Mercurial > repos > dereeper > pangenome_explorer
comparison PanExplorer.xml @ 13:152d7c43478b draft default tip
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author | dereeper |
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date | Thu, 30 May 2024 20:07:55 +0000 |
parents | 38c66e401040 |
children |
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12:38c66e401040 | 13:152d7c43478b |
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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; |