Can't install Transdecoder -

Question

[Pedro]

I was trying to install TransDecoder to do Transcriptome annotation, but when I run make test, this shows up. I've tried to install the module but it is not working. Is there any way around it?

Can't locate URI/Escape.pm in @INC (you may need to install the URI::Escape module) (@INC contains: /home/labpc8c/Documents/Toby/PedroFelix/tools/TransDecoder-TransDecoder-v5.7.0/util/../PerlLib /home/labpc8c/anaconda3/lib/perl5/5.32/site_perl /home/labpc8c/anaconda3/lib/perl5/site_perl /home/labpc8c/anaconda3/lib/perl5/5.32/vendor_perl /home/labpc8c/anaconda3/lib/perl5/vendor_perl /home/labpc8c/anaconda3/lib/perl5/5.32/core_perl /home/labpc8c/anaconda3/lib/perl5/core_perl .) at /home/labpc8c/Documents/Toby/PedroFelix/tools/TransDecoder-TransDecoder-v5.7.0/util/../PerlLib/Gene_obj.pm line 3602.
BEGIN failed--compilation aborted at /home/labpc8c/Documents/Toby/PedroFelix/tools/TransDecoder-TransDecoder-v5.7.0/util/../PerlLib/Gene_obj.pm line 3602.
Compilation failed in require at ../../util/gtf_to_alignment_gff3.pl line 8.
BEGIN failed--compilation aborted at ../../util/gtf_to_alignment_gff3.pl line 8.
Makefile:2: recipe for target 'test' failed
make[2]: *** [test] Error 2
make[2]: Leaving directory '/home/labpc8c/Documents/Toby/PedroFelix/tools/TransDecoder-TransDecoder-v5.7.0/sample_data/cufflinks_example'
Makefile:5: recipe for target 'test' failed                                                                                                                                                                                                                                                                                
make[1]: *** [test] Error 2                                                                                                                                                                                                                                                                                                
make[1]: Leaving directory '/home/labpc8c/Documents/Toby/PedroFelix/tools/TransDecoder-TransDecoder-v5.7.0/sample_data'                                                                                                                                                                                                    
Makefile:10: recipe for target 'test' failed                                                                                                                                                                                                                                                                               
make: *** [test] Error 2

[GenoMax]

Whenever possible use conda to install things: https://anaconda.org/bioconda/transdecoder

It takes care of dependencies and such automatically. Tutorial on installing conda is here (first part): Creating workflows with snakemake and conda

Answer 1

[coreyhowe99]

This code is working for me on google colab to install and run Transdecoder locally:

#install miniconda
! wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.12.0-Linux-x86_64.sh
! chmod +x Miniconda3-py37_4.12.0-Linux-x86_64.sh
! bash ./Miniconda3-py37_4.12.0-Linux-x86_64.sh -b -f -p /usr/local/

#update conda and check version
!conda install --channel defaults conda python=3.10 --yes
!conda update --channel defaults --all --yes


#add channels
!conda config --add channels bioconda
!conda config --add channels conda-forge

#install transdecoder
!conda install -c bioconda transdecoder -y

#run transdecoder 
!TransDecoder.LongOrfs -t example.fasta && TransDecoder.Predict -t  example.fasta