diff --git a/.gitignore b/.gitignore index 17b6f9c4..050e6de3 100644 --- a/.gitignore +++ b/.gitignore @@ -186,7 +186,7 @@ classified_structural_variants /src/frontend_celery/playwright/redis* /Python-* /data_makefile -/.localpython +/.localpython* resources/backups/keycloak_export/dev/*/*-users*.json /resources/backups/database_dumper/dev/data diff --git a/src/annotation_service/annotation_jobs/automatic_classification_job.py b/src/annotation_service/annotation_jobs/automatic_classification_job.py index 518e3d38..c6de0698 100644 --- a/src/annotation_service/annotation_jobs/automatic_classification_job.py +++ b/src/annotation_service/annotation_jobs/automatic_classification_job.py @@ -65,8 +65,7 @@ def save_to_db(self, variant_id, conn: Connection): if autoclass_input is None: return 0, "Not enough information to calculate the automatic classification" - config_path = os.path.join(paths.automatic_classification_path, "config_production.yaml") - returncode, err_msg, classification = self.run_automatic_classification(autoclass_input, config_path) + returncode, err_msg, classification = self.run_automatic_classification(autoclass_input, paths.automatic_classification_config_path) if returncode != 0: raise RuntimeError(err_msg) diff --git a/src/common/paths.py b/src/common/paths.py index 5959410c..345d792d 100644 --- a/src/common/paths.py +++ b/src/common/paths.py @@ -43,6 +43,7 @@ def joinpaths(path, *paths): ngs_bits_path = joinpaths(toolsdir, "ngs-bits/bin") htslib_path = joinpaths(toolsdir, "htslib") automatic_classification_path = joinpaths(toolsdir, "herediclass") + automatic_classification_config_path = os.path.join(automatic_classification_path, "config_pejaver_mult_strength_production.yaml") # config_production.yaml samtools_path = joinpaths(toolsdir, "samtools/samtools") # data @@ -245,6 +246,7 @@ def joinpaths(path, *paths): htslib_path = joinpaths(toolsdir, "htslib-1.16") samtools_path = joinpaths(toolsdir, "samtools/samtools") automatic_classification_path = joinpaths(toolsdir, "herediclass") + automatic_classification_config_path = os.path.join(automatic_classification_path, "config_production.yaml") # data diff --git a/tools/script/install_herediclass_config.sh b/tools/script/install_herediclass_config.sh index 5f16fe99..27b14d1d 100755 --- a/tools/script/install_herediclass_config.sh +++ b/tools/script/install_herediclass_config.sh @@ -52,5 +52,8 @@ for filename in $gene_sepcific_config_path_production/*.yaml; do sed -r -i "s:variant_classification/::g" $filename done - +for filename in $gene_sepcific_config_path_production/pejaver_mult_strength/*.yaml; do + sed -r -i "s:/home/katzkean/:$variant_classification_path/:g" $filename + sed -r -i "s:variant_classification/::g" $filename +done