install_jbrowse.sh

#!/bin/bash

./apollo jbrowse-tools

#done_message () {
#    if [ $? == 0 ]; then
#        echo " done."
#        if [ "x$1" != "x" ]; then
#            echo $1;
#        fi
#    else
#        echo " failed.  See setup.log file for error messages." $2
#    fi
#}
#
#echo > setup.log;
#echo -n "Installing Perl prerequisites ..."
#if [ -f bin/cpanm ]; then
#    echo  "Prerequisites installed, finished.";
#    exit 0;
#fi
#
#if ! ( perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then
#    echo;
#    echo "WARNING: Your Perl installation does not seem to include a complete set of core modules.  Attempting to cope with this, but if installation fails please make sure that at least ExtUtils::MakeMaker is installed.  For most users, the best way to do this is to use your system's package manager: apt, yum, fink, homebrew, or similar.";
#fi;
#( set -x;
#  chmod +x web-app/jbrowse/bin/cpanm
#  cd web-app/jbrowse
#  bin/cpanm -v --notest -l ../../extlib/ --installdeps .< /dev/null;
#  bin/cpanm -v --notest -l ../../extlib/ --installdeps .< /dev/null;
#  set -e;
#  bin/cpanm -v --notest -l ../../extlib/ --installdeps .< /dev/null;
#  cd -
#  cp -r web-app/jbrowse/bin/ bin;
#  chmod +x bin/*.pl;
#  cp -r web-app/jbrowse/src/perl5 src/perl5;
#) >>setup.log 2>&1;
#done_message "" "As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.";