Update hap.py to use jmcdani20/hap.py:v0.3.12

PiperOrigin-RevId: 361879959
serge2016 · Mar 9, 2021 · 650f4c7 · 650f4c7
1 parent 5acd678
commit 650f4c7
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diff --git a/docs/deeptrio-pacbio-case-study.md b/docs/deeptrio-pacbio-case-study.md
@@ -234,15 +234,15 @@ Concordance HG002: F:143838/144142 (99.79%)  M:143867/144177 (99.78%)  F+M:14210
 ```bash
 mkdir -p happy
 
-sudo docker pull pkrusche/hap.py
+sudo docker pull jmcdani20/hap.py:v0.3.12
 
 sudo docker run \
   -v "${PWD}/benchmark":"/benchmark" \
   -v "${PWD}/input":"/input" \
   -v "${PWD}/output":"/output" \
   -v "${PWD}/reference":"/reference" \
   -v "${PWD}/happy:/happy" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /benchmark/HG002_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG002.output.vcf.gz \
   -f /benchmark/HG002_GRCh38_1_22_v4.2_benchmark.bed \
@@ -257,7 +257,7 @@ sudo docker run \
   -v "${PWD}/output":"/output" \
   -v "${PWD}/reference":"/reference" \
   -v "${PWD}/happy:/happy" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG003.output.vcf.gz \
   -f /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.bed \
@@ -272,7 +272,7 @@ sudo docker run \
   -v "${PWD}/output":"/output" \
   -v "${PWD}/reference":"/reference" \
   -v "${PWD}/happy:/happy" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /benchmark/HG004_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG004.output.vcf.gz \
   -f /benchmark/HG004_GRCh38_1_22_v4.2_benchmark.bed \

diff --git a/docs/deeptrio-quick-start.md b/docs/deeptrio-quick-start.md
@@ -272,13 +272,13 @@ sample is compared against the corresponding truth set from GIAB.
 
 ```bash
 # Pull docker image locally
-sudo docker pull pkrusche/hap.py
+sudo docker pull jmcdani20/hap.py:v0.3.12
 
 # Evaluate HG002
 sudo docker run -it \
   -v "${INPUT_DIR}":"/input" \
   -v "${OUTPUT_DIR}:/output" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /input/HG002_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG002.output.vcf.gz \
   -f "/input/HG002_GRCh38_1_22_v4.2_benchmark.bed" \
@@ -291,7 +291,7 @@ sudo docker run -it \
 sudo docker run -it \
   -v "${INPUT_DIR}":"/input" \
   -v "${OUTPUT_DIR}:/output" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /input/HG003_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG003.output.vcf.gz \
   -f "/input/HG003_GRCh38_1_22_v4.2_benchmark.bed" \
@@ -304,7 +304,7 @@ sudo docker run -it \
 sudo docker run -it \
   -v "${INPUT_DIR}":"/input" \
   -v "${OUTPUT_DIR}:/output" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /input/HG004_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG004.output.vcf.gz \
   -f "/input/HG004_GRCh38_1_22_v4.2_benchmark.bed" \

diff --git a/docs/deeptrio-wgs-case-study.md b/docs/deeptrio-wgs-case-study.md
@@ -216,15 +216,15 @@ Concordance HG002: F:133992/134497 (99.62%)  M:134059/134588 (99.61%)  F+M:13267
 ```bash
 mkdir -p happy
 
-sudo docker pull pkrusche/hap.py
+sudo docker pull jmcdani20/hap.py:v0.3.12
 
 sudo docker run \
   -v "${PWD}/benchmark":"/benchmark" \
   -v "${PWD}/input":"/input" \
   -v "${PWD}/output":"/output" \
   -v "${PWD}/reference":"/reference" \
   -v "${PWD}/happy:/happy" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /benchmark/HG002_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG002.output.vcf.gz \
   -f /benchmark/HG002_GRCh38_1_22_v4.2_benchmark.bed \
@@ -239,7 +239,7 @@ sudo docker run \
   -v "${PWD}/output":"/output" \
   -v "${PWD}/reference":"/reference" \
   -v "${PWD}/happy:/happy" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG003.output.vcf.gz \
   -f /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.bed \
@@ -254,7 +254,7 @@ sudo docker run \
   -v "${PWD}/output":"/output" \
   -v "${PWD}/reference":"/reference" \
   -v "${PWD}/happy:/happy" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /benchmark/HG004_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG004.output.vcf.gz \
   -f /benchmark/HG004_GRCh38_1_22_v4.2_benchmark.bed \

diff --git a/docs/deepvariant-case-study.md b/docs/deepvariant-case-study.md
@@ -106,15 +106,15 @@ For running on GPU machines, or using Singularity instead of Docker, see
 ```bash
 mkdir -p happy
 
-sudo docker pull pkrusche/hap.py
+sudo docker pull jmcdani20/hap.py:v0.3.12
 
 sudo docker run \
   -v "${PWD}/benchmark":"/benchmark" \
   -v "${PWD}/input":"/input" \
   -v "${PWD}/output":"/output" \
   -v "${PWD}/reference":"/reference" \
   -v "${PWD}/happy:/happy" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG003.output.vcf.gz \
   -f /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.bed \

diff --git a/docs/deepvariant-exome-case-study.md b/docs/deepvariant-exome-case-study.md
@@ -107,15 +107,15 @@ For running on GPU machines, or using Singularity instead of Docker, see
 ```bash
 mkdir -p happy
 
-sudo docker pull pkrusche/hap.py
+sudo docker pull jmcdani20/hap.py:v0.3.12
 
 sudo docker run \
   -v "${PWD}/benchmark":"/benchmark" \
   -v "${PWD}/input":"/input" \
   -v "${PWD}/output":"/output" \
   -v "${PWD}/reference":"/reference" \
   -v "${PWD}/happy:/happy" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG003.output.vcf.gz \
   -f /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.bed \

diff --git a/docs/deepvariant-hybrid-case-study.md b/docs/deepvariant-hybrid-case-study.md
@@ -161,7 +161,7 @@ sudo docker run \
   -v "${PWD}/output":"/output" \
   -v "${PWD}/reference":"/reference" \
   -v "${PWD}/happy:/happy" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.vcf.gz \
   /output/HG003.output.vcf.gz \
   -f /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.bed \

diff --git a/docs/deepvariant-pacbio-model-case-study.md b/docs/deepvariant-pacbio-model-case-study.md
@@ -151,7 +151,7 @@ singularity exec --bind /usr/lib/locale/ \
 ```bash
 mkdir -p happy
 
-singularity exec docker://pkrusche/hap.py:latest \
+singularity exec docker://jmcdani20/hap.py:v0.3.12:latest \
     /opt/hap.py/bin/hap.py \
         --threads $(nproc) \
         -r reference/GRCh38_no_alt_analysis_set.fasta \
@@ -179,7 +179,7 @@ Benchmarking Summary:
 ```bash
 mkdir -p happy
 
-singularity exec docker://pkrusche/hap.py:latest \
+singularity exec docker://jmcdani20/hap.py:v0.3.12:latest \
     /opt/hap.py/bin/hap.py \
         --threads $(nproc) \
         -r reference/GRCh38_no_alt_analysis_set.fasta \

diff --git a/docs/deepvariant-quick-start.md b/docs/deepvariant-quick-start.md
@@ -228,11 +228,11 @@ program from Illumina to evaluate the resulting 10 kilobase vcf file. This
 serves as a quick check to ensure the three DeepVariant commands ran correctly.
 
 ```bash
-sudo docker pull pkrusche/hap.py
+sudo docker pull jmcdani20/hap.py:v0.3.12
 sudo docker run -it \
   -v "${INPUT_DIR}":"/input" \
   -v "${OUTPUT_DIR}:/output" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   /input/test_nist.b37_chr20_100kbp_at_10mb.vcf.gz \
   /output/output.vcf.gz \
   -f "/input/test_nist.b37_chr20_100kbp_at_10mb.bed" \

diff --git a/docs/deepvariant-training-case-study.md b/docs/deepvariant-training-case-study.md
@@ -428,12 +428,12 @@ format here: `${OUTPUT_DIR}/test_set.vcf.gz`. Next step is to run `hap.py` to
 complete the evaluation on chromosome 20:
 
 ```
-sudo docker pull pkrusche/hap.py
+sudo docker pull jmcdani20/hap.py:v0.3.12
 
 time sudo docker run -it \
 -v "${DATA_DIR}:${DATA_DIR}" \
 -v "${OUTPUT_DIR}:${OUTPUT_DIR}" \
-pkrusche/hap.py /opt/hap.py/bin/hap.py \
+jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
   "${TRUTH_VCF}" \
   "${OUTPUT_DIR}/test_set.vcf.gz" \
   -f "${TRUTH_BED}" \

diff --git a/docs/trio-merge-case-study.md b/docs/trio-merge-case-study.md
@@ -397,14 +397,14 @@ Indel/SNP+MNP ratio          : 0.09 (3716/41873)
 ### Run hap.py to calculate the accuracy of DeepVariant generated call sets
 
 ```
-sudo docker pull pkrusche/hap.py
+sudo docker pull jmcdani20/hap.py:v0.3.12
 
 declare -a trio=(HG002 HG003 HG004)
 for SAMPLE in "${trio[@]}"
 do
   sudo docker run -i \
     -v "${DIR}":"/data" \
-    pkrusche/hap.py /opt/hap.py/bin/hap.py \
+    jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
     "/data/${SAMPLE}_truth.vcf.gz" \
     "/data/${SAMPLE}.vcf.gz" \
     -f "/data/${SAMPLE}_truth.bed" \

diff --git a/scripts/inference_deeptrio.sh b/scripts/inference_deeptrio.sh
@@ -485,15 +485,15 @@ function run_happy() {
   run "zcat <"${INPUT_DIR}/${REF_BASENAME}.gz" >"${INPUT_DIR}/${REF_BASENAME}""
 
   # Pulling twice in case the first one times out.
-  run "sudo docker pull pkrusche/hap.py || \
-    (sleep 5 ; sudo docker pull pkrusche/hap.py)"
+  run "sudo docker pull jmcdani20/hap.py:v0.3.12 || \
+    (sleep 5 ; sudo docker pull jmcdani20/hap.py:v0.3.12)"
   # shellcheck disable=SC2027
   # shellcheck disable=SC2086
   # shellcheck disable=SC2145
   run "sudo docker run -i \
     -v "${INPUT_DIR}":"/input" \
     -v "${OUTPUT_DIR}:/output" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
     "/input/${truth_vcf}" \
     "/output/${vcf_output}" \
     -f "/input/${truth_bed}" \

diff --git a/scripts/inference_deepvariant.sh b/scripts/inference_deepvariant.sh
@@ -486,15 +486,15 @@ function run_happy() {
   # shellcheck disable=SC2086
   run "zcat <"${INPUT_DIR}/$(basename $REF).gz" >"${UNCOMPRESSED_REF}""
 
-  run "sudo docker pull pkrusche/hap.py"
+  run "sudo docker pull jmcdani20/hap.py:v0.3.12"
   # shellcheck disable=SC2027
   # shellcheck disable=SC2046
   # shellcheck disable=SC2086
   # shellcheck disable=SC2145
   run "( sudo docker run -i \
   -v "${INPUT_DIR}:${INPUT_DIR}" \
   -v "${OUTPUT_DIR}:${OUTPUT_DIR}" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
     "${INPUT_DIR}/$(basename $TRUTH_VCF)" \
     "${OUTPUT_DIR}/${OUTPUT_VCF}" \
     -f "${INPUT_DIR}/$(basename $TRUTH_BED)" \

diff --git a/scripts/run_deeptrio_wgs_case_study_binaries.sh b/scripts/run_deeptrio_wgs_case_study_binaries.sh
@@ -238,12 +238,12 @@ function run_happy() {
   zcat <"${REF}" >"${UNCOMPRESSED_REF}"
 
   # Pulling twice in case the first one times out.
-  sudo docker pull pkrusche/hap.py || \
-    (sleep 5 ; sudo docker pull pkrusche/hap.py)
+  sudo docker pull jmcdani20/hap.py:v0.3.12 || \
+    (sleep 5 ; sudo docker pull jmcdani20/hap.py:v0.3.12)
   sudo docker run -i \
   -v "${DATA_DIR}:${DATA_DIR}" \
   -v "${OUTPUT_DIR}:${OUTPUT_DIR}" \
-  pkrusche/hap.py /opt/hap.py/bin/hap.py \
+  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
     "${truth_vcf}" \
     "${vcf_output}" \
     -f "${truth_bed}" \