Using genome tools to convert bed files to gff3 files

Question

[mropri]

Hi,

I am trying to install genome tools using conda on ubuntu. It installs fine but when I try to use the gt command in the terminal it comes out as:

command not found.

Could someone please help in helping me install genome tools because I want to use genome tools command

gt bed_to_gff3 [BED_file]

to convert my bed files to gff3 files.

So if someone knows how I could make that work and if there is another way I could convert my bed files to gff3 files? Lastly, if there is a way to just convert bed files to gff, not gff3? Would appreciate all the help. Thank you!

Answer 1

[Juke34]

You probably installed genometools

# Name                       Version           Build  Channel             
genometools                    1.2.1          py27_0  bioconda

try with genometools-genometools then the gt command will work:

# Name                       Version           Build  Channel             
genometools-genometools           1.5.9               1  bioconda            
genometools-genometools          1.5.10               0  bioconda            
genometools-genometools          1.5.10      h470a237_1  bioconda            
genometools-genometools          1.5.10       nocairo_0  bioconda            
genometools-genometools          1.5.10  py27h08a56e5_2  bioconda            
genometools-genometools          1.5.10  py27h0a44026_3  bioconda            
genometools-genometools          1.5.10  py35h08a56e5_2  bioconda            
genometools-genometools          1.5.10  py36h08a56e5_2  bioconda            
genometools-genometools          1.5.10  py36h0a44026_3  bioconda            
genometools-genometools          1.5.10  py37h0a44026_3  bioconda            
genometools-genometools           1.6.0  py27h6de7cb9_0  bioconda            
genometools-genometools           1.6.0  py36h6de7cb9_0  bioconda            
genometools-genometools           1.6.0  py37h6de7cb9_0  bioconda            
genometools-genometools           1.6.1  py27h6de7cb9_0  bioconda            
genometools-genometools           1.6.1  py36h0130604_1  bioconda            
genometools-genometools           1.6.1  py36h6de7cb9_0  bioconda            
genometools-genometools           1.6.1  py37h570ac47_1  bioconda            
genometools-genometools           1.6.1  py37h6de7cb9_0  bioconda

[mropri]

Thank you for your answer. I tried genometools-genometools in ubuntu but I still get command not found. What could I be doing wrong? I appreciate all the help.

[mropri]

I figured it out. I had to create a python environment in ubuntu with python version 2.7 as genometools is only compatible with this version. Then I used conda to install this version: broad-viral / genometools-genometools 1.5.10. Then when i used the gt command it worked. Thanks for all your help.