Changes between Version 18 and Version 19 of Admin/StandardOperatingProcedures/InstallSoftwareFromSource

Timestamp:

Jun 3, 2019, 1:41:30 PM (6 years ago)

Author:

Mikael Brandström Durling

Comment:

--

Admin/StandardOperatingProcedures/InstallSoftwareFromSource

@@ -29 +29 @@
 The basic Python/Perl interpreter should be installed in the same manner as any other package. Any python/perl package should be installed as modules which then set a `depends_on()` for the specific version of the interpreter it was installed with. The dependent version of the interpreter should be documented in the wiki page. Modules for python packages should be named -py3 if they are installed against python3.
 
-=== Python ===
-In many cases, installation of python packages can be trivial. If they are available in the python package index, then the actual compile/install steps boils down to `pip install --prefix=/opt/sw/SOFTWARE/VERSION SOFTWARE` (maybe with an added -py3 and pip3). The python module you want to install against has to be loaded.
+=== Python Packages===
+In many cases, installation of python packages can be trivial. If they are available in the python package index, then the actual compile/install steps boils down to `pip install --prefix=/opt/sw/SOFTWARE/VERSION SOFTWARE` (maybe with an added -py3 and pip3). The python module you want to install against has to be loaded. In cases where you have to run setup.py yourself, you need to specify a proper prefix to the install command.
 
+If the package you are about to install requires any of our currently available modules, then please load the module first, and then install the package. Don't forget to add the pre-loaded modules as requirements in the new module file. (Check e.g. the biopython-py3 module for how to achieve this.)
 
+=== Perl packages ===
 
+Similar to python packages, the install prefix has to be set when installing perl packages. Packages that can be installed using CPAN, if prefix paths are set first using `o conf makepl_arg PREFIX=/opt/sw/SOFTWARE/VERSION` and `conf mbuildpl_arg "--prefix /opt/sw/bioperl/2.1.8"` and finally `o conf commit`.¨