Mercurial > repos > dereeper > pangenome_explorer
comparison PanExplorer.xml @ 10:d103c41b6931 draft
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author | dereeper |
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date | Thu, 30 May 2024 16:35:22 +0000 |
parents | 24676ef2945d |
children | ae74fc0cb39c |
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9:24676ef2945d | 10:d103c41b6931 |
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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; |
25 | |
25 | 26 |
26 | 27 |
27 | 28 |
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; |