Merge pull request #540 from jemten/feature/installation_dependencies

Moved dependencies, added tests and refactored

definitions/cpanfile

@@ -6,6 +6,8 @@ requires qw{ Archive::Zip 1.59 };                   # VEP
 requires qw{ Array::Utils 0.5 };                    # MIP
 requires qw{ Bio::Root::Version 1.007002 };         # VEP
 requires qw{ CGI 4.37 };                            # VEP
+requires qw{ Clone 0.39 };                          # MIP
+requires qw{ Data::Diver 1.0101 };                  # MIP
 requires qw{ Data::Printer 0.40 };                  # MIP
 requires qw{ DB_File 1.840 };                       # STAR-Fusion
 requires qw{ DBD::mysql 4.043 };                    # VEP

definitions/install_rare_disease_parameters.yaml

@@ -49,10 +49,13 @@ emip:
     bedtools:
       version: 2.25.0
     expansionhunter:
+      conda_dependency:
       version: 2.5.5
     mip_scripts:
       version: Your current MIP version
     picard:
+      conda_dependency:
+        java-jdk:
       version: 2.3.0
     plink2:
       version: 171013
@@ -67,8 +70,18 @@ emip:
         - GRCh38.86
       version: v4_3t
     svdb:
+      conda_dependency:
+        cython:
+        numpy:
+        pip:
+        python: 2.7
       version: 1.1.2
     tiddit:
+      conda_dependency:
+        cmake:
+        gcc:
+        numpy:
+        python: 2.7
       version: 2.2.1
     vcf2cytosure:
       version: gitRepo
@@ -87,6 +100,8 @@ ecnvnator:
   shell:
     cnvnator:
       cnvnator_root_binary: root_v6.06.00.Linux-slc6-x86_64-gcc4.8.tar.gz
+      conda_dependency:
+        gcc:
       version: 0.3.3
 
 # Peddy environment spec
@@ -123,6 +138,9 @@ evep:
   pip:
   shell:
     vep:
+      conda_dependency:
+        bcftools:
+        htslib:
       vep_assemblies:
         - GRCh37
         - GRCh38

definitions/install_rna_parameters.yaml

@@ -35,18 +35,30 @@ emip:
     scipy:
     star: 2.5.4a
   shell:
-    bootstrapann:
+    blobfish:
+      conda_dependency:
+        bioconductor-deseq2:
+        bioconductor-tximport:
+        python: 2.7
+        r-optparse: 
+        r-readr:
       version: git
+      url: https://github.com/J35P312/BlobFish.git
+    bootstrapann:
+      conda_dependency:
+        numpy:
+        pip:
+        scipy:
       url: https://github.com/J35P312/BootstrapAnn.git
+      version: git
     mip_scripts:
       version: Your current MIP version
     picard:
       version: 2.17.11
     star_fusion:
+      conda_dependency:
+        star:
       version: 1.3.2
-    blobfish:
-      version: git
-      url: https://github.com/J35P312/BlobFish.git
 
 # Specify environment names
 environment_name:

lib/MIP/Check/Installation.pm

@@ -20,10 +20,11 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.01;
+    our $VERSION = 1.02;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
+      check_and_add_dependencies
       check_existing_installation
       check_python_compability
     };
@@ -242,7 +243,6 @@ q{Python is not part of the installation. Skipping python compability check.}
         @programs_to_check = unique(
             keys %{ $installation_set_href->{conda} },
             keys %{ $installation_set_href->{shell} },
-            keys %{ $installation_set_href->{bioconda} },
             keys %{ $installation_set_href->{pip} },
         );
     }
@@ -263,4 +263,84 @@ q{Python is not part of the installation. Skipping python compability check.}
     return;
 }
 
+sub check_and_add_dependencies {
+
+## Function : Check if shell program dependencies are already part of the installation
+## Returns  :
+## Arguments: $conda_program_href => Hash with conda programs to be installed {REF}
+##          : $dependency_href    => Hash with dependencies {REF}
+##          : $log                => Log
+##          : $shell_program      => Shell program
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $conda_program_href;
+    my $dependency_href;
+    my $log;
+    my $shell_program;
+
+    my $tmpl = {
+        conda_program_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$conda_program_href,
+            strict_type => 1,
+        },
+        dependency_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$dependency_href,
+            strict_type => 1,
+        },
+        log => {
+            defined  => 1,
+            required => 1,
+            store    => \$log,
+        },
+        shell_program => {
+            defined     => 1,
+            required    => 1,
+            store       => \$shell_program,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+  DEPENDENCY:
+    foreach my $dependency ( keys %{$dependency_href} ) {
+
+        ## Add dependency to conda installation if missing
+        if ( not $conda_program_href->{$dependency} ) {
+            $conda_program_href->{$dependency} =
+              $dependency_href->{$dependency};
+            next DEPENDENCY;
+        }
+
+        ## Check if version is specified, do nothing if the same version is already part of the installation
+        if ( defined $dependency_href->{$dependency} ) {
+
+            ## Exit if the version of the dependency conflicts with what is already part of the conda installation
+            if (
+                ( defined $conda_program_href->{$dependency} )
+                and ( $dependency_href->{$dependency} ne
+                    $conda_program_href->{$dependency} )
+              )
+            {
+                $log->fatal(
+qq{$shell_program is dependent on $dependency version: $dependency_href->{$dependency}}
+                );
+                $log->fatal(
+qq{The conda installation specifies version: $conda_program_href->{$dependency} of $shell_program}
+                );
+                exit 1;
+            }
+        }
+    }
+    return;
+}
+
 1;

lib/MIP/Get/Parameter.pm

@@ -19,7 +19,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.02;
+    our $VERSION = 1.03;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
@@ -641,19 +641,6 @@ sub get_programs_for_shell_installation {
     }
     elsif ( @{$shell_install_programs_ref} ) {
 
-        # Assert that the selected program has shell install instructions.
-        my @faulty_selects =
-          array_minus( @{$shell_install_programs_ref}, @shell_programs );
-        if (@faulty_selects) {
-            $log->fatal(
-                q{No shell installation instructions available for}
-                  . $COLON
-                  . join $SPACE,
-                @faulty_selects
-            );
-            exit 1;
-        }
-
         # Get elements in @shell_programs that are not part of the conda hash
         my @shell_only_programs =
           array_minus( @shell_programs, @conda_programs );