Mercurial > repos > dereeper > pangenome_explorer
comparison PanExplorer.xml @ 6:35d71348e81e draft
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author | dereeper |
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date | Thu, 30 May 2024 12:12:30 +0000 |
parents | 4157f435fa89 |
children | 2c65d4257fe6 |
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5:4157f435fa89 | 6:35d71348e81e |
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18 | 18 |
19 perl ${__tool_directory__}/Perl/generateConfig.pl '$private_genomes' '$input' config.yaml '$private_genomes_fasta'; | 19 perl ${__tool_directory__}/Perl/generateConfig.pl '$private_genomes' '$input' config.yaml '$private_genomes_fasta'; |
20 | 20 |
21 cat config.yaml >$logfile; | 21 cat config.yaml >$logfile; |
22 | 22 |
23 wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif | 23 wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif; |
24 | 24 |
25 | 25 |
26 | 26 |
27 #if $software=="pgap" | 27 #if $software=="pgap" |
28 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile; | 28 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile; |