AMOS installation on 64-bit Linux

[agroster]

I keep banging my head against the keyboard trying to install the AMOS package on my 64-bit Linux system (Ubuntu 9.10). I think I have qt3 installed correctly, but I could be wrong.

If anyone has successfully installed the AMOS package (e.g. to use hawkeye) for a 64-bit system, can you help me walk through the installation?

Any help would be much appreciated!

ariel

[v_kisand]

I guess what you need is:

some modified .cc files from Ariadna Rodriguez Chamorro (ariadna dot rodriguez at unil dot ch).

when you drop your E-mail I can send these replacements

What I learned the short read version is not working, you should use amos v 2.0.8, worked for me on 64 bit Fedora 11

v.

[agroster]

Thanks for the reply, v_kisand. I've sent an email to Ariadna. I have been trying to install amos 2.0.8, not the short tools.

Looking forward to finally getting this resolved.

[agroster]

Thanks for the reply and thanks Arianda for the files. However, there was no change. I type $ ./configure, then "make", and still get the same errors:

IDMap_AMOS.cc: In member function ‘void AMOS::IDMap_t::read(const std::string&)’:
IDMap_AMOS.cc:504: error: ‘fopen’ was not declared in this scope
IDMap_AMOS.cc:509: error: ‘fscanf’ was not declared in this scope
IDMap_AMOS.cc:515: error: ‘fscanf’ was not declared in this scope
IDMap_AMOS.cc:517: error: ‘getc’ was not declared in this scope
IDMap_AMOS.cc:529: error: ‘EOF’ was not declared in this scope
IDMap_AMOS.cc:540: error: ‘EOF’ was not declared in this scope
IDMap_AMOS.cc:557: error: ‘fclose’ was not declared in this scope
make[3]: *** [libAMOS_a-IDMap_AMOS.o] Error 1
make[3]: Leaving directory `/home/bioinformatics/programs/amos-2.0.8/src/AMOS'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/bioinformatics/programs/amos-2.0.8/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/bioinformatics/programs/amos-2.0.8'
make: *** [all] Error 2

qt3 is installed and operational, as judging by "qmake" working.

I think this is a common error, but not sure how to fix it.

ariel

[v_kisand]

hmm, looks like C++ problem...

othrewise I run
./configure --with-Qt-dir= ...

Qt is used for GUIs even when qt3.3 is missing or not directed, the compilation runs fine, non-GUI part will be built

make
make install

v.

[jmarshall]

The interesting information that you can post in situations like these is: what version of which compiler you are using, and the error messages that are produced.

Judging from the error messages you have now posted, you're using GCC 4.4.x or thereabouts.

Add "#include <cstdio>" to the top of src/AMOS/IDMap_AMOS.cc, right after the similar <cstring> line. This file will then compile successfully; you might need to do similar things to other source files.

[agroster]

jmarshall, thanks for your reply. It was helpful - I added the #include <cstdio> in the files that were giving me problems, and this got me through some errors. I indeed have the GCC compiler 4.4.4.1.

My current situation is this:

$ ./configure --prefix=/home/bioinformatics/amos-2.0.8/bin --with-Qt-dir=/usr/lib/qt3 --with-Qt-lib-dir=/usr/lib64/qt3

then

$ make

Quite a few things ran, then it stopped with:

FileSystem.cc: In static member function ‘static bool FileSystem::isCreatableFile(const char*)’:
FileSystem.cc:59: error: invalid conversion from ‘const char*’ to ‘char*’
FileSystem.cc: In static member function ‘static char* FileSystem::getAbsolutePath()’:
FileSystem.cc:138: warning: ignoring return value of ‘char* getcwd(char*, size_t)’, declared with attribute warn_unused_result
make[3]: *** [FileSystem.o] Error 1
make[3]: Leaving directory `/home/bioinformatics/programs/amos-2.0.8/src/Foundation'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/bioinformatics/programs/amos-2.0.8/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/bioinformatics/programs/amos-2.0.8'
make: *** [all] Error 2


I added the #include line in FileSystem.cc, but that doesn't solve the problem. I also added #include <string.h> to Foundation/ConfigFile.cc as suggested by Mike Schatz in the AMOS forum, but that didn't help.

[jmarshall]

It turns out that there are two classes of problem compiling AMOS with GCC 4.4.x, and all instances of both are in fact fixed in AMOS's CVS repository. Hopefully the AMOS people will release a 2.0.9 sometime soon that compiles with current GCC.

In the meantime:

1. As you've found, you need to add "#include <cstdio>" to four source files. This fixes the existing "<blah> was not declared" errors.

2. To fix these "invalid conversion" errors in three files, you need to change "char * p" to "const char * p" in the vicinity of each error, like this:

http://amos.cvs.sourceforge.net/viewvc/amos/AMOS/src/Foundation/FileSystem.cc?r1=1.1&r2=1.2

http://amos.cvs.sourceforge.net/viewvc/amos/AMOS/src/Align/align.cc?r1=1.51&r2=1.52

and similarly in src/Align/align_poly.cc.

-- John

[agroster]

John, (jmarshall) - you are my saviour! I finally got it to install, after weeks of banging my head against the wall! The combination of adding the #include <cstdio> to four or five files and changing "char * p" to "const char * p" in three or four others finally did it. AMOS is now installed and fully functional!

John, if you are ever in Berkeley, I want to take you out for a beer!

ariel

[Eskeww]

Ariel and John,
Thank you very much. It also solved my problem. Fora nyone with the same problem, here is how my problem is solved. I hope in the ext AMOS it will be fixed


First
add "#include <stdio.h>" to these files:

$AMOS$/src/AMOS/IDMap_AMOS.cc
$AMOS$/src/AMOS/Message_AMOS.cc
$AMOS$/src/Common/amp.cc
$AMOS$/src/Foundation/Options.cc

edit AMOS > src > Foundation > FileSystem.cc
const char * end_of_path = strrchr(filename, PATH_DELIMINATOR);

Edit line 250, 288 and 360 of AMOS > src > Align > align.cc
char * p; const char * p;

add
#include <iomanip> to AMOS > src > Align > overlap-align.cc
and edit line 274/5
cout << setw(3) << trace[k].score << endl;

then make and make instell
That was it, It should work
Regards
Eskeatnaf

[[email protected]]

AMOS Input Files

Anyone has tried running sequence data in AMOS. I am unable to find the way to start after installing AMOS since the documentation is so unorganized. I have paried end data from illumina 75bp. Can anybody help how to convert fastq reads to amos format?

[bio-x]

i think you can try soapdenovo

http://soap.genomics.org.cn/soapdenovo.html

[[email protected]]

Thanks for reply Bio-x but i have been assigned to do comparative assembly not denovo but i can try after it. But first i want to look at AMOS since it took 6 banging days to install it and now i want to use it.

[Mathgon]

For me, there is just 2 days of banging my head on the keyboard. I'm also on a Linux-64 with a GCC4.
I tried to apply the modification you mentioned but I'm still under errors, perhaps have I made a mistake somewhere.

Is it possible to send me the modified version of the files, I will later put this files on a server for the other users of AMOS (I think we are not alone to "try" using AMOS on a 64b Linux)!

[Mathgon]

My mail address is dfog22 (at) hotmail.com