problems in installing AMOS

[shuang]

I'm trying to make amos-3.1.0 work on Ubuntu. When I ran ./configure, it gave me a warning in the end

WARNING! Qt4 toolkit malfunctioning but is required to run AMOS GUIs
try compiling GUIs manually or reinstall Qt4 toolkit to build GUIs
see config.log for more information on what went wrong


However, before this, I already (tried to) install qt4 by running
apt-get install libqt4-dev


Need help here!!

[inagy]

amos compiling problem

Hi,
I am wondering, whether somebody has managed to compile amos-3.1.0 on x86_64 linux with a recent kernel (3.5 or above) ?
It looks that Qt4 and all the necessary packages are properly installed on my system. However, make terminates with several warning ending like these:

====================================================
.
.
.
g++ -g -O2 -o count-kmers count-kmers.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a -lz -lc -lm
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -g -O2 -MT find-tandem.o -MD -MP -MF .deps/find-tandem.Tpo -c -o find-tandem.o find-tandem.cc
find-tandem.cc: In function ‘int main(int, char**)’:
find-tandem.cc:243:3: error: ‘optarg’ was not declared in this scope
find-tandem.cc:245:63: error: ‘getopt’ was not declared in this scope
find-tandem.cc:258:55: error: ‘optopt’ was not declared in this scope
make[3]: *** [find-tandem.o] Error 1
make[3]: Leaving directory `/usr/local/amos-3.1.0/src/Align'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/usr/local/amos-3.1.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/usr/local/amos-3.1.0'
make: *** [all] Error 2
======================================================

[mjhsieh]

g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -g -O2 -MT find-tandem.o -MD -MP -MF .deps/find-tandem.Tpo -c -o find-tandem.o find-tandem.cc
find-tandem.cc: In function ‘int main(int, char**)’:
find-tandem.cc:243:3: error: ‘optarg’ was not declared in this scope
find-tandem.cc:245:63: error: ‘getopt’ was not declared in this scope
find-tandem.cc:258:55: error: ‘optopt’ was not declared in this scope

Add this in the front group of src/Align/find-tandem.cc file, yes, this is a hack, but a sensible one.

#include <getopt.h>

[inagy]

Thank you !!!

It was simple, but it really helped ...

[yifangt]

amos (goBambus2) running problem

Hello,
I met all the problems described above, and fixed them according to some suggestions. It seems AMOS3.1.0 has been installed now in my box (Ubuntu12.10), but I always got error when I ran goBambus2:

$ goBambus2 /storage/S050611192024.fasta --all --contigs
Traceback (most recent call last):
  File "/home/download-software/amos-3.1.0/bin/goBambus2", line 68, in <module>
    xopt_dict[sopt] = xopt_dict[sopt] = 1
NameError: name 'sopt' is not defined

I checked the lines around 68 of the file, it is the python module problem.

54         for opt in opt_dict.keys():
 55             opt_dict[opt] = []
 56         for opt in sys.argv[3:]:
 57             opt_list = opt.split(",")
 58             mopt = opt_list[0]
 59             mopt = mopt.replace("-", "")
 60             xopt = opt_list[1:]
 61 
 62             if mopt in opt_dict.keys():
 63                 if len(xopt) == 0:
 64                     xopt = [" "]
 65                 opt_dict[mopt] = xopt
 66             else:
 67                 try:
 68                     xopt_dict[sopt] = xopt_dict[sopt] = 1
 69                 except KeyError:
 70                     pass

Does anybody have a clue of it? Thanks a lot in advacne!

Yifang

[mjhsieh]

According to http://sourceforge.net/p/amos/code/c...e/goBambus2.py , it probably should be:

68                     xopt_dict[mopt] = xopt_dict[opt] = 1

[yifangt]

Thank you so much Hsieh!
You saved my days of head-banging-keyboard......
By the way, where is the update info for AMOS/Bambus2 if you know by chance? I went to the homepage but could not find this information. Sourceforge seems not haveing this either, where all the comments are simply "Excellent software" "Easy for use" etc.

[mjhsieh]

Thank you so much Hsieh!
You saved my days of head-banging-keyboard......
By the way, where is the update info for AMOS/Bambus2 if you know by chance? I went to the homepage but could not find this information. Sourceforge seems not haveing this either, where all the comments are simply "Excellent software" "Easy for use" etc.

I can't find it, either. However I guess we'd have better luck checking out (stalking) the project commit log at http://sourceforge.net/p/amos/code/ci/HEAD/log/

[NatashaPavlovikj]

Add this in the front group of src/Align/find-tandem.cc file, yes, this is a hack, but a sensible one.

#include <getopt.h>

Hi,
Mjhsieh, thank you so much for sharing the tip with us.
You saved me a lot of time while configuring AMOS.

Thank you and have great weekend,
Regards,
Natasha

[pari_89]

Hello, I am trying to install amos-cmp version 3.1.0 as well. Can you please tell me where to download and how to install those packages:

WARNING! BLAT was not found but is required to run minimus2-blat
install BLAT if planning on using minimus2-blat
WARNING! Boost graph toolkit was not found but is required to run parts of the AMOS Scaffolder (Bambus 2)
install Boost or locate Boost with configure to build Scaffolder
see config.log for more information on what went wrong

I am trying to look for a step by step installation but not getting one. Can you please help?

Thank you.

[GenoMax]

Hello, I am trying to install amos-cmp version 3.1.0 as well. Can you please tell me where to download and how to install those packages:

WARNING! BLAT was not found but is required to run minimus2-blat
install BLAT if planning on using minimus2-blat
WARNING! Boost graph toolkit was not found but is required to run parts of the AMOS Scaffolder (Bambus 2)
install Boost or locate Boost with configure to build Scaffolder
see config.log for more information on what went wrong

I am trying to look for a step by step installation but not getting one. Can you please help?

Thank you.

blat: http://genome.ucsc.edu/FAQ/FAQblat.html#blat3
boost libraries: http://www.boost.org/

[NAdia1234]

Thank you so much Hsieh!
You saved my days of head-banging-keyboard......
By the way, where is the update info for AMOS/Bambus2 if you know by chance? I went to the homepage but could not find this information. Sourceforge seems not haveing this either, where all the comments are simply "Excellent software" "Easy for use" etc.

Hi yifangt,

I have the same problem, but not I have another:

I have installed AMOS-3.1.0 in Ubuntu 12.04, it was ok, but when I tried to run goBambus2 it did not work. There were some mistakes that I have to change on the script (according to http://amos.git.sourceforge.net/git/...7bcd40;hb=HEAD
). I continued editing the file until no error warning appeared on the command prompt.
Now, I am trying to check if Bambus runs ok, so I am using some example files from: http://www.ncbi.nlm.nih.gov/pubmed/21400694 and http://sourceforge.net/projects/amos/files/sample_data/, using KVP40 data. And now it says "mate pair info not present". So I do not know what I am doing wrong.

I would appreciate any help

Do you check Bambus2 with any data?

Nadia

[nazen]

mjhsieh
Thanks a lot!!!

[eyeziko]

Hello everyone,
I run into this error and I am not sure what to do. Seem like other users of AMOS do not have the -lexpath in libAMOSFoundation.a but I do in my installation hence cannot find -lexpath.

Your help will be highly appreciated.
Thank you

My ERROR:
make[3]: Leaving directory `/user/amos-3.1.0/src/Validation'
Making all in Converters
make[3]: Entering directory `/user/amos-3.1.0/src/Converters'
g++ -g -O2 -o toAmos_new toAmos_new-toAmos_new.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a -lexpat -lz -lc -lm
/usr/bin/ld: cannot find -lexpat
collect2: error: ld returned 1 exit status
make[3]: *** [toAmos_new] Error 1
make[3]: Leaving directory `/user/amos-3.1.0/src/Converters'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/user/amos-3.1.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/user/amos-3.1.0'
make: *** [all] Error 2

[mjhsieh]

g++ -g -O2 -o toAmos_new toAmos_new-toAmos_new.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a -lexpat -lz -lc -lm
/usr/bin/ld: cannot find -lexpat
collect2: error: ld returned 1 exit status
make[3]: *** [toAmos_new] Error 1
make[3]: Leaving directory `/user/amos-3.1.0/src/Converters'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/user/amos-3.1.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/user/amos-3.1.0'
make: *** [all] Error 2

From a simple grep in the directory, expat doesn't seem to be required. Try remove the -lexpat from the Makefile, that might work.

amos-3.1.0 mjhsieh$ grep -ir expat .
./src/Converters/Makefile.am: -lexpat
./src/Converters/Makefile.in: -lexpat