v1.4.0

Added multiple tools :
- vcfbub
- vcflib
- RTG

PanGeTools.def

@@ -36,13 +36,15 @@ Stage: build
         libjemalloc-dev \
         libhts-dev \
         libbz2-dev \
+        pybind11-dev \
         python3 \
         python3-pandas \
         python3-matplotlib \
         python3-sklearn \
         python3-sklearn-lib \
         python3-scipy \
-        python3-seaborn
+        python3-seaborn \
+        unzip
 
     #Installing RUST
     curl https://sh.rustup.rs -sSf | sh -s -- -y
@@ -148,6 +150,29 @@ Stage: build
     mv minimap2-2.26_x64-linux/paftools.js /apps/bin/paftools.js
     rm -rf /apps/minimap2-2.26_x64-linux
 
+    # Installing vcfbub
+    cd /apps
+    wget --no-check-certificate -c https://github.com/pangenome/vcfbub/releases/download/v0.1.0/vcfbub
+    chmod u+x vcfbub
+    mv vcfbub /apps/bin/vcfbub
+
+    # Installing vcflib
+    cd /apps
+    wget --no-check-certificate -c https://github.com/vcflib/vcflib/releases/download/v1.0.9/vcflib-1.0.9-src.tar.gz
+    tar -zxvf vcflib-1.0.9-src.tar.gz
+    cd vcflib-1.0.9
+    mkdir -p build
+    cd build
+    cmake -DZIG=OFF -DCMAKE_BUILD_TYPE=Debug .. && cmake --build . -- -j $(nproc)
+    for file in ./*; do ln -s $(pwd)/$file /apps/bin/$file; done
+
+    # Installing RTG tools
+    cd /apps
+    wget https://github.com/RealTimeGenomics/rtg-tools/releases/download/3.12.1/rtg-tools-3.12.1-linux-x64.zip
+    unzip rtg-tools-3.12.1-linux-x64.zip
+    sed -i 's/read -r -p "Would you like to enable automatic usage logging (y\/n)? " REPLY/REPLY="n"/g' /apps/rtg-tools-3.12.1/rtg
+    ln -s /apps/rtg-tools-3.12.1/rtg /apps/bin
+
     # Cleaning step
     ## Removing tarballs
     rm /apps/*.tar*
@@ -188,6 +213,15 @@ Stage: build
 %apprun minimap2
     exec minimap2 "$@"
 
+%apprun vcfbub
+    exec vcfbub "$@"
+
+%apprun vcfwave
+    exec vcfwave "$@"
+
+%runscript
+    exec "$@"
+
 %test
     echo 'Looking for GFAffix...'
     gfaffix --version
@@ -213,6 +247,10 @@ Stage: build
     wfmash --version
     echo 'Looking for minimap2...'
     minimap2 --version
+    echo 'Looking for vcfbub...'
+    vcfbub --version
+    echo 'Looking for vcfwave...'
+    vcfwave --version
 
 %labels
     Author alexis.mergez@inrae.fr
@@ -228,6 +266,9 @@ Stage: build
     wfmash.Version 0.10.5
     htslib.Version 1.19.1
     minimap2.Version 2.26
+    vcfbub.Version 0.1.0
+    vcflib.Version 1.0.9
+    rtg.Version 3.12.1
 
 %help
     PanGeTools - Pangenomic General tools - Version VERSION_NUMBER
@@ -244,5 +285,8 @@ Stage: build
         - bgzip         v1.19.1
         - wfmash        v0.10.5
         - minimap2      v2.26
+        - vcfbub        v0.1.0
+        - vcflib        v1.0.9
+        - RTG           v3.12.1
     Use apptainer --app <toolname> <container_path> [command] to run the selected tool.
     Tool names are lowercase : gfaffix, smoothxg, odgi, vg, panacus, etc...