Easybuild: Usage Example

Creating and Using Ecosystem

Flight Env provides quick setup methods to create an easybuild software ecosystem.

To install and use easybuild:

• Activate the flight system

• Create the easybuild installation for the user:

  [flight@gateway1 ~]$ flight env create easybuild
  Creating environment easybuild@default
     > ✅ Verifying prerequisites
     > ✅ Fetching prerequisite (lua)
     > ✅ Extracting prerequisite (lua)
     > ✅ Building prerequisite (lua)
     > ✅ Installing prerequisite (lua)
     > ✅ Fetching prerequisite (tcl)
     > ✅ Extracting prerequisite (tcl)
     > ✅ Building prerequisite (tcl)
     > ✅ Installing prerequisite (tcl)
     > ✅ Fetching prerequisite (lmod)
     > ✅ Extracting prerequisite (lmod)
     > ✅ Configuring prerequisite (lmod)
     > ✅ Installing prerequisite (lmod)
     > ✅ Fetching prerequisite (easybuild)
     > ✅ Bootstrapping EasyBuild environment (easybuild@default)
  Environment easybuild@default has been created
  

• Activate the easybuild ecosystem:

  [flight@gateway1 ~]$ flight env activate easybuild
  <easybuild> [flight@gateway1 ~]$
  

• Check that easybuild can be run:

  <easybuild> [flight@gateway1 ~]$ module load EasyBuild
  <easybuild> [flight@gateway1 ~]$ eb --version
  This is EasyBuild 3.9.4 (framework: 3.9.4, easyblocks: 3.9.4) on host gateway1.pri.basic.cluster.local.
  

Installing and Running Perl

An example workflow using perl is demonstrated below.

• View available versions:

  <easybuild> [flight@gateway1 ~]$ eb -S perl
  CFGS1=/home/flight/.local/share/flight/env/easybuild+default/software/EasyBuild/3.9.4/lib/python2.7/site-packages/easybuild_easyconfigs-3.9.4-py2.7.egg/easybuild/easyconfigs
   * $CFGS1/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb
   * $CFGS1/b/Bio-DB-HTS/Bio-DB-HTS-2.11-foss-2017b-Perl-5.26.0.eb
   * $CFGS1/b/Bio-DB-HTS/Bio-DB-HTS-2.11-foss-2018b-Perl-5.28.0.eb
   * $CFGS1/b/Bio-DB-HTS/Bio-DB-HTS-2.11-intel-2017b-Perl-5.26.0.eb
  <-- snip -->
   * $CFGS1/p/Perl/Perl-5.26.1-GCCcore-6.4.0.eb
   * $CFGS1/p/Perl/Perl-5.26.1-foss-2018a-bare.eb
   * $CFGS1/p/Perl/Perl-5.26.1-foss-2018a.eb
   * $CFGS1/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb
   * $CFGS1/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb
  <-- snip -->
   * $CFGS1/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb
   * $CFGS1/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb
  
  Note: 9 matching archived easyconfig(s) found, use --consider-archived-easyconfigs to see them
  

• Install specific version:

  <easybuild> [flight@gateway1 ~]$ eb Perl-5.28.1-GCCcore-8.2.0.eb --robot
  == temporary log file in case of crash /tmp/eb-MdohD2/easybuild-J6tjhZ.log
  == resolving dependencies ...
  == processing EasyBuild easyconfig /home/flight/.local/share/flight/env/easybuild+default/software/EasyBuild/3.9.4/lib/python2.7/site-packages/easybuild_easyconfigs-3.9.4-py2.7.egg/easybuild/easyconfigs/m/M4/M4-1.4.18.eb
  == building and installing M4/1.4.18...
  == fetching files...
  == creating build dir, resetting environment...
  == unpacking...
  == patching...
  == preparing...
  == configuring...
  == building...
  <-- snip -->
  

• Check installation location:

  <easybuild> [flight@gateway1 ~]$ which perl
  

• Install perl library (this may prompt for initial cpan configuration, once configuration is complete then the library will be installed):

  <easybuild> [flight@gateway1 ~]$ cpan File::Slurp
  Loading internal null logger. Install Log::Log4perl for logging messages
  Reading '/home/flight/.cpan/Metadata'
    Database was generated on Mon, 09 Sep 2019 15:47:03 GMT
  Running install for module 'File::Slurp'
  <-- snip -->
  

• Check installation worked:

  <easybuild> [flight@gateway1 ~]$ cpan File::Slurp
  Loading internal null logger. Install Log::Log4perl for logging messages
  Reading '/home/flight/.cpan/Metadata'
    Database was generated on Mon, 09 Sep 2019 15:47:03 GMT
  File::Slurp is up to date (9999.27).