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METALNX MSI BUILD GUIDE

Build From Source Instructions

Copyright © 2015-2017 Dell EMC.

This software is provided under Apache License 2.0.

The information in this file is provided “as is.” Dell EMC makes no representations or warranties of any kind with respect to the information in this publication, and specifically disclaims implied warranties of merchantability or fitness for a particular purpose.


Introduction

This tutorial guides you through the Metalnx MSI compilation pipeline. It explains how to build Metalnx MSI from scratch.

Building Metalnx MSI RPM and DEB packages

The Metalnx MSI package is an optional package that provides a set of iRODS micro services allowing the data grid to automatically extract metadata from certain kinds of files. It relies on the irods-dev library provided by iRODS.

This package also provides automatic metadata extraction for genetic research files (BAM, SAM, CRAM, VCF and Illumina project manifest). In order to allow iRODS and Metalnx to understand these files formats, you must install additional libraries: * HTSlib * samtools

Installing the irods-dev package, HTSlib and Samtools

Please refer to our INSTALL document before proceeding to the next section.

On DEB-based or RPM-based systems, you will need the basic development tools in order to download, compile and install samtools (C++ compiler, make):

$ wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2    # Getting sources from GitHub
$ tar -xvf samtools-1.3.1.tar.bz2															  # Extracting tarball
$ cd samtools-1.3.1																			  # Entering sources directory
$ ./configure --without-curses																  # Configuring compilation pipeline
$ make																						  # Compiling source code
$ sudo make install																			  # Installing compiled binary
$ sudo cp *.h /usr/local/include/															  # Installing headers

Building package

Once the previous requirements are satisfied, you can build the MSI package. The format of the package will depend on which platform you are executing these commands on.

That happens because the Metalnx MSI packing system is based on EPM (Enterprise Package Manager), which is part of the iRODS compilation pipeline. The EPM automatically manages the package creation depending on which platform it is running on.

The first step is make sure you have the metalnx-msi sources downloaded and a terminal session opened on the source tree root:

$ cd metalnx-msi

Then you have to make sure your Linux user has execution permission on the build.sh script:

$ chmod u+x packaging/build.sh

Note: This build script creates packages according to your OS (*.rpm or *.deb). In order to create RPMs, it needs the rpmbuild package installed. You can install it by running: yum install -y rpmbuild

In order to build the MSI package against different versions of iRODS within the same environment, compilation scripts and make files have changed a little.

The MSI package compilation pipeline now relies on two environment variables that tell which iRODS version you are building the package against and where the iRODS libraries are. Those two variables are IRODSROOT and IRODSVERSION.

Between these two variables, only IRODSVERSION is required. If IRODSROOT is not set, the compilation scripts will look for the iRODS libraries under /usr/include/irods/ as before.

Now, execute the build.sh script

NOTE: This command must be executed from the source tree root, otherwise it will NOT work.":

$ IRODSVERSION=4.1.X IRODSROOT=/tmp/irods-packages/4.1.X ./packaging/build.sh      # building MSI against iRODS libs in a different location
$ IRODSVERSION=4.1.X ./packaging/build.sh                                           # building MSI against iRODS libs in a standard location

Once completed, your resulting package can be found at <metalnx_msi_root>/linux-X.XX-<arch>/RPMS/<arch>metalnx-msi-plugins-4.1.X-1.0-DEV.<arch>.<rpm/deb>.