configuring amos3.1 with Celera (CA8.1)

[akshaya.ramesh]

I am trying to view my .asm file generated by the Celera assembler and plan on using the toAmos_new for the same. To use this script, I need to configure amos using the --with-CA-dir function. I have looked at this thread (http://sourceforge.net/p/amos/mailman/message/29093782/) and realized that I have followed all steps but no luck (I do not think the author had success either).

These are the steps that I followed:

./configure --with-qmake-qt4=/usr/local/lib/qt-4.8.4/bin/qmake NUCMER=/media/raid10/programs/MUMmer3.23/nucmer DELTAFILTER=/media/raid10/programs/MUMmer3.23/delta-filter SHOWCOORDS=/media/raid10/programs/MUMmer3.23/show-coords BLAT=/media/raid10/programs/blat --with-CA-dir=/media/raid10/archive_programs/wgs-8.1/Linux-amd64/

and I still get

checking for CA... yes
checking whether CA works... no

When I look at the following lines from the config file:

CA_DIR="$amos_ca_dir"
CA_LDADD="$amos_ca_dir/lib/libCA.a"
CA_CXXFLAGS="-I$amos_ca_dir/../src -I$amos_ca_dir/../src/AS_MSG -I$amos_ca_dir/../src/AS_UTL -DAMOS_HAVE_CA"
# All variables are defined, report the result

I realize that amos is loking for libCA.a (which exists and the correct path), src (which exists and correct path), AS-MSG and AS-UTL (which also exists and has the correct path). I did compile Celera from source-code so that amos could access the src/ directory (the binaries lack the src/ directory)

Does anyone have any idea or suggestions that can help me fix this problem? Or even an alternate package that I could use to view the .asm files. I did post in the amos-help mailing list and have not heard back.

Thank you in advance for your help.

Best,
Akshaya