[mira_talk] Re: installing Bambus 2.33 on Ubuntu 8.04

Hi Davide:

I think I have some good news for you. I have a Linux box running Ubuntu
9.04. I ran through the install process using the exact procedure I detailed
in the pdf.  There were problems with the make, similar to what you
described, but some executables were created. I ran goBambus, but  grommit
died. I applied the changes you detailed, namely

        ConfigFile.hh  (add the line #include <string.h>)
> Logger.hh   (add the line #include <stdlib.h>)
> OptionResult.hh (add the line #include <stdlib.h>)
> Options.hh (add the line #include <string.h>)
> 
in the src/TIGR_FOUNDATION_CC directory. I ran ³make clean², ³make all², and
finally ³make install².  I then re-ran goBambus and the scripts executed as
described in the pdf. Success.

So, my recommendation to you is to upgrade to Ubuntu 9.04.  Easier said the
done, I realize.  Good luck.

Greg
>   
Gregory P. Harhay, PhD
Computational Biologist
Animal Health Research Unit
USDA-ARS-Roman L. Hruska  U.S. Meat Animal Research Center
Clay Center, NE 68933
v - 402.762.4250

On 9/1/09 5:15 AM, "Davide Sassera" <davide.sassera@xxxxxxxx> wrote:

> Dear all,
> Many thanks to Gregory Harhay for the Bambus primer, which also contains
> bugfixes for the installation,
> 
> Even with this help I still cannot install the software
> 
> Basically when I
> 
> # make all
> 
> I get the following error
> 
> 
> if [ ! -d /usr/local/bioinfo/bambus-2.33 ] ;then mkdir
> /usr/local/bioinfo/bambus-2.33 ;fi
> if [ ! -d /usr/local/bioinfo/bambus-2.33/bin/ ] ;then mkdir
> /usr/local/bioinfo/bambus-2.33/bin ;fi
> if [ ! -d /usr/local/bioinfo/bambus-2.33/lib/ ] ;then mkdir
> /usr/local/bioinfo/bambus-2.33/lib ;fi
> if [ ! -d /usr/local/bioinfo/bambus-2.33/doc/ ] ;then mkdir
> /usr/local/bioinfo/bambus-2.33/doc ;fi
> for i in src doc ;do cd $i ; make install; cd .. ;done
> make[1]: Entering directory `/usr/local/bioinfo/bambus-2.33/src'
> for i in goBambus.pl; do /bin/sed "s,^\#!/usr/bin/perl,\#!/usr/bin/perl," $i |
> /bin/sed "s,^\(my\)*[    ]*\$BAMBUS_BASE.*,\1 \$BAMBUS_BASE =
> \"/usr/local/bioinfo/bambus-2.33\";," >
> /usr/local/bioinfo/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[2]: Entering directory `/usr/local/bioinfo/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/bin/perl," $i |
> /bin/sed "s/^\(use DBI.*\)/\#\1/" | /bin/sed "s,^\(my\)*[
> ]*\$BAMBUS_BASE.*,\1 \$BAMBUS_BASE = \"/usr/local/bioinfo/bambus-2.33\";," >
> /usr/local/bioinfo/bambus-2.33/bin/`expr $i : '\(.*\)\.pl$'`; done
> make[2]: Leaving directory `/usr/local/bioinfo/bambus-2.33/src/IO'
> make[2]: Entering directory `/usr/local/bioinfo/bambus-2.33/src/DotLib'
> cp DotLib.pm /usr/local/bioinfo/bambus-2.33/lib/
> make[2]: Leaving directory `/usr/local/bioinfo/bambus-2.33/src/DotLib'
> make[2]: Entering directory
> `/usr/local/bioinfo/bambus-2.33/src/TIGR_Foundation_CC'
> mkdir -p /export/usr/local/lib
> mkdir -p /export/usr/local/include
> cp libTigrFoundation.a /export/usr/local/lib; \
>  cp CategoryInformation.hh ConfigFile.hh ConfigSection.hh Exceptions.hh
> FileSystem.hh LogCategory.hh LogMsg.hh Logger.hh MessageLevel.hh
> OptionResult.hh Options.hh TIGR_Foundation.hh /export/usr/local/include;
> make[2]: Leaving directory
> `/usr/local/bioinfo/bambus-2.33/src/TIGR_Foundation_CC'
> make[2]: Entering directory `/usr/local/bioinfo/bambus-2.33/src/grommit'
> cp grommit /usr/local/bioinfo/bambus-2.33/bin/
> make[2]: Leaving directory `/usr/local/bioinfo/bambus-2.33/src/grommit'
> make[1]: Leaving directory `/usr/local/bioinfo/bambus-2.33/src'
> make[1]: Entering directory `/usr/local/bioinfo/bambus-2.33/doc'
> cp BAMBUS.README /usr/local/bioinfo/bambus-2.33/doc
> cp: `BAMBUS.README' and `/usr/local/bioinfo/bambus-2.33/doc/BAMBUS.README' are
> the same file 
> make[1]: *** [install] Error 1
> make[1]: Leaving directory `/usr/local/bioinfo/bambus-2.33/doc'
> cp -r lib/* /usr/local/bioinfo/bambus-2.33/lib
> cp: `lib/DotLib.pm' and `/usr/local/bioinfo/bambus-2.33/lib/DotLib.pm' are the
> same file 
> cp: `lib/TIGR' and `/usr/local/bioinfo/bambus-2.33/lib/TIGR' are the same file
> make: *** [install] Error 1
> 
> 
> I asked to the guys at the AMOS list and I was given the following advice
> 
> 
> Apparently, there are some standard C++ headers not
> explicitely included in some of the bambus header files, so standard C++
> functions 
> (like strlen) are not found. I could solve the problem by manually editing the
> following header files:
> 
> ConfigFile.hh  (add the line #include <string.h>)
> Logger.hh   (add the line #include <stdlib.h>)
> OptionResult.hh (add the line #include <stdlib.h>)
> Options.hh (add the line #include <string.h>)
> 
> With this changes I got the
> 
> # make all 
> 
> working, but then I move on to
> 
> #make install 
> 
> I get a new error, shown below. I asked the AMOS guys again, but they gave no
> answer
> 
> thanks in advance
> 
> Davide
> 
> if [ ! -d /usr/local/bin/bambus-2.33 ] ;then mkdir /usr/local/bin/bambus-2.33
> ;fi
> if [ ! -d /usr/local/bin/bambus-2.33/bin/ ] ;then mkdir
> /usr/local/bin/bambus-2.33/bin ;fi
> if [ ! -d /usr/local/bin/bambus-2.33/lib/ ] ;then mkdir
> /usr/local/bin/bambus-2.33/lib ;fi
> if [ ! -d /usr/local/bin/bambus-2.33/doc/ ] ;then mkdir
> /usr/local/bin/bambus-2.33/doc ;fi
> for i in src doc ;do cd $i ; make install; cd .. ;done
> make[1]: Entering directory `/usr/local/bin/bambus-2.33/src'
> for i in goBambus.pl; do /bin/sed
> "s,^\#!/usr/local/bin/perl,\#!/usr/bin/perl," $i | /bin/sed "s,^\(my\)*[
> ]*\$BAMBUS_BASE.*,\1 \$BAMBUS_BASE = \"/usr/local/bin/bambus-2.33\";," >
> /usr/local/bin/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[2]: Entering directory `/usr/local/bin/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/bin/perl," $i |
> /bin/sed "s/^\(use DBI.*\)/\#\1/" | /bin/sed "s,^\(my\)*[
> ]*\$BAMBUS_BASE.*,\1 \$BAMBUS_BASE = \"/usr/local/bin/bambus-2.33\";," >
> /usr/local/bin/bambus-2.33/bin/`expr $i : '\(.*\)\.pl$'`; done
> make[2]: Leaving directory `/usr/local/bin/bambus-2.33/src/IO'
> make[2]: Entering directory `/usr/local/bin/bambus-2.33/src/DotLib'
> cp DotLib.pm /usr/local/bin/bambus-2.33/lib/
> make[2]: Leaving directory `/usr/local/bin/bambus-2.33/src/DotLib'
> make[2]: Entering directory
> `/usr/local/bin/bambus-2.33/src/TIGR_Foundation_CC'
> cp libTigrFoundation.a /export/usr/local/lib; \
>   cp CategoryInformation.hh ConfigFile.hh ConfigSection.hh Exceptions.hh
> FileSystem.hh LogCategory.hh LogMsg.hh Logger.hh MessageLevel.hh
> OptionResult.hh Options.hh TIGR_Foundation.hh /export/usr/local/include;
> make[2]: Leaving directory `/usr/local/bin/bambus-2.33/src/TIGR_Foundation_CC'
> make[2]: Entering directory `/usr/local/bin/bambus-2.33/src/grommit'
> cp grommit /usr/local/bin/bambus-2.33/bin/
> make[2]: Leaving directory `/usr/local/bin/bambus-2.33/src/grommit'
> make[1]: Leaving directory `/usr/local/bin/bambus-2.33/src'
> make[1]: Entering directory `/usr/local/bin/bambus-2.33/doc'
> cp BAMBUS.README /usr/local/bin/bambus-2.33/doc
> cp: `BAMBUS.README' and `/usr/local/bin/bambus-2.33/doc/BAMBUS.README' are the
> same file
> make[1]: *** [install] Error 1
> make[1]: Leaving directory `/usr/local/bin/bambus-2.33/doc'
> cp -r lib/* /usr/local/bin/bambus-2.33/lib
> cp: `lib/DotLib.pm' and `/usr/local/bin/bambus-2.33/lib/DotLib.pm' are the
> same file
> cp: `lib/TIGR' and `/usr/local/bin/bambus-2.33/lib/TIGR' are the same file
> make: *** [install] Error 1
>

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