Update default singularity image dir

molgenis · Sep 14, 2021 · 987465f · 987465f
1 parent 6d32fda
commit 987465f
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Showing 8 changed files with 22 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -27,6 +27,7 @@ config:
   assembly                allowed values: GRCh37, GRCh38 default: GRCh37
   reference               reference sequence file
   cpu_cores               number of CPU cores
+  singularity_image_dir   directory where the singularity images are stored.
   preprocess_*            see 'bash pipeline_preprocess.sh --help' for usage.
   annotate_*              see 'bash pipeline_annotate.sh --help' for usage.
   filter_*                see 'bash pipeline_filter.sh --help' for usage.

diff --git a/config/default.cfg b/config/default.cfg
@@ -3,7 +3,6 @@ assembly=GRCh37
 cpu_cores=4
 preprocess_filter_low_qual=1
 preprocess_filter_read_depth=20
-singularity_image_dir=./singularity/sif/
 annotate_phenotype_matching=hpo
 annotate_vibe_hdt=/apps/data/VIBE/vibe-5.1.0-hdt/vibe-5.1.0.hdt
 annotate_vibe_hpo=/apps/data/VIBE/hp_2020-12-07.owl

diff --git a/pipeline.sh b/pipeline.sh
@@ -38,7 +38,7 @@ config:
   assembly                allowed values: GRCh37, GRCh38 default: GRCh37
   reference               reference sequence file (.fasta.gz, .fna.gz, .ffn.gz, .faa.gz or .frn.gz).
   cpu_cores               number of CPU cores
-  singularity_image_dir   directory where the singularity images are stored
+  singularity_image_dir   directory where the singularity images are stored.
   preprocess_*            see 'bash pipeline_preprocess.sh --help' for usage.
   annotate_*              see 'bash pipeline_annotate.sh --help' for usage.
   filter_*                see 'bash pipeline_filter.sh --help' for usage.
@@ -444,6 +444,8 @@ main() {
 
   if [[ -n "${VIP_CFG_MAP["singularity_image_dir"]+unset}" ]]; then
     singularityImageDir="${VIP_CFG_MAP["singularity_image_dir"]}"
+  else
+    singularityImageDir="${SCRIPT_DIR}/singularity/sif"
   fi
 
   if [[ -n "${VIP_CFG_MAP["cpu_cores"]+unset}" ]]; then

diff --git a/pipeline_annotate.sh b/pipeline_annotate.sh
@@ -46,7 +46,8 @@ config:
   annotate_vep                            Variant Effect Predictor (VEP) options.
   assembly                                see 'bash pipeline.sh --help' for usage.
   reference                               see 'bash pipeline.sh --help' for usage.
-  cpu_cores                               see 'bash pipeline.sh --help' for usage."
+  cpu_cores                               see 'bash pipeline.sh --help' for usage.
+  singularity_image_dir                   see 'bash pipeline.sh --help' for usage."
 }
 
 get_unique_phenotypes() {
@@ -538,6 +539,8 @@ main() {
 
   if [[ -n "${VIP_CFG_MAP["singularity_image_dir"]+unset}" ]]; then
     singularityImageDir="${VIP_CFG_MAP["singularity_image_dir"]}"
+  else
+    singularityImageDir="${SCRIPT_DIR}/singularity/sif"
   fi
 
   if [[ -n "${VIP_CFG_MAP["assembly"]+unset}" ]]; then

diff --git a/pipeline_filter.sh b/pipeline_filter.sh
@@ -34,7 +34,8 @@ config:
   filter_tree             decision tree file (.json) that applies classes 'F' and 'T'.
   filter_annotate_labels  annotate decision tree labels (0 or 1, default: 0).
   filter_annotate_paths   annotate decision tree paths (0 or 1, default: 0).
-  cpu_cores               see 'bash pipeline.sh --help' for usage."
+  cpu_cores               see 'bash pipeline.sh --help' for usage.
+  singularity_image_dir   see 'bash pipeline.sh --help' for usage."
 }
 
 
@@ -209,6 +210,8 @@ main() {
 
   if [[ -n "${VIP_CFG_MAP["singularity_image_dir"]+unset}" ]]; then
     singularityImageDir="${VIP_CFG_MAP["singularity_image_dir"]}"
+  else
+    singularityImageDir="${SCRIPT_DIR}/singularity/sif"
   fi
 
   if [[ -n "${VIP_CFG_MAP["cpu_cores"]+unset}" ]]; then

diff --git a/pipeline_inheritance.sh b/pipeline_inheritance.sh
@@ -33,7 +33,8 @@ usage() {
 -h, --help                optional: Print this message and exit.
 
 config:
-  cpu_cores               see 'bash pipeline.sh --help' for usage."
+  cpu_cores               see 'bash pipeline.sh --help' for usage.
+  singularity_image_dir   see 'bash pipeline.sh --help' for usage."
 }
 
 # arguments:
@@ -224,6 +225,8 @@ main() {
 
   if [[ -n "${VIP_CFG_MAP["singularity_image_dir"]+unset}" ]]; then
     singularityImageDir="${VIP_CFG_MAP["singularity_image_dir"]}"
+  else
+    singularityImageDir="${SCRIPT_DIR}/singularity/sif"
   fi
 
   if [[ -n "${VIP_CFG_MAP["cpu_cores"]+unset}" ]]; then

diff --git a/pipeline_preprocess.sh b/pipeline_preprocess.sh
@@ -38,7 +38,8 @@ config:
   preprocess_filter_low_qual    filter low quality records using filter status and read depth.
   preprocess_filter_read_depth  filter read depth threshold (default: 20)
   reference                     see 'bash pipeline.sh --help' for usage.
-  cpu_cores                     see 'bash pipeline.sh --help' for usage."
+  cpu_cores                     see 'bash pipeline.sh --help' for usage.
+  singularity_image_dir         see 'bash pipeline.sh --help' for usage."
 }
 
 #######################################
@@ -358,6 +359,8 @@ main() {
 
   if [[ -n "${VIP_CFG_MAP["singularity_image_dir"]+unset}" ]]; then
     singularityImageDir="${VIP_CFG_MAP["singularity_image_dir"]}"
+  else
+    singularityImageDir="${SCRIPT_DIR}/singularity/sif"
   fi
 
   if [[ -n "${VIP_CFG_MAP["reference"]+unset}" ]]; then

diff --git a/pipeline_report.sh b/pipeline_report.sh
@@ -349,6 +349,8 @@ main() {
 
   if [[ -n "${VIP_CFG_MAP["singularity_image_dir"]+unset}" ]]; then
     singularityImageDir="${VIP_CFG_MAP["singularity_image_dir"]}"
+  else
+    singularityImageDir="${SCRIPT_DIR}/singularity/sif"
   fi
 
   if [[ -n "${VIP_CFG_MAP["assembly"]+unset}" ]]; then