Mercurial > repos > dereeper > pangenome_explorer

comparison PanExplorer.xml @ 12:38c66e401040 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 19:59:16 +0000
parents ae74fc0cb39c
children 152d7c43478b
comparison
equal deleted inserted replaced
11:ae74fc0cb39c 12:38c66e401040
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 >>$logfile 2>&1;
25 24
25
26 if [ -f \$PANEX_PATH/panexplorer.sif ]; then
27 echo "Singularity file exists."
28 else
29 wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1
30 fi
26 31
27 32
28 33
29 #if $software=="pgap" 34 #if $software=="pgap"
30 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile; 35 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile;