Mercurial > repos > dereeper > pangenome_explorer
comparison PanExplorer.xml @ 12:38c66e401040 draft
Uploaded
author | dereeper |
---|---|
date | Thu, 30 May 2024 19:59:16 +0000 |
parents | ae74fc0cb39c |
children | 152d7c43478b |
comparison
equal
deleted
inserted
replaced
11:ae74fc0cb39c | 12:38c66e401040 |
---|---|
19 | 19 |
20 perl ${__tool_directory__}/Perl/generateConfig.pl '$private_genomes' '$input' config.yaml '$private_genomes_fasta'; | 20 perl ${__tool_directory__}/Perl/generateConfig.pl '$private_genomes' '$input' config.yaml '$private_genomes_fasta'; |
21 | 21 |
22 cat config.yaml >$logfile; | 22 cat config.yaml >$logfile; |
23 | 23 |
24 wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1; | |
25 | 24 |
25 | |
26 if [ -f \$PANEX_PATH/panexplorer.sif ]; then | |
27 echo "Singularity file exists." | |
28 else | |
29 wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1 | |
30 fi | |
26 | 31 |
27 | 32 |
28 | 33 |
29 #if $software=="pgap" | 34 #if $software=="pgap" |
30 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile; | 35 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile; |