Getting the jbrowse/bin scripts to work

[mpoelchau]

To get the scripts in jbrowse/bin to work, we had to do the following:

  bin/cpanm -l extlib --installdeps .
  sudo yum install perl-CPAN.x86_64
  sudo cpan local::lib
  sudo cpan JSON

Then, add /home/vagrant/jbrowse/bin to PATH

This was kind of a convoluted troubleshooting process, so the following may also be necessary:

sudo yum groupinstall "Development Tools" 
sudo yum install zlib-devel perl-ExtUtils-MakeMaker

and then (can break if node is not up to date)

cd ~/jbrowse
./setup.sh

In the future, we'd need to run through the whole process again to see what's absolutely necessary to install, then update the vagrantfile accordingly.

Related issues:

• Workflow: flow_apollo2 Organism_Onboarding#26
• install npm and finish setup of javascript dependencies of genomics-workspace #9 (jbrowse requires node)

[mpoelchau]

This time around setup.sh didn't work. We installed the missing perl modules manually. Had to go in as root and use cpan. Installed the following modules:

Hash::Merge
CGI
Heap::Simple
Heap::Simple:XS

[mpoelchau]

Update - this setup worked after setting up vagrant via kenttools branch. I think having node installed is a prerequisite. I included some notes below about changes that need to be made in order to make this work via vagrant. FYI using jbrowse's setup.sh failed, hence some of the extra installation steps here.

cd ~/jbrowse
bin/cpanm -l extlib --installdeps .
sudo yum install perl-CPAN.x86_64 #note that this is interactive/have to press y
sudo cpan local::lib #note that this is interactive
sudo cpan JSON
sudo yum groupinstall "Development Tools" #also interactive
sudo cpan Hash::Merge #interactive
cpanm CGI --sudo
cpanm  Heap::Simple --sudo
sudo cpan Heap::Simple:XS #interactive