https://bioinformaticsonline.com/snippets/view/37015/install-perl-locally? https://bioinformaticsonline.com/snippets/view/37015/install-perl-locally Fri, 22 Jun 2018 05:26:42 -0500 https://bioinformaticsonline.com/snippets/view/37015/install-perl-locally # To follow these instructions, we'll assume your system admins have already installed these essentials: # Debian/Ubuntu system admins should run: sudo apt-get install -y build-essential libexpat1-dev libssl-dev libmysqlclient-dev libxml2-dev # RHEL/CentOS system admins should run: sudo yum groupinstall -y 'Development Tools' sudo yum install -y expat-devel openssl-devel mysql-devel libxml2-devel # Create a folder where you want to install different Perls, and cd into it: # Note that it doesn't need to be your home folder. Put it wherever you want to maintain such software: export PERL_BASE="$HOME/perl" mkdir -p $PERL_BASE cd $PERL_BASE # Download source tarball into a subfolder named src, and untar: curl --create-dirs -L -o src/perl-5.24.1.tar.gz http://www.cpan.org/src/5.0/perl-5.24.1.tar.gz cd src tar -zxf perl-5.24.1.tar.gz # Configure and build, making sure that this non-standard location is baked into the perl binary: cd perl-5.24.1 ./Configure -des -Dprefix=$PERL_BASE/perl-5.24.1 -Dotherlibdirs=$PERL_BASE/perl-5.24.1/lib/perl5 make make install # Install dependencies for Ensembl API, VEP, OncoKB, and other tools we use here at MSKCC: curl -sL https://cpanmin.us | $PERL_BASE/perl-5.24.1/bin/perl - --notest -l $PERL_BASE/perl-5.24.1 App::cpanminus JSON::Parse XML::Parser XML::Simple LWP LWP::Simple LWP::Protocol::https Archive::Extract Archive::Tar Archive::Zip CGI DBI Time::HiRes DBD::mysql Encode File::Copy::Recursive Perl::OSType Module::Metadata Statistics::Lite Tie::Autotie Tie::IxHash Log::Log4perl FindBin::Real Getopt::Long Catalyst::Runtime Catalyst::Devel List::Util Test::XML::Simple Test::XPath IO::String Bio::Perl version # Set $PERL5LIB to find these libraries, and set $PATH to use this Perl instead of the system Perl: export PERL5LIB="$PERL_BASE/perl-5.24.1/lib/perl5:$PERL_BASE/perl-5.24.1/lib/perl5/x86_64-linux:$PERL5LIB" export PATH="$PERL_BASE/perl-5.24.1/bin:$PATH" # You can add those 2 lines to the end of your `~/.bashrc` to make it persistent. # But be sure to define `$PERL_BASE` in your `~/.bashrc` too.]]> Aaryan Lokwani