

rsync -ruptl /var/www/html/rsat/perl-scripts/lib/js /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY


rsync -ruptl /var/www/html/rsat/public_html/images/program_icons/matrix-clustering_icons /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_query_matrices.tab -from tab -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_data/wt1_input_motifs_processed_1.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_data/wt1_input_motifs_processed_1.tf -from tf -to transfac -prefix_id wt1 -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_data/wt1_input_motifs_processed.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_data/wt1_input_motifs_processed.tf  > /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/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/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_data/input_motifs_processed.tf -split -from tf -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/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/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/pairwise_compa.tab'; hclust.method = 'average'; description.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab'; distance.table = '/var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/distance_table.tab'; alignment.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/alignment_table.tab'; verbosity = 0; metric = 'Ncor'; heatmap.color.palette = 'YlOrRd'; heatmap.color.classes = '9'; export.newick = 0; radial.only = 0; draw.heatmap = 1; draw.consensus = 0; pos.hclust.in.heatmap = 'column'; lthsp = 'cor_0.6_Ncor_0.4_'; out.prefix = '/var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering'; "


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/cluster_1_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_data/cluster_1_transfac_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_aligned_logos/wt1_m1_matrix-clustering_query_matrices.tab_1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_aligned_logos/wt1_m2_matrix-clustering_query_matrices.tab_2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/IC_test_2025-03-20.052032_7QVPF1


cat /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


rm -r /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_pairwise_compa_logos


cp /var/www/html/rsat/public_html/templates_html/display_d3_tree.html /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_logo_tree.html


cp /var/www/html/rsat/public_html/templates_html/display_small_d3_tree.html /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_portable_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_temporary.html /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_portable_logo_tree.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_html/pairwise_compa_matrix_descriptions.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/distance_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/distance_table.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/alignment_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/alignment_table.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/clusters.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/clusters.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/clusters_motif_names.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_tables/clusters_motif_names.html


mv -f /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2025/03/20/matrix-clustering_2025-03-20.052024_Q3NzmY/matrix-clustering_portable_logo_tree.html
