Added Pansel & GraphAligner

Added Pansel
Added GraphAligner
Updated GFAstast

PanGeTools.def

@@ -35,6 +35,13 @@ Stage: build
         libgsl-dev \
         libzstd-dev \
         libjemalloc-dev \
+        libjemalloc2 \
+        libsparsehash-dev \
+        libsdsl-dev \
+        libboost-all-dev \
+        libprotobuf-dev \
+        protobuf-compiler \
+        autoconf \
         libhts-dev \
         libbz2-dev \
         pybind11-dev \
@@ -169,17 +176,42 @@ Stage: build
 
     # 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
+    wget --no-check-certificate -c 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
 
     # Installing mash
     cd /apps
-    wget https://github.com/marbl/Mash/releases/download/v2.3/mash-Linux64-v2.3.tar
+    wget --no-check-certificate -c https://github.com/marbl/Mash/releases/download/v2.3/mash-Linux64-v2.3.tar
     tar -xvf mash-Linux64-v2.3.tar
     mv mash-Linux64-v2.3/mash bin/mash 
 
+    # Installing pansel
+    cd /apps
+    git clone -b v1.0.0 https://forgemia.inra.fr/pepragrodiv/pangenome/pansel.git pansel.src
+    cd pansel.src
+    make -j $(nproc)
+    mv pansel /apps/bin/pansel
+    rm -rf /apps/pansel.src
+
+    # Installing jemalloc
+    cd /apps
+    git clone -b 5.3.0 https://github.com/jemalloc/jemalloc
+    cd jemalloc
+    ./autogen.sh
+    make -j $(nproc)
+    make install -j $(nproc)
+
+    # Installing GraphAligner
+    cd /apps
+    git clone -b v1.0.19 https://github.com/maickrau/GraphAligner
+    cd GraphAligner
+    git submodule update --init --recursive
+    make bin/GraphAligner -j $(nproc)
+    mv bin/GraphAligner /apps/bin/
+    cd /apps && rm -rf GraphAligner
+
     # Cleaning step
     ## Removing tarballs
     rm /apps/*.tar*
@@ -232,6 +264,12 @@ Stage: build
 %apprun mash
     exec mash "$@"
 
+%apprun pansel
+    exec pansel "$@"
+
+%apprun graphaligner
+    exec GraphAligner "$@"
+
 %runscript
     exec "$@"
 
@@ -268,6 +306,8 @@ Stage: build
     vcfwave --version
     echo 'Looking for mash...'
     mash --version
+    echo 'Looking for GraphAligner...'
+    GraphAligner --version
 
 %labels
     Author alexis.mergez@inrae.fr
@@ -279,7 +319,7 @@ Stage: build
     panacus.Version 0.2.3
     gfatools.Version 0.5
     GFAvc.Version 0.2
-    GFAstats.Version 0.2
+    GFAstats.Version 0.3.1
     Samtools.Version 1.19
     wfmash.Version 0.10.5
     htslib.Version 1.19.1
@@ -288,6 +328,8 @@ Stage: build
     vcflib.Version 1.0.9
     rtg.Version 3.12.1
     mash.Version 2.3
+    pansel.version 1.0
+    GraphAligner.version 1.0.19
     about.home https://forgemia.inra.fr/alexis.mergez/pangetools
 
 %help
@@ -301,7 +343,7 @@ Stage: build
         - panacus       v0.2.3
         - gfatools      v0.5
         - GFAvc         v0.2
-        - GFAstats      v0.3
+        - GFAstats      v0.3.1
         - samtools      v1.19
         - bgzip         v1.19.1
         - wfmash        v0.10.5
@@ -310,5 +352,7 @@ Stage: build
         - vcflib        v1.0.9
         - RTG           v3.12.1
         - Mash          v2.3
+        - pansel        v1.0
+        - GraphAligner  v1.0.19
     Use apptainer --app <toolname> <container_path> [command] to run the selected tool.
     Tool names are lowercase : gfaffix, smoothxg, odgi, vg, panacus, etc...