initiate conda

Clinical-Genomics · Nov 21, 2022 · 13cf1b9 · 13cf1b9
1 parent e94cd8a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,10 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [11.0.3]
+
+- Initiate conda prior to activation
+
 ## [11.0.2]
 
 Updates chromograph

diff --git a/lib/MIP/Active_parameter.pm b/lib/MIP/Active_parameter.pm
@@ -656,14 +656,12 @@ sub check_sample_id_in_hash_parameter_path {
                 ## Check sample_id are unique
                 next SAMPLE_ID if ( $seen{$sample_id} < 2 );
 
-                $log->fatal(
-                        q{Sample_id: }
+                $log->fatal( q{Sample_id: }
                       . $sample_id
                       . q{ is not uniqe in '--}
                       . $parameter_name . q{': }
                       . $path . q{=}
-                      . $sample_ids_str,
-                );
+                      . $sample_ids_str, );
                 exit 1;
             }
         }
@@ -677,14 +675,12 @@ sub check_sample_id_in_hash_parameter_path {
 
             my $seen_sample_ids = join $COMMA . $SPACE, ( keys %seen );
 
-            $log->fatal(
-                    q{Could not detect }
+            $log->fatal( q{Could not detect }
                   . $sample_id
                   . q{ for '--}
                   . $parameter_name
                   . q{'. Provided sample_ids are: }
-                  . $seen_sample_ids,
-            );
+                  . $seen_sample_ids, );
             exit 1;
         }
     }
@@ -1042,11 +1038,14 @@ sub get_package_env_cmds {
     }
 
     ## Get env load command
+    my $conda_init_path =
+      catfile( $active_parameter_href->{conda_path}, qw{ etc profile.d conda.sh } );
     my @env_method_cmds = get_env_method_cmds(
         {
-            action     => q{load},
-            env_name   => $env_name,
-            env_method => $env_method,
+            action          => q{load},
+            conda_init_path => $conda_init_path,
+            env_name        => $env_name,
+            env_method      => $env_method,
         }
     );
     return @env_method_cmds;

diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
@@ -81,7 +81,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{11.0.2};
+Readonly our $MIP_VERSION => q{11.0.3};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

diff --git a/lib/MIP/Environment/Manager.pm b/lib/MIP/Environment/Manager.pm
@@ -28,14 +28,16 @@ sub get_env_method_cmds {
 
 ## Function : Get the standard load and unload env command for environment method
 ## Returns  : @env_method_cmds
-## Arguments: $action     => What to do with the environment
-##          : $env_method => Method used to load environment
-##          : $env_name   => Name of environment
+## Arguments: $action          => What to do with the environment
+##          : $conda_init path => path to initialize conda
+##          : $env_method      => Method used to load environment
+##          : $env_name        => Name of environment
 
     my ($arg_href) = @_;
 
     ## Flatten argument(s)
     my $action;
+    my $conda_init_path;
     my $env_method;
     my $env_name;
 
@@ -47,6 +49,10 @@ sub get_env_method_cmds {
             store       => \$action,
             strict_type => 1,
         },
+        conda_init_path => {
+            store       => \$conda_init_path,
+            strict_type => 1,
+        },
         env_method => {
             allow       => [qw{ conda }],
             defined     => 1,
@@ -67,7 +73,13 @@ sub get_env_method_cmds {
 
     my %method_cmd = (
         conda => {
-            load   => [ ( conda_activate( { env_name => $env_name, } ), ) ],
+            load => [
+                (
+                    conda_activate(
+                        { conda_init_path => $conda_init_path, env_name => $env_name, }
+                    ),
+                )
+            ],
             unload => [ ( conda_deactivate( {} ), ) ],
         },
     );

diff --git a/lib/MIP/Program/Conda.pm b/lib/MIP/Program/Conda.pm
@@ -14,7 +14,7 @@ use warnings qw{ FATAL utf8 };
 use warnings;
 
 ## MIPs lib/
-use MIP::Constants qw{ $LOG_NAME $NEWLINE $SPACE };
+use MIP::Constants qw{ $LOG_NAME $NEWLINE $SEMICOLON $SPACE };
 use MIP::Unix::Write_to_file qw{ unix_write_to_file };
 
 BEGIN {
@@ -30,16 +30,22 @@ sub conda_activate {
 
 ##Function : Activate conda environment
 ##Returns  : @commands
-##Arguments: $env_name   => Name of conda environment
-##         : $filehandle => Filehandle to write to
+##Arguments: $conda_init path => path to initialize conda
+##         : $env_name        => Name of conda environment
+##         : $filehandle      => Filehandle to write to
 
     my ($arg_href) = @_;
 
     ## Flatten argument(s)
+    my $conda_init_path;
     my $env_name;
     my $filehandle;
 
     my $tmpl = {
+        conda_init_path => {
+            store       => \$conda_init_path,
+            strict_type => 1,
+        },
         env_name => {
             required    => 1,
             store       => \$env_name,
@@ -52,10 +58,14 @@ sub conda_activate {
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
-    ## Stores commands depending on input parameters
+    my @commands;
+
+    if ($conda_init_path) {
+
+        push @commands, ( q{source}, $conda_init_path, $SEMICOLON );
+    }
 
-    # Basic command
-    my @commands = qw{ conda activate };
+    push @commands, qw{ conda activate };
 
     # Activates env, default base
     push @commands, $env_name;

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;

diff --git a/t/conda_activate.t b/t/conda_activate.t
@@ -5,7 +5,7 @@ use Carp;
 use charnames qw{ :full :short };
 use English qw{ -no_match_vars };
 use File::Basename qw{ dirname };
-use File::Spec::Functions qw{ catdir };
+use File::Spec::Functions qw{ catdir catfile };
 use FindBin qw{ $Bin };
 use open qw{ :encoding(UTF-8) :std };
 use Params::Check qw{ allow check last_error };
@@ -19,19 +19,16 @@ use Modern::Perl qw{ 2018 };
 
 ## MIPs lib/
 use lib catdir( dirname($Bin), q{lib} );
-use MIP::Constants qw{ $COMMA $SPACE };
+use MIP::Constants qw{ $COMMA $SEMICOLON $SPACE };
 use MIP::Test::Commands qw{ test_function };
 
-
 BEGIN {
 
     use MIP::Test::Fixtures qw{ test_import };
 
 ### Check all internal dependency modules and imports
 ## Modules with import
-    my %perl_module = (
-        q{MIP::Program::Conda} => [qw{ conda_activate }],
-);
+    my %perl_module = ( q{MIP::Program::Conda} => [qw{ conda_activate }], );
 
     test_import( { perl_module_href => \%perl_module, } );
 }
@@ -48,7 +45,8 @@ diag(   q{Test conda_activate from Conda.pm}
       . $EXECUTABLE_NAME );
 
 ## Base arguments
-my @function_base_commands = qw{ conda activate };
+my @source_commands = ( q{source}, catfile(qw{path to conda etc profile.d conda.sh}), $SEMICOLON );
+my @function_base_commands = ( @source_commands, qw{ conda activate } );
 
 my %base_argument = (
     filehandle => {
@@ -59,14 +57,22 @@ my %base_argument = (
 
 ## Can be duplicated with %base and/or %specific to enable testing of each individual argument
 my %required_argument = (
-    filehandle => {
-        input           => undef,
-        expected_output => \@function_base_commands,
+    conda_init_path => {
+        input           => catfile(qw{path to conda etc profile.d conda.sh}),
+        expected_output => q{source}
+          . $SPACE
+          . catfile(qw{path to conda etc profile.d conda.sh})
+          . $SPACE
+          . $SEMICOLON,
     },
     env_name => {
         input           => q{test_env},
         expected_output => q{test_env},
     },
+    filehandle => {
+        input           => undef,
+        expected_output => \@function_base_commands,
+    },
 );
 
 ## Coderef - enables generalized use of generate call

diff --git a/t/get_env_method_cmds.t b/t/get_env_method_cmds.t
@@ -5,7 +5,7 @@ use Carp;
 use charnames qw{ :full :short };
 use English qw{ -no_match_vars };
 use File::Basename qw{ dirname };
-use File::Spec::Functions qw{ catdir };
+use File::Spec::Functions qw{ catdir catfile };
 use FindBin qw{ $Bin };
 use open qw{ :encoding(UTF-8) :std };
 use Params::Check qw{ allow check last_error };
@@ -21,16 +21,13 @@ use Modern::Perl qw{ 2018 };
 use lib catdir( dirname($Bin), q{lib} );
 use MIP::Constants qw{ $COMMA $SPACE };
 
-
 BEGIN {
 
     use MIP::Test::Fixtures qw{ test_import };
 
 ### Check all internal dependency modules and imports
 ## Modules with import
-    my %perl_module = (
-        q{MIP::Environment::Manager} => [qw{ get_env_method_cmds }],
-);
+    my %perl_module = ( q{MIP::Environment::Manager} => [qw{ get_env_method_cmds }], );
 
     test_import( { perl_module_href => \%perl_module, } );
 }
@@ -51,12 +48,17 @@ my $env_name   = q{test_env};
 
 my @env_cmds = get_env_method_cmds(
     {
-        action     => q{load},
-        env_name   => $env_name,
-        env_method => $env_method,
+        action          => q{load},
+        conda_init_path => catfile(qw{path to conda etc profile.d conda.sh}),
+        env_name        => $env_name,
+        env_method      => $env_method,
     }
 );
-my @expected_load_cmds = ( qw{ conda activate }, $env_name );
+my @expected_load_cmds = (
+    q{source},
+    catfile(qw{path to conda etc profile.d conda.sh}),
+    qw{ ; conda activate }, $env_name,
+);
 
 ## Then return load env commands
 is_deeply( \@expected_load_cmds, \@env_cmds, q{Got env load cmds} );

diff --git a/t/get_package_env_cmds.t b/t/get_package_env_cmds.t
@@ -54,6 +54,7 @@ my %active_parameter = (
             $program_name => undef,
         },
     },
+    conda_path => catdir(qw{ path to conda }),
 );
 
 ## When no prior to load cmd
@@ -67,7 +68,7 @@ my @program_environment_cmds = get_package_env_cmds(
 ## Then return command to activate environment for package
 is_deeply(
     \@program_environment_cmds,
-    [qw{ conda activate mip_pyv3.6 }],
+    [qw{ source path/to/conda/etc/profile.d/conda.sh ; conda activate mip_pyv3.6 }],
     q{Got package environment command}
 );
 

diff --git a/t/get_recipe_resources.t b/t/get_recipe_resources.t
@@ -57,6 +57,7 @@ test_log( { no_screen => 1, } );
 ## Given a recipe name and active parameter hash
 my %active_parameter =
   test_mip_hashes( { mip_hash_name => q{active_parameter}, recipe_name => q{deepvariant}, } );
+$active_parameter{conda_path} = catdir(qw{path to conda});
 my $recipe_name = q{deepvariant};
 
 my %recipe_resource = get_recipe_resources(
@@ -70,7 +71,7 @@ my %recipe_resource = get_recipe_resources(
 my %expected = (
     core_number  => 35,
     gpu_number   => 1,
-    load_env_ref => [qw{ conda activate test }],
+    load_env_ref => [qw{ source path/to/conda/etc/profile.d/conda.sh ; conda activate test }],
     memory       => 175,
     mode         => 2,
     time         => 10,

diff --git a/t/mip_analyse_rd_dna.test b/t/mip_analyse_rd_dna.test
@@ -163,7 +163,7 @@ while ( my ( $pedigree, $pedigree_path ) = each %pedigree ) {
 }
 
 ## Clean-up
-#remove_tree( catfile( $cluster_constant_path, qw{ 643594-miptest analysis } ) );
+remove_tree( catfile( $cluster_constant_path, qw{ 643594-miptest analysis } ) );
 
 GENOME_BUILD:
 foreach my $genome_build (@genome_builds) {

diff --git a/t/parse_recipe_prerequisites.t b/t/parse_recipe_prerequisites.t
@@ -52,6 +52,7 @@ test_log( { no_screen => 1, } );
 my $recipe_name = q{deepvariant};
 my %active_parameter =
   test_mip_hashes( { mip_hash_name => q{active_parameter}, recipe_name => $recipe_name, } );
+$active_parameter{conda_path} = catdir(qw{path to conda});
 
 ## Given a parameter hash
 my %parameter =
@@ -77,7 +78,7 @@ my %expected_recipe = (
     file_tag       => q{_deepvar},
     gpu_number     => 1,
     job_id_chain   => q{TEST},
-    load_env_ref   => [qw{ conda activate test }],
+    load_env_ref   => [qw{ source path/to/conda/etc/profile.d/conda.sh ; conda activate test }],
     memory         => 175,
     mode           => 2,
     outfile_suffix => q{.g.vcf.gz},

diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
@@ -121,7 +121,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:v11.0.2
+    uri: docker.io/clinicalgenomics/mip:v11.0.3
   multiqc:
     executable:
       multiqc: