rsync -ruptl /var/www/html/rsat/perl-scripts/lib/js /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq


rsync -ruptl /var/www/html/rsat/public_html/images/program_icons/matrix-clustering_icons /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_query_matrices.transfac -from tf -to tf -perm 1 -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_data/Collection_1_random_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_data/Collection_1_random_motifs.tf -from transfac -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_data/Collection_1_input_motifs_processed_1.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_data/Collection_1_input_motifs_processed_1.tf -from tf -to transfac -prefix_id Collection_1 -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_data/Collection_1_input_motifs_processed.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_data/Collection_1_input_motifs_processed.tf  > /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_data/input_motifs_processed.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_data/input_motifs_processed.tf -split -from tf -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_data/motif


 cat /var/www/html/rsat/R-scripts/matrix-clustering.R | /usr/bin/R --slave --no-save --no-restore --no-environ --args " infile = '/var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_tables/pairwise_compa.tab'; hclust.method = 'average'; description.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab'; distance.table = '/var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_tables/distance_table.tab'; alignment.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering_tables/alignment_table.tab'; verbosity = 0; metric = 'Ncor'; heatmap.color.palette = 'YlOrRd'; heatmap.color.classes = '9'; export.newick = 0; radial.only = 1; draw.heatmap = 1; draw.consensus = 0; pos.hclust.in.heatmap = 'column'; lthsp = 'Ncor_0.4_cor_0.6_'; out.prefix = '/var/www/html/rsat/public_html/tmp/www-data/2025/09/15/matrix-clustering_2025-09-15.162039_lIWtuq/matrix-clustering'; "