Mercurial > repos > dereeper > pangenome_explorer

comparison PanExplorer.xml @ 8:f919ffe96425 draft

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Uploaded
author dereeper
date Thu, 30 May 2024 14:31:04 +0000
parents 2c65d4257fe6
children 24676ef2945d
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7:2c65d4257fe6 8:f919ffe96425
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; 24 wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1;
25 25
26 26
27 27
28 #if $software=="pgap" 28 #if $software=="pgap"
29 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile; 29 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile;