Mercurial > repos > dereeper > pangenome_explorer

comparison PanExplorer.xml @ 10:d103c41b6931 draft

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Uploaded
author dereeper
date Thu, 30 May 2024 16:35:22 +0000
parents 24676ef2945d
children ae74fc0cb39c
comparison
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9:24676ef2945d 10:d103c41b6931
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 >>$logfile 2>&1; 24 if [ -f \$PANEX_PATH/panexplorer.sif ]; then; else; wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1; fi;
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28 #if $software=="pgap" 29 #if $software=="pgap"
29 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile; 30 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile;