linking mip_analysis.test

Clinical-Genomics · Nov 11, 2022 · da45cef · da45cef
1 parent 3db1c28
commit da45cef
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Showing 6 changed files with 17 additions and 15 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -27,12 +27,15 @@ COPY . "$MIP_INSTALL_DIR"
 WORKDIR "$MIP_INSTALL_DIR"
 
 # Make executable and add to binary to PATH
-RUN chmod a+x "$MIP_INSTALL_DIR/mip"
+RUN chmod a+x "$MIP_INSTALL_DIR/mip" && \
+    chmod a+x "$MIP_INSTALL_DIR/t/mip_analysis.test" && \
+    ln -s "$MIP_INSTALL_DIR/t/mip_analysis.test" "$MIP_INSTALL_DIR/mip_analysis.test"
+
 ENV PATH "$PATH:$MIP_INSTALL_DIR"
 
 # Remove any outside local from previous carton installs
 RUN rm -rf local
 
 RUN carton install
 
-ENV PERL5LIB="$MIP_INSTALL_DIR"/local/lib/perl5
+ENV PERL5LIB="$MIP_INSTALL_DIR"/local/lib/perl5
diff --git a/lib/MIP/Cli/Mip/Install.pm b/lib/MIP/Cli/Mip/Install.pm
@@ -143,7 +143,7 @@ sub _build_usage {
                         qw{ arriba bedtools blobfish bootstrapann bwa bwakit bwa-mem2 cadd chanjo
                           chromograph cnvnator cyrius deeptrio deepvariant delly expansionhunter fastqc gatk
                           gatk4 genmod gens_preproc gffcompare glnexus hmtnote htslib manta megafusion mip mip_scripts multiqc
-                          pdfmerger perl peddy picard plink preseq python rhocall rseqc rtg-tools salmon sambamba
+                          pdfmerger peddy picard plink preseq python rhocall rseqc rtg-tools salmon sambamba
                           smncopynumbercaller star star-fusion stranger stringtie svdb telomerecat tiddit
                           trim-galore ucsc upd utilities varg vcf2cytosure vcfanno vep vts }
                     ]
@@ -176,7 +176,7 @@ q{Save singularity images to sif and update run instructions for offline mip exe
                         qw{ arriba bedtools blobfish bootstrapann bwa bwakit bwa-mem2 cadd chanjo
                           chromograph cnvnator cyrius deeptrio deepvariant delly expansionhunter fastqc gatk
                           gatk4 genmod gens_preproc gffcompare glnexus hmtnote htslib manta megafusion mip mip_scripts multiqc
-                          pdfmerger perl peddy picard plink preseq python rhocall rseqc rtg-tools salmon sambamba
+                          pdfmerger peddy picard plink preseq python rhocall rseqc rtg-tools salmon sambamba
                           smncopynumbercaller star star-fusion stranger stringtie svdb telomerecat tiddit
                           trim-galore ucsc upd utilities varg vcf2cytosure vcfanno vep vts }
                     ]

diff --git a/lib/MIP/Recipes/Analysis/Analysisrunstatus.pm b/lib/MIP/Recipes/Analysis/Analysisrunstatus.pm
@@ -460,12 +460,8 @@ sub _check_vcf_header_and_keys {
             ## Execute test(s)
             $command .= q?$harness->runtests( ?;
 
-            $command .= q?["?
-              . catfile( $Bin, qw{ t mip_analysis.test } )
-              . q?", "test ?
-              . $mode
-              . $SPACE
-              . $recipe_name . q?"], ?;
+            $command .=
+              q?["? . q{mip_analysis.test} . q?", "test ? . $mode . $SPACE . $recipe_name . q?"], ?;
 
             $command .= q?)'?;
 

diff --git a/lib/MIP/Recipes/Install/Mip_scripts.pm b/lib/MIP/Recipes/Install/Mip_scripts.pm
@@ -162,6 +162,11 @@ sub install_mip_scripts {
 
             path($src_path)->copy($dst_path);
             path($dst_path)->chmod(q{a+x});
+
+            ## Create symlinks to bin
+            if ( $directory eq q{t} ) {
+                symlink $dst_path, catfile( $conda_environment_path, q{bin}, $script );
+            }
         }
     }
     return 1;

diff --git a/t/mip_install.test b/t/mip_install.test
@@ -152,8 +152,8 @@ my %process_return = child_process(
         verbose      => $verbose,
     }
 );
-
 ok( $process_return{success}, q{Executed install} );
+path( catdir( $conda_path, q{envs}, $environment_name ) )->remove_tree;
 
 ## When given option to pull singularity images for local installation
 push @{$cmds_ref}, q{--singularity_local_install};
@@ -166,6 +166,7 @@ push @{$cmds_ref}, q{--singularity_local_install};
 );
 ## Then return true
 ok( $process_return{success}, q{Executed local singularity install} );
+path( catdir( $conda_path, q{envs}, $environment_name ) )->remove_tree;
 
 ## When given option to pull images using docker
 push @{$cmds_ref}, qw{ --container_manager docker };

diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
@@ -125,15 +125,12 @@ container:
   mip:
     executable:
       mip:
+      perl:
     uri: docker.io/clinicalgenomics/mip:v11.1.0
   multiqc:
     executable:
       multiqc:
     uri: docker.io/ewels/multiqc:v1.12
-  perl:
-    executable:
-      perl:
-    uri: docker.io/clinicalgenomics/perl:5.26
   peddy:
     executable:
       peddy: "python -m peddy"