Tutorial:Install AMOS on Ubuntu 13.10

Question

[Medhat]

I was trying to install AMOS I faced some problems and here is the conclusion;

Most of the actions inspired from those two posts

• http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/amos.htm
• http://seqanswers.com/forums/showthread.php?t=17802

for Ubuntu

sudo apt-get install autotools-dev automake
sudo apt-get install libqt4-dev
sudo apt-get install libboost-graph-dev
 nano src/Align/find-tandem.cc
... include this after line #9
#include <getopt.h>

in AMOS directory

./configure
make check
make install

For more options you can read the "install.txt" with the software

[hafiz.talhamalik]

Hi, commenting after quite some time of this post. but I'm trying to install amos and facing the following error. if someone could help me in this regard.

In file included from /usr/include/c++/9/ext/hash_map:60,
                 from ../../src/AMOS/utility_AMOS.hh:48,
                 from ../../src/AMOS/foundation_AMOS.hh:13,
                 from genome-complexity-fast.cc:1:
/usr/include/c++/9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
**genome-complexity-fast.cc:21:74: error: template argument 3 is invalid
   21 |  HASHMAP::hash_multimap<Mer_t, MerVertex_t *, hash<unsigned long> > MerTable_t;
      |                                                                   ^
genome-complexity-fast.cc: In member function ‘MerVertex_t* deBrujinGraph_t::getVertex(const Mer_t&, int, int)’:
genome-complexity-fast.cc:602:26: error: qualified-id in declaration before ‘m’
  602 |     MerTable_t::iterator m = mers_m.find(mer);
      |                          ^
genome-complexity-fast.cc:604:13: error: ‘m’ was not declared in this scope; did you mean ‘tm’?
  604 |     while ((m != mers_m.end()) &&
      |             ^
      |             tm
genome-complexity-fast.cc:604:25: error: request for member ‘end’ in ‘((deBrujinGraph_t*)this)->deBrujinGraph_t::mers_m’, which is of non-class type ‘MerTable_t’ {aka ‘int’}
  604 |     while ((m != mers_m.end()) &&
      |                         ^~~
genome-complexity-fast.cc:617:5: error: ‘m’ was not declared in this scope; did you mean ‘tm’?
  617 |     m = mers_m.insert(make_pair(mer, new MerVertex_t(startpos, endpos)));
      |     ^
      |     tm
genome-complexity-fast.cc:617:16: error: request for member ‘insert’ in ‘((deBrujinGraph_t*)this)->deBrujinGraph_t::mers_m’, which is of non-class type ‘MerTable_t’ {aka ‘int’}
  617 |     m = mers_m.insert(make_pair(mer, new MerVertex_t(startpos, endpos)));
      |                ^~~~~~
genome-complexity-fast.cc: In member function ‘int deBrujinGraph_t::nodeCount()’:
genome-complexity-fast.cc:663:19: error: request for member ‘size’ in ‘((deBrujinGraph_t*)this)->deBrujinGraph_t::mers_m’, which is of non-class type ‘MerTable_t’ {aka ‘int’}
  663 |     return mers_m.size();
      |                   ^~~~
genome-complexity-fast.cc: In member function ‘void deBrujinGraph_t::convertToNodes()’:
genome-complexity-fast.cc:785:31: error: qualified-id in declaration before ‘mi’
  785 |     for (MerTable_t::iterator mi = mers_m.begin();
      |                               ^~
genome-complexity-fast.cc:785:30: error: expected ‘;’ before ‘mi’
  785 |     for (MerTable_t::iterator mi = mers_m.begin();
      |                              ^~~
      |                              ;
genome-complexity-fast.cc:785:31: error: ‘mi’ was not declared in this scope
  785 |     for (MerTable_t::iterator mi = mers_m.begin();
      |                               ^~
genome-complexity-fast.cc:785:43: error: request for member ‘begin’ in ‘((deBrujinGraph_t*)this)->deBrujinGraph_t::mers_m’, which is of non-class type ‘MerTable_t’ {aka ‘int’}
  785 |     for (MerTable_t::iterator mi = mers_m.begin();
      |                                           ^~~~~
genome-complexity-fast.cc:786:23: error: request for member ‘end’ in ‘((deBrujinGraph_t*)this)->deBrujinGraph_t::mers_m’, which is of non-class type ‘MerTable_t’ {aka ‘int’}
  786 |          mi != mers_m.end();
      |                       ^~~
genome-complexity-fast.cc:786:28: error: expected ‘)’ before ‘;’ token
  786 |          mi != mers_m.end();
      |                            ^
      |                            )
genome-complexity-fast.cc:785:9: note: to match this ‘(’
  785 |     for (MerTable_t::iterator mi = mers_m.begin();
      |         ^
genome-complexity-fast.cc:787:10: error: ‘mi’ was not declared in this scope
  787 |          mi++)
      |          ^~
genome-complexity-fast.cc:799:12: error: request for member ‘clear’ in ‘((deBrujinGraph_t*)this)->deBrujinGraph_t::mers_m’, which is of non-class type ‘MerTable_t’ {aka ‘int’}
  799 |     mers_m.clear();
      |            ^~~~~
make[3]: *** [Makefile:1139: genome-complexity-fast.o] Error 1
make[3]: Leaving directory '/media/pc/Bay2/Softwares/amos/src/Align'
make[2]: *** [Makefile:424: all-recursive] Error 1
make[2]: Leaving directory '/media/pc/Bay2/Softwares/amos/src'
make[1]: *** [Makefile:413: all-recursive] Error 1
make[1]: Leaving directory '/media/pc/Bay2/Softwares/amos'
make: *** [Makefile:354: all] Error 2**

Answer 1

[majidgeek]

Try these steps on my blog:

http://blog.rahimi.id.ir/post/2016/07/21/installing-amos-for-next-generation-sequence-assembly-in-ubuntu-linux