Building Tophat Release 1.2.0Beta

Question

[Laurent Gautier]

Hi,

We are having trouble to build TopHat from source, and do not know where to report the issue (the email address given on the site did not return any answer)

The configure step appears all fine:

-- tophat 1.2.0 Configuration Results --
C compiler:          gcc -Wall -m64 -O3  -DNDEBUG
C++ compiler:        g++ -Wall -m64 -O3  -DNDEBUG -I/usr/local/include
GCC version:         gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
Host System type:    x86_64-unknown-linux-gnu

but running make ends with:

In file included from ./SeqAn-1.1/seqan/sequence.h:51,
                  from juncs_db.cpp:26:
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::clear(seqan::String<TValue, TSpec>&) [with TValue = char, TSpec = seqan::CStyle]’:
./SeqAn-1.1/seqan/sequence/string_cstyle.h:492:   instantiated from ‘static void seqan::_Assign_String_2_StringArray<TExpand, true>::assign_(seqan::String<char, seqan::CStyle>&, seqan::String<char, TSourceSpec>&) [with TSourceSpec = seqan::Alloc<void>, TExpand = const seqan::Tag<seqan::TagExact_>]’
./SeqAn-1.1/seqan/sequence/string_cstyle.h:522:   instantiated from ‘void seqan::assign(seqan::String<TTargetValue, seqan::CStyle>&, seqan::String<TValue, TSpec>&, seqan::Tag<TTag>) [with TValue = char, TSourceSpec = seqan::Alloc<void>, TExpand = seqan::TagExact_]’
./SeqAn-1.1/seqan/sequence/string_base.h:737:   instantiated from ‘void seqan::assign(seqan::String<TValue, TSpec>&, TSource&) [with TTargetValue = char, TTargetSpec = seqan::CStyle, TSource = seqan::String<char, seqan::Alloc<void> >]’
./SeqAn-1.1/seqan/sequence/string_cstyle.h:97:   instantiated from ‘seqan::String<TTargetValue, seqan::CStyle>::String(TString&) [with TString = seqan::String<char, seqan::Alloc<void> >, TValue = char]’
./SeqAn-1.1/seqan/sequence/string_cstyle.h:798:   instantiated from ‘typename seqan::Value<T, 0>::Type* seqan::toCString(T&) [with T = seqan::String<char, seqan::Alloc<void> >]’
juncs_db.cpp:327:   instantiated from here
./SeqAn-1.1/seqan/sequence/string_base.h:207: error: no matching function for call to ‘_setLength(seqan::String<char, seqan::CStyle>&, int)’
make[2]: *** [juncs_db.o] Error 1

Answer 1

[Brad Chapman]

Ran into this one as well and SeqAnswers helped out.

Remove the included SeqAn in src/SeqAn-1.1 and replace it with the latest release.

There is an automated build of this as part of CloudBioLinux: https://github.com/chapmanb/bcbb/blob/master/ec2/biolinux/custom/bio_nextgen.py

So you could install with:

fab -f fabfile.py install_custom:tophat -H localhost

[Laurent Gautier]

Thanks. It does build with Seqan 1.2. Somehow did not find the seqanswers thread when looking for earlier reports of the issue. Reporting problems to TopHat developpers also appears difficult to others.