TopHat on a 32 bit machine

[poisson200]

Dear Bioinformaticians.

Can TopHat be installed on a 32bit Ubuntu (Linux ubuntu 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:04:26 UTC 2009 i686 GNU/Linux) installation? I tried and get the following:

g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp
In file included from /usr/include/features.h:378,
from /usr/include/assert.h:37,
from /usr/include/c++/4.4/cassert:45,
from reads.cpp:14:
/usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory

It looks like the configure script is expecting the system to be 64bit. I tried make clean, edited all files to change -m64 to -m32 but when I run configure, it always ends up with:

-- TopHat 1.0.13 Configuration Results --
C compiler: gcc -Wall -g -m64 -O3 -DNDEBUG
C++ compiler: g++ -Wall -g -m64 -O3 -DNDEBUG
GCC version: gcc (Ubuntu 4.4.1-4ubuntu9) 4.4.1
Host System type: i686-pc-linux-gnu
Install prefix: /home/john/Documents/software/tophat-1.0.13
Install eprefix: ${prefix}

Both the gcc and g++ have the -m64 flag. Does anyone know how I can fix this? I saw another 2 threads about similar problems installing MAQ but the fixes don't work for TopHat.

Thanks a lot for any help.

Kind regards,

P

[jmarshall]

Both the gcc and g++ have the -m64 flag. Does anyone know how I can fix this? I saw another 2 threads about similar problems installing MAQ but the fixes don't work for TopHat.

Have you tried the tophat configure patch suggested in this thread: http://seqanswers.com/forums/showthread.php?t=3781 ?

You can try changing CFLAGS="-m64" on line 4028 of configure to CXXFLAGS="-m64" and rerunning configure, which will hopefully cause different flags to be shown on the "C compiler" and "C++ compiler" lines shown above and will build a 32-bit executable, which you do have a compiler for.

[poisson200]

Have you tried the tophat configure patch suggested in this thread: http://seqanswers.com/forums/showthread.php?t=3781 ?

Hello Marshall,
Thank you for the suggestion, I just tried it but, alas, it did not work, just the same result:

g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp
In file included from /usr/include/features.h:378,
from /usr/include/assert.h:37,
from /usr/include/c++/4.4/cassert:45,
from reads.cpp:14:
/usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory

As you can see, g++ is still running with -m64 option.

Kind regards,

P

[jmarshall]

Curious. It works for me, and apparently it worked for the person who was asking in that other thread. Did you "make clean" and rerun configure? Probably best to start from a freshly unpacked tophat directory, edit configure, and only then run configure etc.

If the worst comes to the worst, you could just remove the three occurrences of -m64 in each of Makefile and src/Makefile by hand...

John

[poisson200]

Thanks for your advice John.
I have tried all variants, including editing the Makefiles themselves. Now I get:
john@ubuntu:~/Documents/software/tophat-1.0.13$ make
make all-recursive
make[1]: Entering directory `/home/john/Documents/software/tophat-1.0.13'
Making all in src
make[2]: Entering directory `/home/john/Documents/software/tophat-1.0.13/src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m32 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m32 -O3 -DNDEBUG -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp
In file included from /usr/include/c++/4.4/bits/stl_algobase.h:61,
from /usr/include/c++/4.4/bits/char_traits.h:41,
from /usr/include/c++/4.4/string:42,
from reads.cpp:15:
/usr/include/c++/4.4/cstddef:52: error: expected unqualified-id before ‘unsigned’
/usr/include/c++/4.4/cstddef:52: error: expected ‘;’ before ‘unsigned’
/usr/include/c++/4.4/cstddef:52: error: declaration does not declare anything
In file included from /usr/include/c++/4.4/string:42,
from reads.cpp:15:

As you see the -m32 is there but now something else is broken. It could be idiot syndrome in the sense I am missing something obvious.

Thanks.

P.

[aghazalp]

same problem here

Hi,

it seems like I have the same problem and I tried to change the CFLAGS to CXXFLAGS but it doesnt seem to work for me either. I am using Ubuntu 8.1

[Life_Dogma]

How to install Tophat-2.0.2 on ubuntu 12.04 32bit????

[arvid]

I'm not quite sure why you really want to do that. Why not spend the time on installing a 64-bit Ubuntu as dual boot instead, in case you really have to stick to your 32-bit installation?

IMHO I don't quite see the point on working with NGS data on 32-bit OSs these days - you'll run into installation and RAM issues with many software packages, and you'll probably spend more time (=money) on fixing your setup than it would cost (in time and money) to get an appropriate setup. Just my 2 cents.

[Life_Dogma]

So your advice is to change to ubuntu 64-bit????? since im working on NGS data.

[arvid]

Yes, or any other 64-bit distribution. You do have a 64-bit processor, don't you (I haven't seen a 32-bit processor in years in new PCs)? How much RAM do you have on the machine?

Though some people keep saying there are 32-bit programs that don't run on 64-bit Linux, I haven't encountered anything since 2008 causing real problems on my 64-bit installs. On Windows it's another story, however...

[Life_Dogma]

Thank you so much for your help arvid, you saved me time and money