All Hive scripts now detect $::hive_root_dir and use it for setting the @INC...

All Hive scripts now detect $::hive_root_dir and use it for setting the @INC so manual setting of PERL5LIB is only needed if using API directly

modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm

@@ -11,7 +11,7 @@ Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf
 init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf -password <mypass>
 
     # Example 2: specifying the mandatory options as well as overriding some defaults:
-init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf -hive_root_dir ~/ensembl_main/ensembl-hive-new -pipeline_db -host <myhost> -pipeline_db -dbname <mydbname> -password <mypass>
+init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf -pipeline_db -host <myhost> -pipeline_db -dbname <mydbname> -password <mypass>
 
 =head1 DESCRIPTION
 
@@ -73,9 +73,10 @@ use base ('Bio::EnsEMBL::Hive::DependentOptions');
 sub default_options {
     my ($self) = @_;
     return {
-        'ensembl_cvs_root_dir'  => $self->o('ENV', 'ENSEMBL_CVS_ROOT_DIR'),             # it will make sense to set this variable if you are going to use ehive frequently
-        'hive_root_dir'         => $self->o('ensembl_cvs_root_dir').'/ensembl-hive',    # but you may want to have Hive elsewhere, which is perfectly legitimate
-        'password'              => $self->o('ENV', 'ENSADMIN_PSW'),                     # people will have to make an effort NOT to insert it into config files like .bashrc etc
+        'ensembl_cvs_root_dir'  => $self->o('ENV', 'ENSEMBL_CVS_ROOT_DIR'),                     # it will make sense to set this variable if you are going to use ehive with ensembl
+        'hive_root_dir'         => $::hive_root_dir                                             # this value is set up automatically if this code is run by init_pipeline.pl
+                                    || $self->o('ENV', 'ENSEMBL_CVS_ROOT_DIR').'/ensembl-hive', # otherwise we have to rely on other means
+        'password'              => $self->o('ENV', 'ENSADMIN_PSW'),                             # people will have to make an effort NOT to insert it into config files like .bashrc etc
 
         'host'                  => 'localhost',
         'pipeline_name'         => 'hive_generic',

scripts/beekeeper.pl

@@ -2,11 +2,17 @@
 
 use strict;
 use warnings;
-use Getopt::Long;
 
-use Cwd 'abs_path';             # both are needed to pick 'our' runWorker.pl
-use File::Basename 'dirname';   #
+    # Finding out own path in order to reference own components (including own modules):
+use Cwd            ();
+use File::Basename ();
+our $hive_root_dir;
+BEGIN {
+    $hive_root_dir = File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) );
+    unshift @INC, "$hive_root_dir/modules";
+}
 
+use Getopt::Long;
 use Bio::EnsEMBL::Hive::Utils ('script_usage', 'destringify');
 use Bio::EnsEMBL::Hive::Utils::Config;
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
@@ -275,8 +281,7 @@ sub main {
 sub generate_worker_cmd {
     my ($self, $run_analysis, $run_job_id, $force) = @_;
 
-    my $beekeeper_fullpath = abs_path($0);
-    my $worker_cmd = dirname($beekeeper_fullpath).'/runWorker.pl';
+    my $worker_cmd = "$::hive_root_dir/scripts/runWorker.pl";
 
     unless(-x $worker_cmd) {
         print("Can't run '$worker_cmd' script for some reason, please investigate.\n");

scripts/generate_graph.pl

@@ -5,6 +5,16 @@ package Script;
 use strict;
 use warnings;
 
+    # Finding out own path in order to reference own components (including own modules):
+use Cwd            ();
+use File::Basename ();
+our $hive_root_dir;
+BEGIN {
+    $hive_root_dir = File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) );
+    unshift @INC, "$hive_root_dir/modules";
+}
+
+
 use Getopt::Long;
 use Pod::Usage;
 

scripts/hoover_pipeline.pl

@@ -2,8 +2,17 @@
 
 use strict;
 use warnings;
-use Getopt::Long;
 
+    # Finding out own path in order to reference own components (including own modules):
+use Cwd            ();
+use File::Basename ();
+our $hive_root_dir;
+BEGIN {
+    $hive_root_dir = File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) );
+    unshift @INC, "$hive_root_dir/modules";
+}
+
+use Getopt::Long;
 use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;

scripts/init_pipeline.pl

 #!/usr/bin/env perl
-#
+
 # A generic loader of hive pipelines.
 #
 # Because all of the functionality is hidden in Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf
@@ -8,8 +8,18 @@
 
 use strict;
 use warnings;
-use Bio::EnsEMBL::Hive::Utils ('script_usage', 'load_file_or_module');
 
+    # Finding out own path in order to reference own components (including own modules):
+use Cwd            ();
+use File::Basename ();
+our $hive_root_dir;
+BEGIN {
+    $hive_root_dir = File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) );
+    unshift @INC, "$hive_root_dir/modules";
+}
+
+
+use Bio::EnsEMBL::Hive::Utils ('script_usage', 'load_file_or_module');
 
 sub main {
     my $file_or_module = shift @ARGV or script_usage(0);

scripts/lsf_report.pl

@@ -4,8 +4,17 @@
 
 use strict;
 use warnings;
-use Getopt::Long;
 
+    # Finding out own path in order to reference own components (including own modules):
+use Cwd            ();
+use File::Basename ();
+our $hive_root_dir;
+BEGIN {
+    $hive_root_dir = File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) );
+    unshift @INC, "$hive_root_dir/modules";
+}
+
+use Getopt::Long;
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Hive::Utils ('script_usage');
 

scripts/runWorker.pl

@@ -2,6 +2,16 @@
 
 use strict;
 use warnings;
+
+    # Finding out own path in order to reference own components (including own modules):
+use Cwd            ();
+use File::Basename ();
+our $hive_root_dir;
+BEGIN {
+    $hive_root_dir = File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) );
+    unshift @INC, "$hive_root_dir/modules";
+}
+
 use Getopt::Long;
 use Bio::EnsEMBL::Hive::Utils ('script_usage');
 use Bio::EnsEMBL::Registry;

scripts/seed_pipeline.pl

@@ -2,8 +2,17 @@
 
 use strict;
 use warnings;
-use Getopt::Long;
 
+    # Finding out own path in order to reference own components (including own modules):
+use Cwd            ();
+use File::Basename ();
+our $hive_root_dir;
+BEGIN {
+    $hive_root_dir = File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) );
+    unshift @INC, "$hive_root_dir/modules";
+}
+
+use Getopt::Long;
 use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;

scripts/standaloneJob.pl

@@ -2,14 +2,22 @@
 
 use strict;
 use warnings;
+
+    # Finding out own path in order to reference own components (including own modules):
+use Cwd            ();
+use File::Basename ();
+our $hive_root_dir;
+BEGIN {
+    $hive_root_dir = File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) );
+    unshift @INC, "$hive_root_dir/modules";
+}
+
 use Getopt::Long qw(:config pass_through);
 use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Hive::Process;
 use Bio::EnsEMBL::Hive::AnalysisJob;
 use Bio::EnsEMBL::Hive::Utils ('script_usage', 'load_file_or_module', 'parse_cmdline_options', 'stringify', 'destringify');
 
-use Data::Dumper;
-
 my ($reg_conf, $help, $debug, $no_write, $no_cleanup, $flow_into, $input_id);
 
 my $module_or_file = shift @ARGV or script_usage();