Trying to use the gff_to_gtf utiilty in genomeTools

Question

[oma219]

Hello,

I downloaded the genomeTools package so I could use the utility gff3_to_gtf utility but I'm having trouble finding it. I have looked at the documentation online and the READMEs but I cannot seem to locate the script. Does anyone know where it would be located? Thanks.

    ubuntu@ip-172-31-19-217:~/software/genometools-1.5.9$ ls
CHANGELOG  CONTRIBUTORS  doc  gtdata  gtpython  gtruby  gtscripts  INSTALL  LICENSE  Makefile  obj  README  README.md  scripts  src  VERSION

[h.mon]

try: less INSTALL.

[oma219]

I keep getting this error. Do you know what this means?

ubuntu@ip-172-31-19-217:~/software/genometools-1.5.9$ make prefix=/usr 64bit=no cairo=no install
grep: src/tools/*.c: No such file or directory
grep: src/tools/*.c: No such file or directory
grep: src/tools/*.c: No such file or directory
grep: src/tools/*.c: No such file or directory
grep: src/tools/*.c: No such file or directory
grep: src/tools/*.c: No such file or directory
grep: src/tools/*.c: No such file or directory
grep: src/tools/*.c: No such file or directory
[compile condenseq_creator.o]
In file included from /usr/include/string.h:25:0,
                 from src/extended/condenseq_creator.c:18:
/usr/include/features.h:367:25: fatal error: sys/cdefs.h: No such file or directory
compilation terminated.
Makefile:809: recipe for target 'obj/src/extended/condenseq_creator.o' failed
make: *** [obj/src/extended/condenseq_creator.o] Error 1

[Malcolm.Cook]

For another approach to this conversion problem I recommend gffread http://ccb.jhu.edu/software/stringtie/gff.shtml

Answer 1

[h.mon]

if you want to install on a system-wide location, I suggest you use the package manager:

sudo apt-get install genometools

If you really want to compile GenomeTools, the key error message (so far) is "sys/cdefs.h: No such file or directory", check this page for possible solutions.

P.S.: you will find genometools binaries here.