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  • #46
    If you have no tclConfig.sh or tkConfig.sh it's possible you miss a "-dev" package. I'm not sure how SUSE handles this, but on debian they split packages into run-time and development components.

    Eg from dpkg -l | grep tcl:

    Code:
    ii  itcl3                                       3.2.1-3.1                                [incr Tcl] OOP extension for Tcl - run-time files
    ii  tcl8.4                                      8.4.12-1.1                               Tcl (the Tool Command Language) v8.4 - run-time files
    ii  tcl8.4-dev                                  8.4.12-1.1                               Tcl (the Tool Command Language) v8.4 - development files
    I'd expect something similar to be true of SUSE, which may make life simpler than compiling from scratch.

    If I had to pin the problems on a specific package then I'd say it's somewhere in the itcl/itk/iwidgets area. The three are all from the same stable so it's hard to say which, but I'd imagine tcl itself to work fine. You can test this by manually editing your $STADENROOT/share/staden/etc/gap5rc file. You should see something to load Iwidgets (which in turn will pull in itcl/itk as a dependency). Most functionality will work without them - I can't recall which bit I needed it for now - so as a test to see if that's the cause of your conflict try commenting them out. Ie at the start of gap5rc edit it to:

    Code:
    #-----------------------------------------------------------------------------
    # Packages required
    #-----------------------------------------------------------------------------
    load_package tk_utils
    #if {[info commands tk] != ""} {
    #   package require Iwidgets
    #}

    Comment


    • #47
      I solved the problem.

      You were absolutely right as the actually installed itcl/itk/iwidgets packages had problems with my manually installed tcl/tk8.5.8 packages. So I made a rollback to version 8.5.2 , installed all devel-packages too, and everything works fine. Now I can test gap5 and especially its improved contig joining. Thanks!

      Jens

      Comment


      • #48
        After my first steps with gap5 and just reading about how to transform assembly projects from different ngs platforms and gap4, I wonder if it is a bug that I cannot create a new gap5 database. Or is it not implemented yet? The error message I get is "invalid command name 'open_db'". I'm able to open projects created with tg_index so the function seems to work. but I'm a bit confused at the moment.

        Comment


        • #49
          Apologies for that - I forgot it was even there (likely just ripped straight out of Gap4).

          You are correct that tg_index is currently the way to create new databases, or to append to existing ones. The File->New dialogue in gap5 shouldn't be there as I haven't implemented it within the GUI yet. Sorry about that.

          James

          PS. My current work has been focusing on fixing a whole raft of contig editing bugs, especially surrounding Undo. I plan on a new release soon(TM).

          Comment


          • #50
            No functioning samtools found

            Hello,

            Is anyone else getting this error when configuring Gap5?

            configure: WARNING: No functioning samtools found
            configure: WARNING: Gap5/tg_index will have reduced functionality

            I've got it to configure with all the other dependent libraries & originally I put --with-samtools=DIR (adding my home directory where I'd installed it) & got the above message.

            So then I got synaptic package manager to install samtools but get the same message.

            It seems to find samtools, but says that it is not functioning. I can use samtools on my computer so do not understand where I am going wrong.

            Can anybody help please?

            thanks alig

            Comment


            • #51
              AFAIR there must be a directory structure like this, e.g.,

              samtools/lib samtools/include
              and the samtools binary itself must be placed in 'samtools' (not in samtools/bin for example).

              You will see this if you look into the configure script.

              hth,
              Sven

              Comment


              • #52
                It's... complicated!

                The problem here is that samtools doesn't have an official make install target, so people who do install it tend to just copy over the binary to <some_package_root>/bin/samtools. We can try and specify that root via --with-samtools, but I need more than just the binary - infact I don't need the binary at all! Then there's the issue about include files. Do people bother to actually install them (normally not). If so, where? Eg should "sam.h" should be included via #include <sam.h>, #include <samtools/sam.h>, #include <sam/sam.h>, etc.

                The only logical conclusion I had with all of this is to not bother installing it at all. Instead unpack samtools, build (with -fPIC, see later), and then point gap5 configure at the samtools source tree where you just did the compilation. It's the only foolproof way of picking up the dependencies until a proper samtools installation mechanism exists.

                Regarding compilation, note that Gap5 makes use of the library - libbam.a. However it links this into Gap5 run-time libraries; libgap5.so infact. This is implemented as a Tcl plugin and so is a dynamic library that gets loaded at runtime. On many systems that means all code has to be compiled as "position independent code" so it can be moved around in memory. This is enabled via "-fPIC". Unfortunately samtools does not build using that by default as it's only interest is in created a static binary and library, not a dynamic one.

                The easiest way to fix this is to edit the samtools Makefile and add -fPIC to the CFLAGS line (before the # mark as everything after that is a comment).

                I suspect this is why the configure script is finding samtools directory but failing to consider it as a valid installation. Sorry it's all so complex.

                Comment


                • #53
                  Re: no functioning samtools when configuring gap5

                  Hi James,

                  Thank you very much for your quick reply. I had an earlier version of samtools which didn't have a Makefile to edit.
                  After downloading samtools-0.1.8 & editing the Makefile by adding -fPIC, then using --with-samtools=DIR with configure, it finds a functioning samtools.

                  Thanks a bunch, looking forward to using Gap5

                  alig

                  Comment


                  • #54
                    problems lauching gap5 and installing manual

                    Hi,
                    sorry me again.
                    I get the following message when try to launch gap5
                    couldn't read file "/home/neuro/Documents/Gap5/staden-2.0.0b7-src/gap5/../share/staden/tcl/gap5/gap.tcl": no such file or directory
                    Have tried to set STADENROOT in .bashrc file but doesn't help

                    Also cannot install gap5 manual as get following error when make unix

                    ! Font \circle=lcircle10 not loadable: Metric (TFM) file not found.
                    <to be read again>
                    \allocationnumber
                    \alloc@ ...ifnum \count 1#1 < #4\allocationnumber
                    =\count 1#1 \global \advan...
                    l.5802 \newdimen\circthick

                    ?
                    ! Emergency stop.
                    <to be read again>
                    \allocationnumber
                    \alloc@ ...ifnum \count 1#1 < #4\allocationnumber
                    =\count 1#1 \global \advan...
                    l.5802 \newdimen\circthick

                    No pages of output.
                    Transcript written on txiversion.log.

                    kpathsea: Running mktextfm lcircle10
                    /usr/share/texmf/web2c/mktexnam: Could not map source abbreviation for lcircle10.
                    /usr/share/texmf/web2c/mktexnam: Need to update ?
                    mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input lcircle10
                    This is METAFONT, Version 2.718281 (TeX Live 2009/Debian)

                    kpathsea: Running mktexmf lcircle10

                    ! I can't find file `lcircle10'.
                    <*> ...jfour; mag:=1; nonstopmode; input lcircle10

                    Please type another input file name
                    ! Emergency stop.
                    <*> ...jfour; mag:=1; nonstopmode; input lcircle10

                    Transcript written on mfput.log.
                    grep: lcircle10.log: No such file or directory
                    mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input lcircle10' failed to make lcircle10.tfm.
                    kpathsea: Appending font creation commands to missfont.log.
                    /usr/bin/texi2dvi: texinfo.tex appears to be broken, quitting.
                    make[1]: *** [manual.pdf] Error 1
                    rm manual.texinfo
                    make[1]: Leaving directory `/home/neuro/Documents/Gap5/staden_doc-2.0.0b1-src/manual'
                    make: *** [common] Error 2

                    any help gratefully appreciated
                    alig

                    Comment


                    • #55
                      tk_utils Error when make gap5

                      Hi,

                      I still cannot launch gap5 & really want to get on & use the program to view my Next Gen data.

                      When I type ./gap5 to launch it I still get
                      couldn't read file "/usr/local/staden-2.0.0b7-src/gap5/../share/staden/tcl/gap5/gap.tcl": no such file or directory

                      I'm also now getting an error when I run make

                      /usr/local/staden-2.0.0b7-src/build.linux/../tk_utils/misc.c:6:30: error: io_lib/traceType.h: No such file or directory
                      make[1]: *** [misc.o] Error 1
                      make[1]: Leaving directory `/usr/local/staden-2.0.0b7-src/build.linux/tk_utils'
                      make: *** [tk_utils] Error 2

                      Can anyone help me please

                      alig

                      Comment


                      • #56
                        Originally posted by alig View Post
                        Hi,

                        I still cannot launch gap5 & really want to get on & use the program to view my Next Gen data.

                        When I type ./gap5 to launch it I still get
                        couldn't read file "/usr/local/staden-2.0.0b7-src/gap5/../share/staden/tcl/gap5/gap.tcl": no such file or directory

                        I'm also now getting an error when I run make

                        /usr/local/staden-2.0.0b7-src/build.linux/../tk_utils/misc.c:6:30: error: io_lib/traceType.h: No such file or directory
                        make[1]: *** [misc.o] Error 1
                        make[1]: Leaving directory `/usr/local/staden-2.0.0b7-src/build.linux/tk_utils'
                        make: *** [tk_utils] Error 2

                        Can anyone help me please

                        alig
                        So there are two problems here. The first seems to be implying you're compiling it and then attempting to run in situ. You need to run configure with a --prefix option (or let it default to, umm, somewhere - probably /usr/local) and then do a "make install" after compiling. This will copy the compiled bits and tcl files out of the source tree and place them into a directory. Granted I should probably add something to allow running directly out of the build directory as it'd help me a lot too.

                        The second issue, with io_lib, is less clear. Did you install the staden io_lib library somewhere? Was this by compiling it yourself or by using some prepackaged distribution (eg via synaptic or yum)? If the latter, it's possible that you installed the binaries/libraries but not the development package that contains the header files (eg "io_lib/traceType.h" in this case). The configure script ought to spot this though - I'll investigate.

                        Finally, I've been reacting to the many issues people have with linking against samtools and iwidgets libraries and have now managed to rewrite the bits of code that depend on these. The next release should therefore have far fewer dependencies and be easier to build. The subversion (svn) copy has these features already if you want to try the bleeding edge release.

                        James

                        Comment


                        • #57
                          tk_utils Error when make gap5

                          Hi James,

                          Thank you for your quick response. I installed the dev package for staden io_lib using synaptic package manager. I now have a different error.

                          make install
                          mkdir -p /usr/local/lib/staden
                          mkdir -p /usr/local/bin
                          mkdir -p /usr/local/share/staden/etc
                          mkdir -p /usr/local/share/staden
                          mkdir -p /usr/local/share/staden/scripts
                          mkdir -p /usr/local/share/staden/tcl
                          mkdir -p /usr/local/share/doc
                          mkdir -p /usr/local/share/man
                          cp shlib.conf /usr/local/share/staden/etc
                          cp ../staden.profile /usr/local/share/staden
                          make JOB=install
                          make[1]: Entering directory `/usr/local/staden-2.0.0b7-src/build.linux'
                          cd Misc && make -f /usr/local/staden-2.0.0b7-src/build.linux/../Misc/Makefile -w BUILD=/usr/local/staden-2.0.0b7-src/build.linux SRC=/usr/local/staden-2.0.0b7-src/build.linux/../Misc SUBDIR=Misc install
                          make[2]: Entering directory `/usr/local/staden-2.0.0b7-src/build.linux/Misc'
                          cp /usr/local/staden-2.0.0b7-src/build.linux/lib/libmisc.so /usr/local/lib/staden
                          make[2]: Leaving directory `/usr/local/staden-2.0.0b7-src/build.linux/Misc'
                          cd tk_utils && make -f /usr/local/staden-2.0.0b7-src/build.linux/../tk_utils/Makefile -w BUILD=/usr/local/staden-2.0.0b7-src/build.linux SRC=/usr/local/staden-2.0.0b7-src/build.linux/../tk_utils SUBDIR=tk_utils install
                          make[2]: Entering directory `/usr/local/staden-2.0.0b7-src/build.linux/tk_utils'
                          cp /usr/local/staden-2.0.0b7-src/build.linux/lib/libtk_utils.so /usr/local/lib/staden
                          cp: cannot stat `/usr/local/staden-2.0.0b7-src/build.linux/lib/libtk_utils.so': No such file or directory
                          make[2]: *** [install] Error 1
                          make[2]: Leaving directory `/usr/local/staden-2.0.0b7-src/build.linux/tk_utils'
                          make[1]: *** [tk_utils] Error 2
                          make[1]: Leaving directory `/usr/local/staden-2.0.0b7-src/build.linux'
                          make: *** [install] Error 2

                          I have tried putting STADENROOT in my .bashrc file, but hasn't helped.

                          STADENROOT=/usr/local/staden-2.0.0b7-src
                          export STADENROOT

                          Any guidance would be greatly received

                          alig

                          Comment


                          • #58
                            Did the initial "make" work without errors? It looks like it's missing one of the things it should have just built.

                            Note that "make install" here doesn't automatically test whether the software have been fully built, and rebuild it if not (unlike many packages).

                            Comment


                            • #59
                              installing gap5

                              Hi,
                              Thank you for pointing me in all the right directions. I got confused and did make install after configure.
                              All good now, looking forward to using gap5
                              cheers alig

                              Comment


                              • #60
                                how search for unpadded positions in gap5

                                Hi,

                                I would like to search for unpadded positions in gap5 as none of my variant positions match up in gap5 as the search position box within edit contig view includes pads.

                                How do I search for an unpadded position in gap5?

                                Thanks

                                alig

                                Comment

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