10 17:18 My.fasta

                    Comment


                    • #25
                      Originally posted by sklages View Post
                      Is this error message complete? I can only see one ".

                      Sven
                      Yes it is the only error message I get.

                      Comment


                      • #26
                        OK, next step, how does your config look like?

                        Comment


                        • #27
                          Originally posted by sklages View Post
                          OK, next step, how does your config look like?
                          ubuntu 12.04
                          16 cpu
                          > 100 Gigs of Ram

                          Is that what you're asking?

                          Comment


                          • #28
                            No, I was asking for the tgicl.cfg file. But OK .. after years of abstinence I have downloaded and installed current TGICL 2.1 on my Ubuntu 12.04 (64bit) notebook :-)

                            After reading a few lines in
                            perldoc tgicl
                            I found pretty fast, that the program has to be called with the parameter '-F':

                            -F <fasta_db> the EST file in fasta format.
                            I just successfully clustered a small sanger dataset (7600 seqs) this way.

                            If you want to get rid of the warning for your TGICL installation, just add
                            no warnings 'deprecated';
                            to DBDrv.pm.

                            TGICL is not suited for huge (sanger) datasets IMHO; there is no active development.

                            An alternative may be (also for sanger) wcdest (http://code.google.com/p/wcdest/); that's what we were using some years ago after we ran into problems with TGICL. But it is just a clusterer; you still need an assembler and will still need some scripting.
                            You may also want to have a look at MIRA assembler for *assembling* EST datasets; it is not a clustering tool, but an assembler.

                            But there may be others.

                            hth,
                            Sven

                            Comment


                            • #29
                              Thanks a lot Sven!

                              Comment


                              • #30
                                Hi,
                                I was having the same problem and I did all those steps.
                                But now,when I run tgicl :

                                tgicl -F teste.fasta

                                this appear in console:

                                not available in PATH!

                                This could be something wrong with environment variable? I'm confused.

                                Thanks.

                                Comment

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