Help with bambus

[roshanbernard]

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  ;then mkdir /usr/home/bambus-2.33 ;fi
if  ;then mkdir /usr/home/bambus-2.33/bin ;fi
if  ;then mkdir /usr/home/bambus-2.33/lib ;fi
if  ;then mkdir /usr/home/bambus-2.33/doc ;fi
for i in src doc ;do cd $i ; make install; cd .. ;done
make: 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: 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: Leaving directory `/home/rosh/bambus-2.33/src/IO'
make: Entering directory `/home/rosh/bambus-2.33/src/DotLib'
cp DotLib.pm /usr/home/bambus-2.33/lib/
make: Leaving directory `/home/rosh/bambus-2.33/src/DotLib'
make: 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: ***  Error 1
make: Leaving directory `/home/rosh/bambus-2.33/src/TIGR_Foundation_CC'
make: 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: ***  Error 1
make: Leaving directory `/home/rosh/bambus-2.33/src/grommit'
make: Leaving directory `/home/rosh/bambus-2.33/src'
make: 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: 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

[Yifang Tan]