Mercurial > repos > dereeper > pangenome_explorer

comparison PanExplorer.xml @ 13:152d7c43478b draft default tip

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author dereeper
date Thu, 30 May 2024 20:07:55 +0000
parents 38c66e401040
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12:38c66e401040 13:152d7c43478b
21 21
22 cat config.yaml >$logfile; 22 cat config.yaml >$logfile;
23 23
24 24
25 25
26 if [ -f \$PANEX_PATH/panexplorer.sif ]; then 26 if [ ! -f \$PANEX_PATH/panexplorer.sif ]; then wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1;fi;
27 echo "Singularity file exists."
28 else
29 wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1
30 fi
31 27
32 28
33 29
34 #if $software=="pgap" 30 #if $software=="pgap"
35 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile; 31 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile;