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Breakdancer installing problem

Hi guys

I am trying to install breakdancer on my opensuse distro. When I run make I receive the following error:

[ 14%] Built target boost-libs
[ 15%] Performing build step for 'samtools-lib'
make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Errore 2
make[1]: *** [CMakeFiles/samtools-lib.dir/all] Errore 2
make: *** [all] Errore 2
salvo@linux-t9bq:~/breakdancer/build> su -x "make clean"
su: opzione non valida -- "x"
Try 'su --help' for more information.
salvo@linux-t9bq:~/breakdancer/build> su -c "make clean"
Password:
salvo@linux-t9bq:~/breakdancer/build> su -c "make"
Password:
[  1%] Creating directories for 'boost-libs'
[  3%] Performing download step (verify and extract) for 'boost-libs'
-- verifying file...
     file='/home/salvo/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
-- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
-- extracting...
     src='/home/salvo/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
     dst='/home/salvo/breakdancer/build/vendor/boost/boost-src'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[  5%] No patch step for 'boost-libs'
[  7%] No update step for 'boost-libs'
[  8%] Performing configure step for 'boost-libs'
Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
Detecting Python version... 2.7
Detecting Python root... /usr
Unicode/ICU support for Boost.Regex?... not found.
Generating Boost.Build configuration in project-config.jam...

Bootstrapping is done. To build, run:

    ./b2

To adjust configuration, edit 'project-config.jam'.
Further information:

   - Command line help:
     ./b2 --help

   - Getting started guide:
     http://www.boost.org/more/getting_started/unix-variants.html

   - Boost.Build documentation:
     http://www.boost.org/boost-build2/doc/html/index.html

[ 10%] Performing build step for 'boost-libs'
[ 12%] No install step for 'boost-libs'
[ 14%] Completed 'boost-libs'
[ 14%] Built target boost-libs
[ 15%] Creating directories for 'samtools-lib'
[ 17%] Performing download step (verify and extract) for 'samtools-lib'
-- verifying file...
     file='/home/salvo/breakdancer/vendor/samtools-0.1.19.tar.gz'
-- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
-- extracting...
     src='/home/salvo/breakdancer/vendor/samtools-0.1.19.tar.gz'
     dst='/home/salvo/breakdancer/build/vendor/samtools'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 19%] No patch step for 'samtools-lib'
[ 21%] No update step for 'samtools-lib'
[ 22%] Performing configure step for 'samtools-lib'
Building samtools, build log at /home/salvo/breakdancer/build/vendor/samtools/build.log
[ 24%] Performing build step for 'samtools-lib'
make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Errore 2
make[1]: *** [CMakeFiles/samtools-lib.dir/all] Errore 2
make: *** [all] Errore 2

Any suggestion?

Thanks for the help!

softwareerror
• 5,699 views • link
updated by Ram Ram • written by salvocamiolo • salvocamiolo

Quick question: Why are you using su for make?

• 0 views • link
written by Ram Ram

That was just a try. Since I got the same error by running just make I tried also running make with super user.

• 0 views • link
updated by Ram Ram • written by salvocamiolo • salvocamiolo

make usually never requires super user permissions. su make can prove troublesome. Could you maybe try installing samtools-lib first? May I ask what OS+version you're using?

• 0 views • link
written by Ram Ram

Thanks for the reply! I am running opensuse 12.2

• 0 views • link
updated by Ram Ram • written by salvocamiolo • salvocamiolo

I'd suggest installing samtools independently and editing the makefile to point to the installed samtools. Instructions from the manual:

.. open 'Makefile' in the 'cpp' directory, redirect '-I/gsc/pkg/bio/samtools/samtools-0.1.6/' to the place you installed your samtools. Then 'make' again, in which case you generate your own binary, which will overwrite the downloaded one.

• 0 views • link
written by Ram Ram

Did you follow the install instructions?

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updated by Ram Ram • written by nnutter nnutter

Hi there,

Yes I followed those instructions and get the error upon trying the make step.

• 0 views • link
updated by Ram Ram • written by salvocamiolo • salvocamiolo

1 answer

Ok Guys, I thing I sorted it out. The installing instructions generated the error I reported on opensuse 12.2.

I then downloaded the cpp/perl package from sourceforgenet. In order to compile the cpp part I had to change the path of the samtools package as suggested by RamRS (thanks for that). Moreover compiling failed again. I had to add also the flag -lpthread in the Makefile in order to make it work.

For the perl part the script did not work straight away because of some module missing. I had to install the following modules from CPAN:

Now everything seems to work fine.

Thanks everyone for your useful suggestions!

• 0 views • link
updated by Ram Ram • written by salvocamiolo • salvocamiolo

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