[mira_talk] Re: installing Bambus 2.33 on Ubuntu 8.04
- From: Giuseppe DAuria <giuseppe.dauria@xxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 02 Sep 2009 16:46:59 +0200
Ok, it works,
Just a suggestion about the line
$BAMBUS_BASE = "/usr/local/share/apps/bambus";
You should add a comment to remember users to point to Bambus directory,
(for example mine is different from that).
Bye
Giuseppe
On Wed, 2009-09-02 at 09:38 -0500, Gregory Harhay wrote:
> Hi Giuseppe:
>
> Thanks for pointing this out. I should put this fix in the pdf. To maintain
> consistency with the other scripts, I think the fix should look something
> like this at the top of untangle
> ====
>
> my $BAMBUS_BASE ;
> BEGIN{
> $BAMBUS_BASE = "/usr/local/share/apps/bambus";
> }
>
> my $DETECTIVE = $BAMBUS_BASE . "/bin/detective";
> my $PREGROMMIT = $BAMBUS_BASE . "/bin/xml2grommit";
> my $GROMMIT = $BAMBUS_BASE . "/bin/grommit";
> my $DISPLAY = $BAMBUS_BASE . "/bin/printScaff";
> my $CATXML = $BAMBUS_BASE . "/bin/catXML";
>
> $ENV{PERL5LIB} .= ":$BAMBUS_BASE/lib";
> use lib "$BAMBUS_BASE/lib";
> ===============
>
> to enhance of the "readability" code as well as getting the script to run.
>
>
>
> On 9/2/09 8:54 AM, "Giuseppe DAuria" <giuseppe.dauria@xxxxx> wrote:
>
> > Hi Davide, Greg,
> >
> > I have a fresh Ubuntu 9.04 on a new computer and I perfectly installed
> > Babmus only after changes you suggested.
> >
> > I think to have found a bug in the "untangle" script that seems to be
> > useful to reduce Bambus results.
> > The error starts with
> >
> > "Can't locate TIGR/Foundation.pm in @INC"
> >
> > I just
> >
> > $ locate Foundation.pm
> > /path/to/Foundation
> >
> > and added
> >
> > use lib '/path/to/Foundation';
> >
> > at the beginning of the script.
> >
> > I do not know if this is a real bug or is some misconfiguration but it
> > worked for me.
> >
> > By
> >
> > Giuseppe
> >
> > On Tue, 2009-09-01 at 14:34 -0500, Gregory Harhay wrote:
> >> 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
> >>
> >>
> >>
> >>
> >>
>
> 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
>
>
>
>
--
***************************************************************
Dr. Giuseppe D'Auria
.........................................
Cavanilles Institute for Biodiversity and Evolutionary Biology,
University of Valencia, "Poligono de la Coma" s/n
46980 Paterna (Valencia), Spain
tel: +34 963 5 43270
E-mail: giuseppe.dauria@xxxxx
.........................................
Centro Superior de Investigación en Salud Pública CSISPAvda. de
Cataluña, 21, 46020 Valencia
Tel.: +34 961 92 5929
E-mail: dauria_giu@xxxxxx
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