[mira_talk] installing Bambus 2.33 on Ubuntu 8.04
- From: Davide Sassera <davide.sassera@xxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 01 Sep 2009 12:15:30 +0200
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
--
Davide Sassera
Sezione di Patologia Generale e Parassitologia
Dipartimento di Patologia Animale,
Igiene e Sanità Pubblica Veterinaria
Facoltà di Veterinaria
Università degli Studi di Milano
Via Celoria 10, 20133, Milano, ITALY
Tel: +39 0250318094
Fax: +39 0250318095
Other related posts:
