Breakdancer installation problem

[opulcy97]

Hi,

I was trying to install the latest version of breakdancer tool (breakdancer-1.1.2_2013_03_08). However, the compilation with cpp version failed. It gave me the following error:


/usr/bin/ld: cannot find -lbam
collect2: ld returned 1 exit status
make: *** [all] Error 1

Can anyone please tell me how to overcome the problem? I got stuck with it for quite a while.

Many thanks in advance.

[GenoMax]

Looks like you are missing libbam.a that is included in Samtools.

Simple instructions to install that library are included in "Installing SAMtools" on this page: http://cufflinks.cbcb.umd.edu/tutorial.html

[opulcy97]

Thanks GenoMax. It worked like a charm.

[binlangman]

Error while installing breakdancer

I installed breakdancer by running the following command:
cd breakdancer-1.1.2/cpp
make
But erros occurred:

g++ -g -Wall -O2 -I/Users/kchen3/pkg/samtools/samtools-0.1.6 BreakDancerMax.cpp AlnParser.cpp Poisson.cpp -o breakdancer-max -lm -lz -L/Users/kchen3/pkg/samtools/samtools-0.1.6 -lbam
In file included from /usr/local/gcc/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/backward/strstream:52:0,
from BreakDancerMax.h:3,
from BreakDancerMax.cpp:1:
/usr/local/gcc/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/backward/backward_warning.h:33:2: Warning：#warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
In file included from BreakDancerMax.cpp:1:0:
BreakDancerMax.h:17:17: fatal error：sam.h：No such file or directory
compile interrupted。
In file included from AlnParser.cpp:1:0:
AlnParser.h:17:17: fatal error：sam.h：No such file or directory
compile interrupted。
In file included from Poisson.h:1:0,
from Poisson.cpp:1:
AlnParser.h:17:17: fatal error：sam.h：No such file or directory
compile interrupted。
make: *** [all] error 1

What should I do to install breakdancer?

[GenoMax]

Did you compile samtools on this computer yourself? You may be trying to use a very old version of samtools (v.0.1.6, if the file path reflects the correct version in your command line). Latest samtools is at v0.1.19 (http://sourceforge.net/projects/samt...d?source=files). I suggest getting that version and compiling it before trying to install breakdancer.

[jugpreet]

Breakdancer make file error

Hi guys,

I am trying to install latest version of breakdance (1.1.2) and getting following error. does anyone know whats going on here. Thanks in Advance.


In file included from /usr/include/c++/4.4/backward/strstream:47,
from BreakDancerMax.h:3,
from BreakDancerMax.cpp:1:
/usr/include/c++/4.4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
In file included from BreakDancerMax.cpp:1:
BreakDancerMax.h:17:17: error: sam.h: No such file or directory
BreakDancerMax.h:18:17: error: bam.h: No such file or directory
BreakDancerMax.h:19:19: error: ksort.h: No such file or directory
BreakDancerMax.h:20:19: error: khash.h: No such file or directory
In file included from BreakDancerMax.h:21,
from BreakDancerMax.cpp:1:
AlnParser.h:23: error: ‘bam1_t’ was not declared in this scope
AlnParser.h:23: error: ‘b’ was not declared in this scope
AlnParser.h:23: error: expected primary-expression before ‘format’
AlnParser.h:23: error: expected primary-expression before ‘alt’

[GenoMax]

Have you installed samtools?

[jugpreet]

yes...i did....it seems like there is a problem in the C++ compiler

[louis_ly]

Hi everyone,
Hi,

I was trying to install the latest version of breakdancer tool (breakdancer-1.1.2_2013_03_08). However, the compilation with cpp version failed. It gave me the following error:

~/software/breakDancer/breakdancer-1.1.2/cpp$ make
g++ -g -Wall -O2 -I/Users/kchen3/pkg/samtools/samtools-0.1.6 BreakDancerMax.cpp AlnParser.cpp Poisson.cpp -o breakdancer-max -lm -lz -L/Users/kchen3/pkg/samtools/samtools-0.1.6 -lbam
In file included from /usr/include/c++/4.8/backward/strstream:51:0,
from BreakDancerMax.h:3,
from BreakDancerMax.cpp:1:
/usr/include/c++/4.8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
#warning \
^
In file included from BreakDancerMax.cpp:1:0:
BreakDancerMax.h:17:17: fatal error: sam.h: No such file or directory
#include "sam.h"
^
compilation terminated.
In file included from AlnParser.cpp:1:0:
AlnParser.h:17:17: fatal error: sam.h: No such file or directory
#include "sam.h"
^
compilation terminated.
In file included from Poisson.h:1:0,
from Poisson.cpp:1:
AlnParser.h:17:17: fatal error: sam.h: No such file or directory
#include "sam.h"
^
compilation terminated.
make: *** [all] Error 1


Is there anyone can help me? Thanks.

[yueluo]

Try installing a newer version of samtools.

http://cole-trapnell-lab.github.io/cufflinks/getting_started/#installing-the-sam-tools