Mercurial > repos > dereeper > pangenome_explorer
changeset 18:716821f47909 draft default tip
Uploaded
| author | dereeper |
|---|---|
| date | Tue, 17 Dec 2024 13:19:43 +0000 |
| parents | db83eb7c8f78 |
| children | |
| files | PanExplorer.xml |
| diffstat | 1 files changed, 11 insertions(+), 9 deletions(-) [+] |
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--- 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;