trying to remove conda from analysisrunstatus

Clinical-Genomics · Nov 10, 2022 · 3db1c28 · 3db1c28
1 parent e82203a
commit 3db1c28
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Showing 3 changed files with 31 additions and 25 deletions.
diff --git a/definitions/analyse_parameters.yaml b/definitions/analyse_parameters.yaml
@@ -271,6 +271,8 @@ analysisrunstatus:
   data_type: SCALAR
   default: 1
   file_tag: nofile_tag
+  program_executables:
+    - perl
   type: recipe
 ## Sacct
 sacct:

diff --git a/lib/MIP/Recipes/Analysis/Analysisrunstatus.pm b/lib/MIP/Recipes/Analysis/Analysisrunstatus.pm
@@ -140,16 +140,15 @@ sub analysis_analysisrunstatus {
     ## Creates recipe directories (info & data & script), recipe script filenames and writes sbatch header
     my ($recipe_file_path) = setup_script(
         {
-            active_parameter_href           => $active_parameter_href,
-            core_number                     => $recipe{core_number},
-            directory_id                    => $case_id,
-            filehandle                      => $filehandle,
-            job_id_href                     => $job_id_href,
-            memory_allocation               => $recipe{memory_allocation},
-            process_time                    => $recipe{time},
-            recipe_directory                => $recipe_name,
-            recipe_name                     => $recipe_name,
-            source_environment_commands_ref => $recipe{load_env_ref},
+            active_parameter_href => $active_parameter_href,
+            core_number           => $recipe{core_number},
+            directory_id          => $case_id,
+            filehandle            => $filehandle,
+            job_id_href           => $job_id_href,
+            memory_allocation     => $recipe{memory_allocation},
+            process_time          => $recipe{time},
+            recipe_directory      => $recipe_name,
+            recipe_name           => $recipe_name,
         }
     );
 
@@ -410,8 +409,11 @@ sub _check_vcf_header_and_keys {
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
+    use MIP::Environment::Executable qw{ get_executable_base_command };
     use MIP::File::Path qw{ remove_file_path_suffix };
 
+    my @commands = ( get_executable_base_command( { base_command => q{perl}, } ), );
+
   RECIPE:
     foreach my $recipe_name ( keys %{$vcf_file_href} ) {
 
@@ -427,45 +429,47 @@ sub _check_vcf_header_and_keys {
                     file_suffixes_ref => [qw{ .gz}],
                 }
             );
+            my $command = join q{ }, @commands;
 
-            print {$filehandle} q?perl -MTest::Harness -e ' ?;
+            $command .= q? -MTest::Harness -e ' ?;
 
             ## Adjust arguments to harness object
-            print {$filehandle} q?my %args = (?;
+            $command .= q?my %args = (?;
 
             ## Print individual test results to STDOUT
-            print {$filehandle} q?verbosity => 1, ?;
+            $command .= q?verbosity => 1, ?;
 
             ##Argument to test script
-            print {$filehandle} q?test_args => { ?;
+            $command .= q?test_args => { ?;
 
             ## Add test for select file using alias
-            print {$filehandle} q?"test ? . $mode . $SPACE . $recipe_name . q?" => [ ?;
+            $command .= q?"test ? . $mode . $SPACE . $recipe_name . q?" => [ ?;
 
             ## Infile
-            print {$filehandle} q?"? . $vcf_file_path . q?", ?;
+            $command .= q?"? . $vcf_file_path . q?", ?;
 
             ##ConfigFile
-            print {$filehandle} q?"? . $analysis_config_file . q?", ?;
-            print {$filehandle} q?], ?;
+            $command .= q?"? . $analysis_config_file . q?", ?;
+            $command .= q?], ?;
 
-            print {$filehandle} q?}); ?;
+            $command .= q?}); ?;
 
             ## Create harness using arguments provided
-            print {$filehandle} q?my $harness = TAP::Harness->new( \%args ); ?;
+            $command .= q?my $harness = TAP::Harness->new( \%args ); ?;
 
             ## Execute test(s)
-            print {$filehandle} q?$harness->runtests( ?;
+            $command .= q?$harness->runtests( ?;
 
-            print {$filehandle} q?["?
+            $command .= q?["?
               . catfile( $Bin, qw{ t mip_analysis.test } )
               . q?", "test ?
               . $mode
               . $SPACE
               . $recipe_name . q?"], ?;
 
-            print {$filehandle} q?)'?;
-            say   {$filehandle} $NEWLINE;
+            $command .= q?)'?;
+
+            say {$filehandle} $command . $NEWLINE;
         }
     }
     return;

diff --git a/lib/MIP/Script/Setup_script.pm b/lib/MIP/Script/Setup_script.pm
@@ -663,7 +663,7 @@ sub setup_script {
         {
             bash_bin_path      => catfile( rootdir(), qw{ bin bash } ),
             filehandle         => $filehandle,
-            invoke_login_shell => 1,
+            invoke_login_shell => 0,
         }
     );
     print {$filehandle} $NEWLINE;