[AMOS-help] Help needed with bambus installation

[Roshan <ros...@ya...>]

hi,



i am using ubuntu 10.10 OS....and i am trying to install Bambus 2.33.



i have installed Amos and all other required file for the installation.But i am getting following error.



when i give command 'make all' it gives me this message





if [ ! -d /usr/home/bambus-2.33 ] ;then mkdir /usr/home/bambus-2.33 ;fi

if [ ! -d /usr/home/bambus-2.33/bin/ ] ;then mkdir /usr/home/bambus-2.33/bin ;fi

if [ ! -d /usr/home/bambus-2.33/lib/ ] ;then mkdir /usr/home/bambus-2.33/lib ;fi

if [ ! -d /usr/home/bambus-2.33/doc/ ] ;then mkdir /usr/home/bambus-2.33/doc ;fi

for i in src doc ;do cd $i ; make install; cd .. ;done

make[1]: Entering directory `/home/rosh/bambus-2.33/src'

for i in goBambus.pl; do /bin/sed 
"s,^\#!/usr/local/bin/perl,\#!/usr/local/bin/perl," $i | /bin/sed 
"s,^\(my\)*[ ]*\$BAMBUS_BASE.*,\1 \$BAMBUS_BASE = 
\"/usr/home/bambus-2.33\";," > /usr/home/bambus-2.33/bin/`expr $i : 
'\(.*\)\.pl$'`; done

for i in IO DotLib TIGR_Foundation_CC grommit ;do cd $i ; make install; cd .. ;done

make[2]: Entering directory `/home/rosh/bambus-2.33/src/IO'

for i in bacEnd.pl detective.pl printScaff.pl xml2grommit.pl catXML.pl 
untangle.pl; do /bin/sed 
"s,^\#!/usr/local/bin/perl,\#!/usr/local/bin/perl," $i | /bin/sed 
"s/^\(use DBI.*\)/\#\1/" | /bin/sed "s,^\(my\)*[ ]*\$BAMBUS_BASE.*,\1 
\$BAMBUS_BASE = \"/usr/home/bambus-2.33\";," > 
/usr/home/bambus-2.33/bin/`expr $i : '\(.*\)\.pl$'`; done

make[2]: Leaving directory `/home/rosh/bambus-2.33/src/IO'

make[2]: Entering directory `/home/rosh/bambus-2.33/src/DotLib'

cp DotLib.pm /usr/home/bambus-2.33/lib/

make[2]: Leaving directory `/home/rosh/bambus-2.33/src/DotLib'

make[2]: Entering directory `/home/rosh/bambus-2.33/src/TIGR_Foundation_CC'

g++ -D_HAS_GETOPT -c -o FileSystem.o FileSystem.cc

FileSystem.cc: In static member function ‘static bool FileSystem::isCreatableFile(const char*)’:

FileSystem.cc:58: error: invalid conversion from ‘const char*’ to ‘char*’

make[2]: *** [FileSystem.o] Error 1

make[2]: Leaving directory `/home/rosh/bambus-2.33/src/TIGR_Foundation_CC'

make[2]: Entering directory `/home/rosh/bambus-2.33/src/grommit'

g++ -Wl -L../TIGR_Foundation_CC/ -o grommit grommit.o -L. -lgraph -lTigrFoundation

/usr/bin/ld: cannot find -lTigrFoundation

collect2: ld returned 1 exit status

make[2]: *** [grommit] Error 1

make[2]: Leaving directory `/home/rosh/bambus-2.33/src/grommit'

make[1]: Leaving directory `/home/rosh/bambus-2.33/src'

make[1]: Entering directory `/home/rosh/bambus-2.33/doc'

cp BAMBUS.README /usr/home/bambus-2.33/doc

cp Manual.html /usr/home/bambus-2.33/doc

cp xml2grommit.README /usr/home/bambus-2.33/doc

cp scaffold.dtd /usr/home/bambus-2.33/doc

cp evidence.dtd /usr/home/bambus-2.33/doc

cp -r Manual_files /usr/home/bambus-2.33/doc

make[1]: Leaving directory `/home/rosh/bambus-2.33/doc'

cp -r lib/* /usr/home/bambus-2.33/lib

chmod -R a+rx /usr/home/bambus-2.33/bin







could u please tell me, how do i go about this..I have folllowed all the
 instructions given in manual and also i found some info in 
'Instructions for scaffolding MIRA 454 contigs using 454 

paired-end data and BAMBUS' pdf file written by gregory harhay. i did 
all the necessory changes.But i am stil not able to resolve the issue.



I have invested weeks on this.. can anyone help me out..



regards



roshan