Mercurial > repos > dereeper > pangenome_explorer

comparison PanExplorer.xml @ 5:4157f435fa89 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Thu, 30 May 2024 12:11:25 +0000
parents 97e4e3e818b6
children 35d71348e81e
comparison
equal deleted inserted replaced
4:53df1177ff97 5:4157f435fa89
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 if [ -f \$PANEX_PATH/panexplorer.sif ]; then; else; wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif; fi; 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;