update inheritance matcher 3.1.1 (#637)

* update inheritance matcher 3.1.1 * update inheritance match md5 sum
molgenis · Sep 6, 2024 · 28a7bad · 28a7bad
1 parent fbe7e60
commit 28a7bad
Show file tree

Hide file tree

Showing 5 changed files with 6 additions and 6 deletions.
diff --git a/config/nxf_vcf.config b/config/nxf_vcf.config
@@ -9,7 +9,7 @@ env {
   CMD_STRANGER = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/stranger-0.8.1.sif stranger"
   CMD_VCFREPORT="apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-report-7.0.0.sif"
   CMD_VCFDECISIONTREE = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-decision-tree-4.1.1.sif"
-  CMD_VCFINHERITANCEMATCHER = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-inheritance-matcher-3.1.0.sif"
+  CMD_VCFINHERITANCEMATCHER = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-inheritance-matcher-3.1.1.sif"
 
   // workaround for SAMtools https://github.com/samtools/samtools/issues/1366#issuecomment-769170935
   REF_PATH = ":"

diff --git a/install.sh b/install.sh
@@ -88,7 +88,7 @@ download_files() {
   urls+=("8f6e06847776448e004df8b863571109" "images/straglr-1.4.4_vip_v3.sif")
   urls+=("bcc157242cd9b09c66f015c52ef2d61d" "images/stranger-0.8.1.sif")
   urls+=("57401e7b835fed2f52fafadc0dd744d4" "images/vcf-decision-tree-4.1.1.sif")
-  urls+=("9c4d7b48138f29651cdd45eb8d0cc4b6" "images/vcf-inheritance-matcher-3.1.0.sif")
+  urls+=("231b9369cdfdb080455a3eddb2e0019b" "images/vcf-inheritance-matcher-3.1.1.sif")
   urls+=("53f9265acb2041b2b93c692177d91d74" "images/vcf-report-7.0.0.sif")
   urls+=("7bffc236a7c65b2b2e2e5f7d64beaa87" "images/vep-111.0.sif")
   urls+=("82be3c18406e7c027ee4cec83a723d71" "nextflow-24.04.2-all")

diff --git a/utils/apptainer/build.sh b/utils/apptainer/build.sh
@@ -97,7 +97,7 @@ main() {
   images+=("stranger-0.8.1")
   images+=("straglr-1.4.4_vip_v3")
   images+=("vcf-decision-tree-4.1.1")
-  images+=("vcf-inheritance-matcher-3.1.0")
+  images+=("vcf-inheritance-matcher-3.1.1")
   images+=("vcf-report-7.0.0")
 
   for i in "${!images[@]}"; do

diff --git a/...ner/def/vcf-inheritance-matcher-3.1.0.def → ...ner/def/vcf-inheritance-matcher-3.1.1.def b/...ner/def/vcf-inheritance-matcher-3.1.0.def → ...ner/def/vcf-inheritance-matcher-3.1.1.def
@@ -8,15 +8,15 @@ From: sif/build/openjdk-17.sif
 %post
     version_major=3
     version_minor=1
-    version_patch=0
+    version_patch=1
 
     # install
     apk update
     apk add --virtual=.build-dependencies curl
 
     mkdir -p /opt/vcf-inheritance-matcher/lib
     curl -Ls -o /opt/vcf-inheritance-matcher/lib/vcf-inheritance-matcher.jar "https://github.com/molgenis/vip-inheritance-matcher/releases/download/v${version_major}.${version_minor}.${version_patch}/vcf-inheritance-matcher.jar"
-    echo "1b4b9f33542ce0e19c7bc22542e857137ca12f2e62f68f4d7f0254da43f2143b  /opt/vcf-inheritance-matcher/lib/vcf-inheritance-matcher.jar" | sha256sum -c
+    echo "f7afe980c217efe7b5b5ec932c1bf885f4e812e7814b2b58bf002db98a3c58a2  /opt/vcf-inheritance-matcher/lib/vcf-inheritance-matcher.jar" | sha256sum -c
 
     # cleanup
     apk del .build-dependencies

diff --git a/vip.sh b/vip.sh
@@ -7,7 +7,7 @@ SCRIPT_NAME="$(basename "$0")"
 # SCRIPT_DIR is incorrect when vip.sh is submitted as a Slurm job that is submitted as part of another Slurm job
 VIP_DIR="${VIP_DIR:-"${SCRIPT_DIR}"}"
 
-VIP_VERSION="7.9.0"
+VIP_VERSION="7.9.1"
 
 display_version() {
   echo -e "${VIP_VERSION}"