perl-admix

Perl and its modules RPMS created via YAML2RPM

Prerequisites

1. Make sure the development RPMs are installed. Follow the Quickstart section of the guide in https://github.com/RCIC-UCI-Public/yaml2rpm/blob/master/README.md

2. Check environment an unset if any of the PERL related are set. Specifically,

   unset PERL5LIB PERL_MB_OPT PERL_LOCAL_LIB_ROOT PERL_MM_OPT

   When these variabls are set it can change the default options for perl build and create an incompatibility.

Build Perl

These include packages perl, its environment module and a set of modules that are needed to bootstrap building environment for using MetaCPAN::Client.

1. Download the repo

   git clone https://github.com/RCIC-UCI-Public/perl-admix

2. Create a directory for distribution soruces and download sources for perl and its bootstrap packages from CPAN.

   cd perl-admix/
   make sources
   
   cd yamlspecs/
   make prep

   After this step, sources/ is created at the top level directory and all source distribution files for packages are downloaded.

3. Compile and install perl and its bootstrap packages

   make bootstrap | tee out 2>&1
   make bootstrap  SET=meta | tee out-meta 2>&1

   After this step, perl, perl environment module and 95 additional RPMS are build. They contain a basic perl with additional packages to use MetaCpan::Client module.

   In addition, a single RPM perl_VERSION-metacpan is created. It installs a single README.metacpan file in the perl base install directory and includes all other RPMs from bootstrap build as dependencies. This allows to install all perl bootstrap RPMs via simply installing this one RPM (assuming yum points to the repo where all created perl boostrap RPMS are).

Build BioPerl and its dependencies

1. A BioPerl module requires a large number of prerequisites which are not cleanly defined in CPAN dependencies. We provide a way to to install all checked dependencies. Required yaml files are in bioperl/ and the following commands wil build and install all needed RPMS. This aassumes that Perl and its metacpan RPMs were already built and installed. The following command will build and install RPMS in the correct dependency order.

   cd yamlspecs/
   make bootstrap SET=bio | tee out 2>&1
   
   To erase all built and installed BioPerl RPMS
   ```bash
   make bioerase

Building RPMS for additional modules

The steps below outline how one can automate to a large degree creation of the additiona perl modules RPMs. Because the perl modules do not always obey the build process and do not provide all the dependency information, there will be always case that will need a manual adjustment.

This usually involves overwriting requires/provides or changing the order in a buildorder file. For the requires/provides see examples of the filters in the metacpan/Package-Stash.yaml or metacpan/ExtUtils-Helpers.yaml or other yaml files that contain filter_requires or filter_provides directives.

For the buildorder updates, follow error messages during RPMs build and check for errors in the out file, then adjust the buildprder and rerun build RPM command.

The standard, no change outline is:

1. Create a file that lists desired perl modules names one per line using perl module name schema, For example, a default file name is desired and the file content is:

   A::B
   C
   F::K

2. Before the next step make sure there is ~/.cpan/CPAN/MyConfig.pm file The template for this file is generated when running cpan -l command but is doen interactively. We can generate this file before running any cpan commands via:

   make MyConfig.pm
   mkdir -p  ~/.cpan/CPAN/
   cp MyConfig.pm  ~/.cpan/CPAN/MyConfig.pm

3. Run a program that will query CPAN for the modules and their prerequisites and create yaml files for found modules. In some instances, a module will be provided by the parent modules distribution. Use perl version for which you are building the the modules. For example:

   cd yamspecs/
   module load perl/X.Y.Z
   make desired-yaml

   Ater the execution, the following files are generated:

   • NAME.yaml for each desired module NAME and any found dependent modules
   • buildorder, shows in what order RPMS will need to be built. This file will need to be included in a new set-SOMENAME,yaml file.
   • versions-bootstrap, with versions and distro location in cpan. This file will need to be included in versions-SOMENAME.yaml file and referenced in above set-SOMENAME.yaml
   • versions-desired, summary information about order and versions.

4. To download all source distributions for generated yaml files one can execute

   make desired-download

5. To build and install RPMS for desired modules:

   make desired-build | tee out 2>&1

   If the build goes well a new set and its version file can be created and the set can be added to packages.yaml.

6. To remove built and install RPMs

   make desired-erase