Bash Install Script

[hoelzer]

I was able to run the INSTALL.sh script on my local Linux System with the following adjustments:

1) I manually soft-linked pip to pip3 because the install script is checking for pip3 explicitly

2) I installed prokka via conda because the install script was failing (maybe due to the tbl2asn binary)

3) I manually run

cpanm  Array::Utils Bio::Perl Exception::Class File::Basename File::Copy File::Find::Rule File::Grep File::Path File::Slurper File::Spec File::Temp File::Which FindBin Getopt::Long Graph Graph::Writer::Dot List::Util Log::Log4perl Moose Moose::Role Text::CSV PerlIO::utf8_strict Devel::OverloadInfo Digest::MD5::File 

after ROARY install failed.

Then everything was working.

[hoelzer]

again what worked for me (I redid the install)

conda create -n ribap python=3.7
ln -s /home/martin/miniconda3/envs/ribap/bin/pip /home/martin/miniconda3/envs/ribap/bin/pip3
conda install -c bioconda prokka
./INSTALL.sh

export PATH=$PATH:/home/martin/ribap/bin
export PERL5LIB=$PERL5LIB:/home/martin/ribap/lib

Likely, I did not have to do again

cpanm  Array::Utils Bio::Perl Exception::Class File::Basename File::Copy File::Find::Rule File::Grep File::Path File::Slurper File::Spec File::Temp File::Which FindBin Getopt::Long Graph Graph::Writer::Dot List::Util Log::Log4perl Moose Moose::Role Text::CSV PerlIO::utf8_strict Devel::OverloadInfo Digest::MD5::File 

[hoelzer]

... and then I run into

/home/martin/ribap/bin/ribap.sh: line 254: /home/martin/ribap/bin/bin/blast2tsv.py: No such file or directory

so I

cp -r bin /home/martin/ribap/bin/

[klamkiew]

To be honest, I think we can also kick the shell scripts or at least flag them as "not maintained" It was a nice exercise back in 2018 to do both, the install and the main script in bash, but it doesn't make any sense to use those in my eyes :)

[hoelzer]

+1