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Old 01-08-2012, 03:04 AM   #1
xxb0316
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Default breakdancer compilation help

I am a beginner for BreakDancer. When I downloaded the breakdancer (v1.3.5.1.zip) source file from https://github.com/genome/breakdancer/tags, I don't know how to compile properly these files to get the command 'breakdancer_max'. My working server is x86_64, Red Hat 4.4.5-6. Could any one help me? Thanks.
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Old 04-26-2012, 05:50 AM   #2
maria.b
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did you finally succeded to compile breakdancer? I really don't understand anything......
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Old 08-04-2015, 02:35 AM   #3
simobioinfo
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Hi,
I have problems in installing breakdancer.
I downloaded the zip file from sourceforce and decompressed it.
I found two suddirectories, perl and cpp.
I try to make in cpp directory but I'm not able to compile breakdancer.
Could anyone help me for this issue?
Thanks
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Old 08-04-2015, 03:50 AM   #4
GenoMax
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Quote:
Originally Posted by simobioinfo View Post
Hi,
I have problems in installing breakdancer.
I downloaded the zip file from sourceforce and decompressed it.
I found two suddirectories, perl and cpp.
I try to make in cpp directory but I'm not able to compile breakdancer.
Could anyone help me for this issue?
Thanks
What OS are you using? Post the error(s) that are generated after "make".
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Old 08-04-2015, 05:26 AM   #5
sklages
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Quote:
Originally Posted by simobioinfo View Post
Hi,
I have problems in installing breakdancer.
I downloaded the zip file from sourceforce and decompressed it.
I found two suddirectories, perl and cpp.
I try to make in cpp directory but I'm not able to compile breakdancer.
Could anyone help me for this issue?
Thanks
Why don't you read the docs?
INSTALL.md states:

Code:
    $ cd breakdancer
    $ mkdir build
    $ cd build

    $ cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
    ...
    -- Build files have been written to: .../breakdancer/build

    $ make
    ...
    Linking CXX executable ../../../../bin/breakdancer-max
    [100%] Built target breakdancer-max

    $ sudo make install
Change CMAKE_INSTALL_PREFIX as needed.

Last edited by sklages; 08-04-2015 at 05:47 AM. Reason: reduced code to relevant section
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Old 08-10-2015, 02:50 AM   #6
simobioinfo
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Hi,
I read documentation and the message error was:
[ 10%] Performing build step for 'boost-libs'
[ 12%] No install step for 'boost-libs'
[ 14%] Completed 'boost-libs'
[ 14%] Built target boost-libs
Scanning dependencies of target samtools-lib
[ 15%] Creating directories for 'samtools-lib'
[ 17%] Performing download step (verify and extract) for 'samtools-lib'
-- verifying file...
file='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
-- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
-- extracting...
src='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
dst='/root/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 /root/breakdancer/build/vendor/samtools/build.log
[ 24%] Performing build step for 'samtools-lib'
make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Error 2
make[1]: *** [CMakeFiles/samtools-lib.dir/all] Error 2
make: *** [all] Error 2

Can anyone help me to understand?
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Old 08-10-2015, 03:14 AM   #7
GenoMax
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Is the samtools source included in breakdancer otherwise you will need to download it and then put the file in /root/breakdancer/build/vendor/ directory (http://sourceforge.net/projects/samt...r.bz2/download).
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Old 08-10-2015, 04:15 AM   #8
simobioinfo
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So if understand you suggest me to:
-download samtools
-to put the tar.bz2 file into /root/breakdancer/build/vendor/ directory
and then?
Do I have to install it into that directory?
If yes. These steps are correct?
tar -jxvf samtools-0.1.19.tar.bz2
- $ cd samtools-0.1.19
- $ make
- $ export SAMTOOLS_ROOT=$(pwd)
- $ cd ..
Then:
cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
make
sudo make install.

Are these steps correct?
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Old 08-10-2015, 04:32 AM   #9
GenoMax
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That sounds right (if you are following the install document). Give it a try and see what happens.
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Old 08-10-2015, 04:40 AM   #10
simobioinfo
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in the /root/breakdancer/build/vendor/ directory I found a directory named samtools.
Do I have to remove it before to install samtools?
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Old 08-10-2015, 04:56 AM   #11
GenoMax
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What happens if you try to do the breakdancer install again?

BTW: What OS are you doing this on? When you cloned the source from github did you use the "--recursive" option since that is important as indicated in the INSTALL.md file.
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Old 08-10-2015, 06:27 AM   #12
simobioinfo
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I'm working with ubuntu.
I restart from the beginning.
I tried to install samtools but I failed.
I tried to put the tar.bz2 file into the vendor directory changing extension in tar.gz and launched the make command but I have had an error:
Scanning dependencies of target boost-libs
[ 1%] Creating directories for 'boost-libs'
[ 3%] Performing download step (verify and extract) for 'boost-libs'
-- verifying file...
file='/root/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
-- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
-- extracting...
src='/root/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
dst='/root/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_st...-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
Scanning dependencies of target samtools-lib
[ 15%] Creating directories for 'samtools-lib'
[ 17%] Performing download step (verify and extract) for 'samtools-lib'
-- verifying file...
file='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
-- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
-- extracting...
src='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
dst='/root/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 /root/breakdancer/build/vendor/samtools/build.log
[ 24%] Performing build step for 'samtools-lib'
make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Error 2
make[1]: *** [CMakeFiles/samtools-lib.dir/all] Error 2
make: *** [all] Error 2


In the vendor directory now I have these subdirectories:
boost gtest160-build samtools samtools-0.1.1.19.tar.gz src tmp

the directory samtools it was created afte the command
cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local

samtools-0.1.1.19.tar.gz file was introduced by me.

I followed the install.md commands but I failed.

Could you help me step by step?
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Old 08-10-2015, 07:22 AM   #13
GenoMax
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Can you show us the commands you are using to do the install? It is difficult to understand exactly what is happening looking at the logs you posted above. It will also help if you can provide a recursive listing of the directory

Code:
$ ls -lhR /root/breakdancer/vendor/
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Old 08-11-2015, 11:05 PM   #14
simobioinfo
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and finally I got it... I installed samtools independently from breakdancer installation.
Then I modified the cmakefile eliminating the part regarding samtools installation and so I solved my problems...
Thank you
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