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Old 08-25-2013, 08:25 PM   #1
will.jackson
Junior Member
 
Location: Australia

Join Date: Aug 2012
Posts: 9
Default 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
http://computationalgenomicsiicb.blo...ing-cegma.html

http://korflab.ucdavis.edu/datasets/...ructions_1.txt

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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bioinfomatics, bugs, cegma, genewise, installation info

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