I have created a docker Galaxy container from bgruening/galaxy-stable (UBUNTU 18.04, Galaxy 19.05). The non-Tool Shed tool example script toolExample.pl works successfully running:
sudo docker run -d -p 8080:80 -v /home/wedlerh/mygalaxy_storage2/:/export/ -v /home/wedlerh/my_galaxy_tools/:/local_tools/ -e GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/shed_tool_conf.xml,/local_tools/my_tools.xml --name mygalaxy2 wedlerh/mygalaxy
Now I want to install non-Tool Shed tools which require perl modules such as:
Data::Dump::Color, File::Slurp, File::Temp, Pod::Usage, Template, Getopt::Long::Descriptive, Getopt::Lucid, Statistics::Descriptive, Data::Dumper etc.
Unfortunately, I get error messages such as:
Can’t locate Data/Dump/Color.pm in @INC (you may need to install the Data::Dump::Color module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /local_tools/binned_reads.pl line 4.
BEGIN failed–compilation aborted at /local_tools/binned_reads.pl line 4.
My custom perl scripts run successfully on the system outside of the container including their dependencies.
How do I install perl scripts with module dependencies running docker Galaxy?