Merge pull request #63 from Danzelot/software-installation

Software installation

software/applications.rst

@@ -8,14 +8,6 @@ To find out what software packages are available, type::
   module avail
 
 
-Missing or new software
------------------------
-
-If there is any software missing on this list that you would like to have
-installed on Stallo, or you need help to install your own software, please
-feel free to contact the support personal about this: support@metacenter.no.
-
-
 Changes in application software
 -------------------------------
 
@@ -33,3 +25,70 @@ List all software available::
 List all version of a specific software::
 
   module avail software-name
+
+
+Missing or new software
+========================
+
+If there is any software missing on this list that you would like to have
+installed on Stallo, or you need help to install your own software, please
+feel free to contact the support personal about this: support@metacenter.no.
+
+If there is software missing on Stallo that you would like to have, there are
+different options to install it:
+* Use our installation framework EasyBuild
+* Use a package manager like Conda or especially for bioinformatic software Bioconda
+* Compile it yourself and install into your home directory
+* Ask us to install for you
+
+In this document we will show some ways of installing a new software.
+If you run into problems, need help or have question, please
+feel free to contact the support personal about this: support@metacenter.no.
+
+
+Installing new software using EasyBuild
+-----------------------------------------
+
+Our building and installation framework, `EasyBuild <https://easybuild.readthedocs.io/en/latest/Using_the_EasyBuild_command_line.html>`_ 
+can be used by you to install software into your own home directory.
+This is especially interesting for you if you need a software but it is probably
+not used by other users of Stallo, so a systemwide installation doesn't make much sense.
+
+To see if your software is available via the EasyBuild system have a look into the
+`easyconfig github repository <https://github.com/easybuilders/easybuild-easyconfigs>`_.
+if you can find a version of your software there.
+
+Let's assume you want to install the genome aligner Kraken2.
+We find a easyconfig file with the name `Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb <https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb`_ 
+in the easyconfig repository.
+
+Before we start the installation process we first have to load the necessary modules::
+  
+  ml purge
+  ml EasyBuild
+
+Before we actually build we can check the building process by adding
+`--dry-run-short` or `-D` to the build command::
+
+  eb Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb --dry-run-short
+
+As you probably see, a long list of packages is printed with some packages being marked as missing. To automatically install all necessary dependencies we can add `--robot` and then 
+run the installation::
+
+  eb Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb --robot
+
+Before we can load your newly installed module, we have to add the path to the Lmod search path.
+You might have to do this from time to time, or even every time you use your software, as your local cache is regularly updated. ::
+ 
+  ml use ~/.local/easybuild/modules/all
+  ml Kraken2/2.0.7
+
+
+Conda/ Bioconda
+-------------------
+
+Many software packages, especially if they are python based, can be easily installed using
+the Conda package manager.
+For many bioinformatics software, Bioconda has become a nice solution.
+
+A small tutorial can be found in the `Python`_ section of this documentation.

software/python_r_perl.rst

@@ -167,17 +167,14 @@ Load R
 Using R on Stallo is quite straightforward.
 First check which versions are available::
 
-  ml avail R/
+  ml avail -r '^R/'
 
 To load a version::
 
   ml R/3.5.0-iomkl-2018a-X11-20180131
 
 Now you can use R from the command line just as you would on your local computer.
 
-On Stallo you can also always load the newest R version by simply using ``ml R``
-but be aware that this might break your scripts in case a new R version is installed.
-
 
 Install Packages
 -----------------