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  • Problems with CEGMA dependency installation

    Hi everyone,
    I am having trouble installing wise2.2.3-rc7 for running CEGMA. This is the version that the authors of CEGMA recommend but I run into the following error when I run $make all


    (cd base ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --cflags glib-2.0`" libwisebase.a )
    make[1]: Entering directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/base'
    make[1]: `libwisebase.a' is up to date.
    make[1]: Leaving directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/base'
    (cd HMMer2 ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --cflags glib-2.0`" libhmmer.a )
    make[1]: Entering directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/HMMer2'
    make[1]: `libhmmer.a' is up to date.
    make[1]: Leaving directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/HMMer2'
    (cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --cflags glib-2.0`" libdyna.a )
    make[1]: Entering directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/dynlibsrc'
    make[1]: `libdyna.a' is up to date.
    make[1]: Leaving directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/dynlibsrc'
    (cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --cflags glib-2.0`" libdyna_glib.a )
    make[1]: Entering directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/dynlibsrc'
    make[1]: `libdyna_glib.a' is up to date.
    make[1]: Leaving directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/dynlibsrc'
    (cd external ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --cflags glib-2.0`" all )
    make[1]: Entering directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/external'
    (cd mott; make CC="gcc" CFLAGS="-c -O2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include " all)
    make[2]: Entering directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/external/mott'
    make[2]: Nothing to be done for `all'.
    make[2]: Leaving directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/external/mott'
    make[1]: Leaving directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/external'
    (cd models ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --cflags glib-2.0`" EXTRALIBS="" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all )
    make[1]: Entering directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/models'
    gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm
    dnal.o: file not recognized: File format not recognized
    collect2: ld returned 1 exit status
    make[1]: *** [dnal] Error 1
    make[1]: Leaving directory `/home/willj/10_260813_CEGMA/dependencies/wise2.2.3-rc7/src/models'
    make: *** [realall] Error 2

    I have already got over a few problems with the help of
    Installing CEGMA can be a bit of a challenge for most of the users including me! I had installed it earlier, but this time it really gave m...




    But can't seem to find anything on my current problem.

    Also, a lot of the help pages recommend changing a few lines in src/models/phasemodels.c but I don't see this file in src/models, has this been updated?

    Thanks very much

    Will

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