Bambus:- Installation Error

Question

[ajaybioinfo]

Dear all,

i am new in the linux and want to install bambus standalone scaffolder but getting this error , please help me to solve this error so that i can make use of this software.,

or if you know any other contigs scaffolder which can do the scaffolding using the assembled contigs files and paired end data in fasta format kindly tell me your help will be highly appreciated in this regard.

Below is The error during the bambus installation

ajay@ajay ~/Desktop/scaffold/bambus-2.33 $ make

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

make[1]: Entering directory `/home/ajay/Desktop/scaffold/bambus-2.33/src'

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

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

make[2]: Nothing to be done for `all'.

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

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

make[2]: Nothing to be done for `all'.

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

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

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

ConfigFile.cc: In member function ‘void ConfigFile::parseConfig()’:

ConfigFile.cc:113:34: error: ‘strlen’ was not declared in this scope

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

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

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

g++ -I../TIGR_Foundation_CC/ -g -c grommit.cc

grommit.cc: In function ‘int main(int, char**)’:

grommit.cc:236:45: warning: format ‘%s’ expects type ‘char*’, but argument 3 has type ‘char (*)[1024]’

grommit.cc:317:5: error: ‘abort’ was not declared in this scope

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

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

make[1]: Leaving directory `/home/ajay/Desktop/scaffold/bambus-2.33/src'

make[1]: Entering directory `/home/ajay/Desktop/scaffold/bambus-2.33/doc'

make[1]: Nothing to be done for `all'.

make[1]: Leaving directory `/home/ajay/Desktop/scaffold/bambus-2.33/doc'

Thanks in advance Ajay

Answer 1

[fo3c]

It would seem that ConfigFile.cc needs an #include <cstring> at the top, and grommit.cc needs an #include <cstdlib>. If those lines are indeed present, you might be missing some headers, in which case you might want to check your g++ installation.

Answer 2

[ajaybioinfo]

Thanks a lot sir, for valuable suggestions. i have edited the necessary files which you have suggested. sir for you kind information i am installing this on umbuntu mint katya. after reading the suggestion from this MIRA manual (http://mira-assembler.sourceforge.net/docs/scaffoldingMIRABAMBUS.pdf) i have edited my files In Con5igFile.hh, Logger.hh,OptionResult.hh,Options.hh and rerun the make all command but still getting error regarding (invalid conversion from ‘const char’ to ‘char’ And g++ -Wl -L../TIGRFoundationCC/ -o grommit grommit.o -L. -lgraph-lTigrFoundation/usr/bin/ld: cannot find -lTigrFoundation)

Sir kindly help me out to solve this problem and also if possible suggest me some other scaffoding software which can do similar job like BAMBUS.

Please find below the error during installation:-

ajay bambus-2.33 # make all

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

make[1]: Entering directory `/home/ajay/Desktop/scaffold/bambus-2.33/src'

for i in IO DotLib TIGRFoundationCC grommit ;do cd $i ; make all; cd .. ; done

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

make[2]: Nothing to be done for `all'.

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

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

make[2]: Nothing to be done for `all'.

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

make[2]: Entering directory `/home/ajay/Desktop/scaffold/bambus-2.33/src/TIGRFoundationCC'

g++ -DHASGETOPT -c -o CategoryInformation.o CategoryInformation.cc

g++ -DHASGETOPT -c -o ConfigFile.o ConfigFile.cc

g++ -DHASGETOPT -c -o ConfigSection.o ConfigSection.cc

g++ -DHASGETOPT -c -o Exceptions.o Exceptions.cc

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

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

FileSystem.cc:58:60: error: invalid conversion from ‘const char’ to ‘char’

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

make[2]: Leaving directory `/home/ajay/Desktop/scaffold/bambus-2.33/src/TIGRFoundationCC'

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

g++ -I../TIGRFoundationCC/ -g -c grommit.cc

grommit.cc: In function ‘int main(int, char**)’:

grommit.cc:237:45: warning: format ‘%s’ expects type ‘char’, but argument 3 has type ‘char ()[1024]’

g++ -I../TIGRFoundationCC/ -g -c Node.cc

g++ -I../TIGRFoundationCC/ -g -c GrpNode.cc

g++ -I../TIGRFoundationCC/ -g -c GrpLink.cc

g++ -I../TIGRFoundationCC/ -g -c Edge.cc

g++ -I../TIGRFoundationCC/ -g -c GrpEdge.cc

g++ -I../TIGRFoundationCC/ -g -c Component.cc

g++ -I../TIGRFoundationCC/ -g -c GrpComponent.cc

g++ -I../TIGRFoundationCC/ -g -c GrpGraph.cc

ar -r libgraph.a Node.o GrpNode.o GrpLink.o Edge.o GrpEdge.o Component.o GrpComponent.o GrpGraph.o ar: creating libgraph.a

g++ -Wl -L../TIGRFoundationCC/ -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/ajay/Desktop/scaffold/bambus-2.33/src/grommit' make[1]: Leaving directory/home/ajay/Desktop/scaffold/bambus-2.33/src' make[1]: Entering directory /home/ajay/Desktop/scaffold/bambus-2.33/doc' make[1]: Nothing to be done forall'. make[1]: Leaving directory `/home/ajay/Desktop/scaffold/bambus-2.33/doc

Thanking you Ajay