Merge pull request #55 from mathiasbockwoldt/master

Added installing Perl modules and bundled with Python modules

help/faq.rst

@@ -66,37 +66,7 @@ If we don't have it installed, and installing it yourself is not a good solution
 Can I install Python software as a normal user without sudo rights?
 -------------------------------------------------------------------
 
-Yes. The recommended way to achieve this is using
-`virtual environments <https://docs.python.org/3/tutorial/venv.html>`_
-
-As an example we install the Biopython package (and here we use
-the `Python/3.6.4-intel-2018a` module as an example)::
-
-  $ module load Python/3.6.4-intel-2018a
-  $ virtualenv venv
-  $ source venv/bin/activate
-  $ pip install biopython
-
-Next time you log into the machine you have to activate
-the virtual environment::
-
-  $ source venv/bin/activate
-
-If you want to leave the virtual environment again, type::
-
-  $ deactivate
-
-And you do not have to call it "venv". It is no problem to have many
-virtual environments in your home directory. Each will start as a clean
-Python setup which you then can modify. This is also a great system to have
-different versions of the same module installed side by side.
-
-If you want to inherit system site packages into your virtual
-environment, do this instead::
-
-  $ virtualenv --system-site-packages venv
-  $ source venv/bin/activate
-  $ pip install biopython
+Yes. Please see :doc:`/software/local_script_modules`.
 
 
 Compute and storage quota

index.rst

@@ -75,6 +75,7 @@ HPC-UiT Services User Documentation
 
    software/applications
    software/modules
+   software/local_script_modules
    account/linux
    help/AboutLicenses
    news/new_sw

software/local_script_modules.rst

@@ -0,0 +1,77 @@
+.. _local_script_modules:
+
+Local script modules
+====================
+
+Scripting languages often support modules or libraries for additional functionality or convenience functions. We encourage users to install modules locally for only the current user.
+
+
+Python
+------
+
+For Python, the recommended way to install modules locally is using
+`virtual environments <https://docs.python.org/3/tutorial/venv.html>`_
+
+As an example we install the Biopython package (and here we use
+the ``Python/3.6.4-intel-2018a`` module as an example)::
+
+  $ module load Python/3.6.4-intel-2018a
+  $ virtualenv venv
+  $ source venv/bin/activate
+  $ pip install biopython
+
+Next time you log into the machine you have to activate
+the virtual environment::
+
+  $ source venv/bin/activate
+
+If you want to leave the virtual environment again, type::
+
+  $ deactivate
+
+And you do not have to call it "venv". It is no problem to have many
+virtual environments in your home directory. Each will start as a clean
+Python setup which you then can modify. This is also a great system to have
+different versions of the same module installed side by side.
+
+If you want to inherit system site packages into your virtual
+environment, do this instead::
+
+  $ virtualenv --system-site-packages venv
+  $ source venv/bin/activate
+  $ pip install biopython
+
+
+Perl
+----
+
+We will use Perl 5.28 and use the standard paths.
+This follows the general instruction given here: https://metacpan.org/pod/local::lib.
+
+::
+
+  $ module load Perl/5.28.0-GCCcore-7.3.0
+  $ mkdir my_perl_installs   # or however you want to call this temporary folder
+  $ cd my_perl_installs
+
+  # Check the newest version on metacpan.org and search for local::lib
+  $ wget https://cpan.metacpan.org/authors/id/H/HA/HAARG/local-lib-2.000024.tar.gz
+
+  $ tar xzf local-lib-2.000024.tar.gz
+  $ cd local-lib-2.000024
+  $ perl Makefile.PL --bootstrap
+  $ make test
+  $ make install
+  $ echo 'eval "$(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)"' >> ~/.bashrc
+  $ source ~/.bashrc
+
+Now, the module local::lib is installed and the ``~/.bashrc`` changed such that Perl should now recognize your local folder as module folder.
+All future modules will be installed to ``~/perl5``.
+
+If you want to install, for example, the module Math::Vector::Real, just call cpan::
+
+  $ cpan Math::Vector::Real
+
+Remember to load the right Perl version first (``module load ...``).
+The first time you call cpan, it will ask you to do some configurations.
+Just press enter (let it do its configurations).