Error By Installing Cufflinks

Question

[Lisanne]

Dear All,

I want to use cufflinks to analyze RNA-seq Data. Therefore I first installed Boost148_0.tar.gz and built it with this code:

tar -zxf boost_1_48_0.tar.gz
cd boost_1_48_0
./bootstrap.sh
./b2
./bjam --prefix-/home/lisanne/Downloads/boost toolset=gcc link=static runtime-link=static stage install

It seems like the correct way for building. After the installation of boots, i installed cufflinks and buit it with this code:

tar -zxf cufflinks-0.7.0.tar.gz
cd cufflinks-0.7.0
./configure --with-boost=/home/lisanne/Downloads/boost
make

The last "make" command gives the following error:

make  all-recursive
make[1]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0'
Making all in src
make[2]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
g++ -DHAVE_CONFIG_H -I. -I..  -I../src    -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3  -DNDEBUG  -pthread -I/home/lisanne/Downloads/boost/include -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.cpp
mv -f .deps/common.Tpo .deps/common.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I../src    -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3  -DNDEBUG  -pthread -I/home/lisanne/Downloads/boost/include -MT assemble.o -MD -MP -MF .deps/assemble.Tpo -c -o assemble.o assemble.cpp
assemble.cpp:37:41: fatal error: boost/vector_property_map.hpp: No such file or directory
compilation terminated.
make[2]: *** [assemble.o] Error 1
make[2]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0'
make: *** [all] Error 2

The file vectorpropertymap.hpp is not is the map boost, but in the map propertymap. I changed the file assemble.cpp on line 37 from the boost/vectorpropertymap.hpp to boost/propertymap.hpp. That solve this error, but by running the command again, there is another error in the file hits.cpp that i don't understand.

make  all-recursive
make[1]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0'
Making all in src
make[2]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
g++ -DHAVE_CONFIG_H -I. -I..  -I../src    -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3  -DNDEBUG  -pthread -I/home/lisanne/Downloads/boost/include -MT hits.o -MD -MP -MF .deps/hits.Tpo -c -o hits.o hits.cpp
hits.cpp: In member function ‘virtual bool SAMHitFactory::get_hit_from_buf(const char*, ReadHit&, bool, char*, char*)’:
hits.cpp:262:32: error: invalid conversion from ‘const char*’ to ‘char*’
hits.cpp:270:33: error: invalid conversion from ‘const char*’ to ‘char*’
make[2]: *** [hits.o] Error 1
make[2]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0'
make: *** [all] Error 2

and this is the code in the hits.cpp file where it is all about:

// Copy the tag out of the name field before we might wipe it out
char* pipe = strrchr(name, '|');
if (pipe)
{
    if (name_tags)
        strcpy(name_tags, pipe);
    *pipe = 0;
}
// Stripping the slash and number following it gives the insert name
char* slash = strrchr(name, '/');
if (strip_slash && slash)
    *slash = 0;

Can anyone help me with this kind of error? Many thanks! :)

Answer 1

[Docroberson]

My first recommendation would be to download and try to install the most recent version of cufflinks (I believe it is up to version 1.3.0). It appears you are using version 0.7.0. Many bugs have been fixed and features added since then. A new version may appropriately address the issue.

Also, if the samtools install files are not in your PATH, you may want to add to the configure: --with-bam=/path/to/samtools/compiled/source/folder.