Merge e158067 into 806d599

containers/perl/Dockerfile

@@ -0,0 +1,22 @@
+################## BASE IMAGE ######################
+
+FROM perl:5.26
+
+################## METADATA ######################
+
+LABEL base_image="perl:5.26"
+LABEL version="1"
+LABEL software="perl"
+LABEL software.version="5.26"
+LABEL extra.binaries="perl"
+LABEL maintainer="Clinical-Genomics/MIP"
+
+RUN apt-get update && apt-get install -y --no-install-recommends locales locales-all \
+ && apt-get clean \
+ && rm -rf /var/lib/apt/lists/*
+
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US.UTF-8
+
+WORKDIR /data/

definitions/analyse_parameters.yaml

@@ -47,6 +47,13 @@ case_id:
     - mip
   data_type: SCALAR
   type: mip
+install_config_file:
+  associated_recipe:
+    - mip
+  data_type: SCALAR
+  default: 0
+  type: path
+  update_path: absolute_path
 java_use_large_pages:
   associated_recipe:
     - varianteffectpredictor

definitions/dragen_rd_dna_parameters.yaml

@@ -9,6 +9,7 @@ custom_default_parameters:
     - conda_path
     - exome_target_bed
     - infile_dirs
+    - install_config_file
     - pedigree_fam_file
     - picardtools_path
     - reference_dir

definitions/rd_dna_panel_parameters.yaml

@@ -11,6 +11,7 @@ custom_default_parameters:
     - bwa_mem2_build_reference
     - exome_target_bed
     - infile_dirs
+    - install_config_file
     - pedigree_fam_file
     - picardtools_path
     - reference_dir

definitions/rd_dna_parameters.yaml

@@ -11,6 +11,7 @@ custom_default_parameters:
     - bwa_mem2_build_reference
     - exome_target_bed
     - infile_dirs
+    - install_config_file
     - pedigree_fam_file
     - picardtools_path
     - reference_dir

definitions/rd_dna_vcf_rerun_parameters.yaml

@@ -9,6 +9,7 @@ custom_default_parameters:
     - conda_path
     - exome_target_bed
     - infile_dirs
+    - install_config_file
     - pedigree_fam_file
     - picardtools_path
     - reference_dir

definitions/rd_rna_parameters.yaml

@@ -9,6 +9,7 @@ custom_default_parameters:
     - analysis_type
     - conda_path
     - infile_dirs
+    - install_config_file
     - pedigree_fam_file
     - picardtools_path
     - reference_dir

lib/MIP/Active_parameter.pm

@@ -28,7 +28,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.32;
+    our $VERSION = 1.33;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
@@ -55,6 +55,7 @@ BEGIN {
       set_default_conda_path
       set_default_human_genome
       set_default_infile_dirs
+      set_default_install_config_file
       set_default_parameter
       set_default_pedigree_fam_file
       set_default_program_test_file
@@ -2108,6 +2109,39 @@ sub set_include_y {
     return;
 }
 
+sub set_default_install_config_file {
+
+## Function : Set default install config file to active parameters
+## Returns  :
+## Arguments: $active_parameter_href => Holds all set parameter for analysis {REF}
+##          : $parameter_name        => Parameter name
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $active_parameter_href;
+    my $parameter_name;
+
+    my $tmpl = {
+        active_parameter_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$active_parameter_href,
+            strict_type => 1,
+        },
+        parameter_name => { defined => 1, required => 1, store => \$parameter_name, },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    ## Build default for mip install config
+    my $path = catfile( $Bin, qw{ templates mip_install_config.yaml } );
+
+    $active_parameter_href->{$parameter_name} = $path;
+    return;
+}
+
 sub set_parameter_reference_dir_path {
 
 ## Function : Set path for supplied reference(s) associated with parameter that should

lib/MIP/Cli/Mip/Analyse.pm

@@ -21,7 +21,7 @@ use Moose::Util::TypeConstraints;
 use MIP::Cli::Utils qw{ run };
 
 # Set the version for version checking
-our $VERSION = 1.15;
+our $VERSION = 1.16;
 
 extends(qw{ MIP::Cli::Mip });
 
@@ -132,6 +132,14 @@ q{Check analysis output and sets the analysis run status flag to finished in sam
         )
     );
 
+    option(
+        q{install_config_file} => (
+            documentation => q{File with install configuration parameters in YAML format},
+            is            => q{rw},
+            isa           => Str,
+        )
+    );
+
     option(
         q{java_use_large_pages} => (
             documentation => q{Use large page memory},

lib/MIP/Config.pm

@@ -23,10 +23,11 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.06;
+    our $VERSION = 1.07;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ check_cmd_config_vs_definition_file
+      get_install_containers
       parse_config
       parse_dynamic_config_parameters
       set_config_to_active_parameters
@@ -94,6 +95,37 @@ sub check_cmd_config_vs_definition_file {
     return;
 }
 
+sub get_install_containers {
+
+## Function : Get install containers from install config file
+## Returns  : $install_config{container}
+## Arguments: $install_config_file => File with containers from install config
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $install_config_file;
+
+    my $tmpl = {
+        install_config_file => {
+            defined     => 1,
+            required    => 1,
+            store       => \$install_config_file,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    my %install_config = read_from_file(
+        {
+            format => q{yaml},
+            path   => $install_config_file,
+        }
+    );
+    return %{ $install_config{container} };
+}
+
 sub parse_config {
 
 ## Function : Parse config by loading from cli, removing prior dynamic entries,

lib/MIP/Constants.pm

@@ -4,6 +4,7 @@ use 5.026;
 use Carp;
 use charnames qw{ :full :short };
 use English qw{ -no_match_vars };
+use File::Spec::Functions qw{ catfile };
 use open qw{ :encoding(UTF-8) :std };
 use Params::Check qw{ allow check last_error };
 use strict;
@@ -37,6 +38,7 @@ BEGIN {
       $COLON
       $COMMA
       @CONTAINER_BIND_PATHS
+      %CONTAINER_CMD
       $CONTAINER_MANAGER
       $DASH
       $DOLLAR_SIGN
@@ -64,6 +66,7 @@ BEGIN {
       $SPACE
       $TAB
       $UNDERSCORE
+      set_container_cmd
       set_container_constants
       set_genome_build_constants
       set_log_name_constant
@@ -349,6 +352,34 @@ Readonly our $SPACE             => q{ };
 Readonly our $TAB               => qq{\t};
 Readonly our $UNDERSCORE        => q{_};
 
+sub set_container_cmd {
+
+## Function : Set container commands for each executable
+## Returns  :
+## Arguments: $container_cmd_href => Analysis recipe hash {REF}
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $container_cmd_href;
+
+    my $tmpl = {
+        container_cmd_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$container_cmd_href,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    Readonly our %CONTAINER_CMD => %{$container_cmd_href};
+
+    return;
+}
+
 sub set_container_constants {
 
 ## Function : Set container constants
@@ -372,12 +403,17 @@ sub set_container_constants {
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
+    use MIP::Language::Shell qw{ quote_bash_variable };
     use MIP::Environment::Path qw{ reduce_dir_paths };
 
+    my $temp_directory_quoted = quote_bash_variable(
+        { string_with_variable_to_quote => $active_parameter_href->{temp_directory}, } );
+    my $xdg_runtime_dir =
+      $temp_directory_quoted . $COLON . catfile( $EMPTY_STR, qw{ run user $(id -u)} );
+
     my @container_bind_paths = (
-        $active_parameter_href->{reference_dir},
-        $active_parameter_href->{outdata_dir},
-        $active_parameter_href->{temp_directory},
+        $active_parameter_href->{reference_dir},  $active_parameter_href->{outdata_dir},
+        $active_parameter_href->{temp_directory}, $xdg_runtime_dir,
     );
 
     @container_bind_paths = reduce_dir_paths(