# HG changeset patch
# User dereeper
# Date 1734441583 0
# Node ID 716821f47909c534d66590ae9cdc3537ce8cfc23
# Parent  db83eb7c8f788e222f126eadd5ba5b3baabc71bb
Uploaded

diff -r db83eb7c8f78 -r 716821f47909 PanExplorer.xml
--- a/PanExplorer.xml	Sun Dec 15 21:31:25 2024 +0000
+++ b/PanExplorer.xml	Tue Dec 17 13:19:43 2024 +0000
@@ -10,7 +10,7 @@
  -->
     <requirement type="package" version="1.30">perl-yaml</requirement>
     <requirement type="package" version="3.8.7">singularity</requirement>
-    <!--    <container type="docker">ghcr.io/pangenome/pggb:latest</container> -->
+    <container type="docker">docker.io/dereeper/panexplorer_workflow:latest</container>
  </requirements>
 
     <command><![CDATA[
@@ -27,25 +27,27 @@
 
 cat config.yaml >$logfile;
 
-if [ ! -f ${__tool_directory__}/panexplorer.sif ]; then wget -O ${__tool_directory__}/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1;fi;
+if [ ! -f ${__tool_directory__}/panexplorer_workflow_latest.sif ]; then wget -O ${__tool_directory__}/panexplorer_workflow_latest.sif https://panexplorer.southgreen.fr/singularity/panexplorer_workflow_latest.sif >>$logfile 2>&1;fi;
+
+
 
 
 
 #if $software=="pgap"
-singularity exec ${__tool_directory__}/panexplorer.sif sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG 1>snakefile 2>>$logfile;
+singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG 1>snakefile 2>>$logfile;
 #else if $software=="roary"
-singularity exec ${__tool_directory__}/panexplorer.sif sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG 1>snakefile 2>>$logfile;
+singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG 1>snakefile 2>>$logfile;
 #else if $software=="orthofinder"
-singularity exec ${__tool_directory__}/panexplorer.sif sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset 1>snakefile 2>>$logfile;
+singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset 1>snakefile 2>>$logfile;
 #else if $software=="cactus"
-	    singularity exec ${__tool_directory__}/panexplorer.sif cp -rf \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 1>snakefile 2>>$logfile;
+	    singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 1>snakefile 2>>$logfile;
 #else if $software=="pggb"
-singularity exec ${__tool_directory__}/panexplorer.sif sed "s/identity\=30/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG 1>snakefile 2>>$logfile;
+singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG 1>snakefile 2>>$logfile;
 #else
-	    singularity exec ${__tool_directory__}/panexplorer.sif sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG 1>snakefile 2>>$logfile;
+	    singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG 1>snakefile 2>>$logfile;
 #end if
 
-singularity exec ${__tool_directory__}/panexplorer.sif snakemake --cores 1 -s snakefile >>$logfile 2>&1;
+singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif snakemake --cores 1 --config identity=$min_identity -s snakefile >>$logfile 2>&1;
 
 
 cp -rf outputs/upsetr.svg $upset;