

rsync -ruptl /var/www/html/rsat/perl-scripts/lib/js /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A


rsync -ruptl /var/www/html/rsat/public_html/images/program_icons/matrix-clustering_icons /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_query_matrices.meme -from meme -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/iegs_input_motifs_processed_1.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/iegs_input_motifs_processed_1.tf -from tf -to transfac -prefix_id iegs -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/iegs_input_motifs_processed.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/iegs_input_motifs_processed.tf  > /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/input_motifs_processed.tf -split -from tf -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/pairwise_compa.tab'; hclust.method = 'average'; description.file = '/var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab'; distance.table = '/var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/distance_table.tab'; alignment.file = '/var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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 = 'Ncor_0.4_cor_0.6_'; out.prefix = '/var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering'; "


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/cluster_1_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/cluster_1_transfac_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/cluster_2_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/cluster_2_transfac_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/cluster_3_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/cluster_3_transfac_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/cluster_4_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_data/cluster_4_transfac_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/iegs_m5_MA0472.2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/iegs_m7_MA0732.2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/iegs_m2_MA0147.4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/iegs_m8_MA1464.2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/iegs_m1_MA0099.4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/iegs_m6_MA0476.2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_2 -name cluster_2 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_3 -name cluster_3 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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/2026/01/30/IC_test_2026-01-30.191211_Owgzh5


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/IC_test_2026-01-30.191211_0P4Q2o


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/IC_test_2026-01-30.191211_dwRWS3


cat /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/iegs_m3_MA0162.5_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/iegs_m5_MA0472.2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/iegs_m7_MA0732.2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_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/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_nb_motifs_3.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/IC_test_2026-01-30.191212_59LDHl


cat /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/iegs_m4_MA0466.4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices_temp.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices_temp.tf -from tf -to tf  -attr name cluster_4 -attr accession cluster_4 -set_attr merged_AC 'iegs:::MA0466.4' -set_attr merged_ID 'MA0466.4' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


rm -r /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_portable_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_temporary.html /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/distance_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/alignment_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/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/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/clusters.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/clusters.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/clusters_motif_names.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_tables/clusters_motif_names.html


mv -f /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2026/01/30/matrix-clustering_2026-01-30.191204_fXds4A/matrix-clustering_portable_logo_tree.html
