Merge 9ce0e5c into 50d54ff

.travis.yml

@@ -30,11 +30,11 @@ install:
 ## Test installation script and gather coverage information
   - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_install.test
 ## Generate rare disease installation script
-  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl mip install rd_dna --bash_set_errexit --install emip epeddy eperl5 epy3 esvdb etiddit --envn emip=mip_travis --snpg GRCh37.75 --skip gatk --skip snpeff
+  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl mip install rd_dna --bash_set_errexit --install emip epeddy eperl5 epy3 esvdb etiddit --envn emip=mip_travis epeddy=mip_travis_peddy eperl5=mip_travis_perl5 epy3=mip_travis_py3 esvdb=mip_travis_svdb etiddit=mip_travis_tiddit --skip gatk --skip snpeff
 ## Install MIP rare disease
   - bash mip.sh
 ## Generate rna installation script
-  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl mip install rd_rna --bash_set_errexit --install emip epy3 eperl5
+  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl mip install rd_rna --bash_set_errexit --install emip epy3 eperl5 
 ## Install MIP rna
   - bash mip.sh
 
@@ -58,8 +58,8 @@ script:
 ## Set-up test coverage for mip_analyse_vcf_rerun.test
   - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_dragen_rd_dna.test
 ## Set-up test coverage for mip_analyse_rna.test
-  - conda activate MIP_rd_rna
-  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_rd_rna.test 
+  - conda activate mip7_rd-rna
+  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_rd_rna.test
 ## Get some coverage statistics
   - cover
 

definitions/install_rd_dna_parameters.yaml

@@ -28,7 +28,7 @@ emip:
     htslib: 1.9=hc238db4_4
     libstdcxx-ng: 8.2
     ldc: 1.11.0=hb2c9046_0
-    manta: 1.5.0=py27_0 
+    manta: 1.5.0=py27_0
     numpy:
     picard: 2.18.14=0
     pip:
@@ -204,17 +204,24 @@ evep:
         - homo_sapiens_merged
       version: 95
 
-# Specify environment names
+## Default base name
+environment_base_name: mip7_rd-dna
+
+# Specify default environment names
 environment_name:
-  emip: MIP_rd_dna
-  ecnvnator:
-  edelly:
-  epeddy:
-  eperl5:
-  epy3:
-  esvdb:
-  etiddit:
-  evep:
+  emip: mip7_rd-dna
+  ecnvnator: mip7_rd-dna_cnvnator
+  edelly: mip7_rd-dna_delly
+  epeddy: mip7_rd-dna_peddy
+  eperl5: mip7_rd-dna_perl5
+  epy3: mip7_rd-dna_py3
+  esvdb: mip7_rd-dna_svdb
+  etiddit: mip7_rd-dna_tiddit
+  evep: mip7_rd-dna_vep
+
+# Optional addons to env names
+environment_prefix:
+environment_suffix:
 
 # Environments to install
 installations:

definitions/install_rd_rna_parameters.yaml

@@ -112,12 +112,19 @@ evep:
         - homo_sapiens_merged
       version: 95
 
+## Default base name
+environment_base_name: mip7_rd-rna
+
 # Specify environment names
 environment_name:
-  emip: MIP_rd_rna
-  epy3: MIP_rd_rna_py3
-  eperl5: MIP_rd_rna_perl5
-  evep: MIP_rd_rna_vep
+  emip: mip7_rd-rna
+  epy3: mip7_rd-rna_py3
+  eperl5: mip7_rd-rna_perl5
+  evep: mip7_rd-rna_vep
+
+# Optional addons to env names
+environment_prefix:
+environment_suffix:
 
 # Environments and their recipes
 installations:

lib/MIP/Cli/Mip/Install.pm

@@ -22,7 +22,7 @@ use lib catdir( dirname($Bin), q{lib} );
 use MIP::Cli::Utils qw{ run }
   ;    # MooseX::App required sub. Called internally by MooseX::App
 
-our $VERSION = 1.05;
+our $VERSION = 1.06;
 
 extends(qw{ MIP::Cli::Mip });
 
@@ -85,6 +85,25 @@ sub _build_usage {
         ),
     );
 
+    option(
+        q{environment_prefix} => (
+            cmd_aliases => [qw{ ep }],
+            documentation =>
+              q{Prepend this to environment names. Separated by underscore},
+            is  => q{rw},
+            isa => Str,
+        )
+    );
+
+    option(
+        q{environment_suffix} => (
+            cmd_aliases   => [qw{ es }],
+            documentation => q{Append this to environment names. Separated by underscore},
+            is            => q{rw},
+            isa           => Str,
+        )
+    );
+
     option(
         q{noupdate} => (
             cmd_aliases   => [qw{ nup }],
@@ -96,6 +115,17 @@ sub _build_usage {
         ),
     );
 
+    option(
+        q{add_environment_date} => (
+            cmd_aliases   => [qw{ aed }],
+            cmd_flag      => q{add_environment_date},
+            documentation => q{Add creation date to environment},
+            is            => q{rw},
+            isa           => Bool,
+            required      => 0,
+        ),
+    );
+
     option(
         q{prefer_shell} => (
             cmd_aliases => [qw{ psh }],

lib/MIP/Cli/Mip/Install/Rd_dna.pm

@@ -27,7 +27,7 @@ use MIP::Main::Install qw{ mip_install };
 use MIP::Get::Parameter qw{ get_install_parameter_attribute };
 use MIP::Script::Utils qw{ nest_hash print_parameter_defaults update_program_versions};
 
-our $VERSION = 1.05;
+our $VERSION = 1.06;
 
 extends(qw{ MIP::Cli::Mip::Install });
 
@@ -107,8 +107,11 @@ sub _build_usage {
 
     option(
         q{environment_name} => (
-            cmd_aliases   => [qw{ envn }],
-            cmd_flag      => q{environment_name},
+            cmd_aliases => [qw{ envn }],
+            cmd_flag    => q{environment_name},
+            cmd_tags    => [
+q{Default: mip7_rd-dna mip7_rd-dna_cnvnator mip7_rd-dna_delly mip7_rd-dna_peddy mip7_rd-dna_perl5 mip7_rd-dna_py3 mip7_rd-dna_svdb mip7_rd-dna_tiddit mip7_rd-dna_vep}
+            ],
             documentation => q{Set environment names},
             is            => q{rw},
             isa           => Dict [

lib/MIP/Cli/Mip/Install/Rd_rna.pm

@@ -26,7 +26,7 @@ use MIP::File::Format::Yaml qw{ load_yaml };
 use MIP::Main::Install qw{ mip_install };
 use MIP::Script::Utils qw{ nest_hash print_parameter_defaults update_program_versions };
 
-our $VERSION = 1.08;
+our $VERSION = 1.09;
 
 extends(qw{ MIP::Cli::Mip::Install });
 
@@ -93,8 +93,10 @@ sub _build_usage {
 
     option(
         q{environment_name} => (
-            cmd_aliases   => [qw{ envn }],
-            cmd_flag      => q{environment_name},
+            cmd_aliases => [qw{ envn }],
+            cmd_flag    => q{environment_name},
+            cmd_tags =>
+              [q{Default: mip7_rd-rna mip7_rd-rna_py3 mip7_rd-rna_perl5 mip7_rd-rna_vep}],
             documentation => q{Set environment names},
             is            => q{rw},
             isa           => Dict [

lib/MIP/Main/Install.pm

@@ -59,7 +59,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = q{1.4.1};
+    our $VERSION = q{1.4.2};
 
     # Functions and variables that can be optionally exported
     our @EXPORT_OK = qw{ mip_install };
@@ -137,7 +137,6 @@ sub mip_install {
     ## Set environment names and environment specific conda paths
     set_conda_env_names_and_paths(
         {
-            log            => $log,
             parameter_href => \%parameter,
         }
     );

lib/MIP/Package_manager/Pip.pm

@@ -93,7 +93,7 @@ sub check_pip_package {
 
             # Test if the program already exists in that environment
             $command =
-qq{conda list -n $conda_environment | grep 'pip' | $check_pip_package_regexp};
+qq{conda list -n $conda_environment 2> /dev/null | grep '<pip>' | $check_pip_package_regexp};
             run(
                 command => $command,
                 buffer  => \$status
@@ -102,13 +102,12 @@ qq{conda list -n $conda_environment | grep 'pip' | $check_pip_package_regexp};
         return $status;
     }
 
-    # Test if the program is already installed in the root env
-    $command = qq{pip list --format columns | $check_pip_package_regexp};
+    # Test if the program is already installed in the active env
+    $command = qq{pip list --format columns 2> /dev/null | $check_pip_package_regexp};
     run(
         command => $command,
         buffer  => \$status
     );
-
     return $status;
 }
 
@@ -294,7 +293,7 @@ sub _build_package_check_regexp {
           . q?'if( ($_=~/? . $package . q?/) && ($_=~/? . $version . q?/) )?
 
           # Print 1 in case of match
-          . q?{print 1}'?;
+          . q?{print 1}' ?;
     }
     else {
 

lib/MIP/Parse/Parameter.pm

@@ -18,7 +18,7 @@ use List::Util qw{ any };
 use Readonly;
 
 ## MIPs lib/
-use MIP::Constants qw{ $SPACE };
+use MIP::Constants qw{ $SPACE $UNDERSCORE };
 
 BEGIN {
 
@@ -29,9 +29,96 @@ BEGIN {
     our $VERSION = 1.03;
 
     # Functions and variables which can be optionally exported
-    our @EXPORT_OK =
-      qw{ parse_download_reference_parameter parse_infiles parse_nist_parameters parse_prioritize_variant_callers parse_start_with_recipe parse_toml_config_parameters };
+    our @EXPORT_OK = qw{
+      parse_conda_env_name
+      parse_download_reference_parameter
+      parse_infiles
+      parse_nist_parameters
+      parse_prioritize_variant_callers
+      parse_start_with_recipe
+      parse_toml_config_parameters
+    };
+
+}
+
+sub parse_conda_env_name {
+
+## Function : Build conda environment names depending on input parameters
+## Returns  : $conda_environment_name
+## Arguments: $base_name     => Degfault base environment name
+##          : $date          => Date
+##          : $environment   => Installation environment
+##          : parameter_href => Parmeter hash {REF}
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $base_name;
+    my $date;
+    my $environment;
+    my $parameter_href;
+
+    my $tmpl = {
+        base_name => {
+            defined     => 1,
+            required    => 1,
+            store       => \$base_name,
+            strict_type => 1,
+        },
+        date => {
+            defined     => 1,
+            required    => 1,
+            store       => \$date,
+            strict_type => 1,
+        },
+        environment => {
+            defined     => 1,
+            required    => 1,
+            store       => \$environment,
+            strict_type => 1,
+        },
+        parameter_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$parameter_href,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    my $environment_name = $parameter_href->{environment_name}{$environment};
+
+    ## Give the env a default name if not given
+    if ( not $environment_name ) {
+
+        ## Strip the first character, i.e. 'e' from the environment string
+        my $env_postfix = substr $environment, 1;
+        $environment_name = $base_name . $UNDERSCORE . $env_postfix;
+    }
+
+    ## Prepend environemnt prefix
+    if ( $parameter_href->{environment_prefix} ) {
+
+        $environment_name =
+          $parameter_href->{environment_prefix} . $UNDERSCORE . $environment_name;
+    }
+
+    ## Add environment date
+    if ( $parameter_href->{add_environment_date} ) {
+
+        $environment_name = $environment_name . $UNDERSCORE . $date;
+    }
+
+    ## Append environment suffix
+    if ( $parameter_href->{environment_suffix} ) {
+
+        $environment_name =
+          $environment_name . $UNDERSCORE . $parameter_href->{environment_suffix};
+    }
 
+    return $environment_name;
 }
 
 sub parse_download_reference_parameter {