

rsync -ruptl /var/www/html/rsat/perl-scripts/lib/js /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb


rsync -ruptl /var/www/html/rsat/public_html/images/program_icons/matrix-clustering_icons /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_query_matrices.tab -from tab -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_data/3.1293_input_motifs_processed_1.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_data/3.1293_input_motifs_processed_1.tf -from tf -to transfac -prefix_id 3.1293 -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_data/3.1293_input_motifs_processed.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_data/3.1293_input_motifs_processed.tf  > /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_data/input_motifs_processed.tf -split -from tf -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/pairwise_compa.tab'; hclust.method = 'average'; description.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab'; distance.table = '/var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/distance_table.tab'; alignment.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering'; "


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/cluster_2_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/cluster_1_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/cluster_3_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_data/cluster_3_transfac_motifs.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_aligned_logos/3.1293_m1_matrix-clustering_query_matrices.tab_1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_1/cluster_1_matrices_temp.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_aligned_logos/3.1293_m3_matrix-clustering_query_matrices.tab_3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_2/cluster_2_matrices_temp.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_aligned_logos/3.1293_m2_matrix-clustering_query_matrices.tab_2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_3/cluster_3_matrices_temp.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_1/cluster_1_matrices_temp.tf -from tf -to tf  -attr name cluster_1 -attr accession cluster_1 -set_attr merged_AC '3.1293:::matrix-clustering_query_matrices.tab_1' -set_attr merged_ID 'matrix-clustering_query_matrices.tab_1' -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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_1/cluster_1_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_2/cluster_2_matrices_temp.tf -from tf -to tf  -attr name cluster_2 -attr accession cluster_2 -set_attr merged_AC '3.1293:::matrix-clustering_query_matrices.tab_3' -set_attr merged_ID 'matrix-clustering_query_matrices.tab_3' -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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_2/cluster_2_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_3/cluster_3_matrices_temp.tf -from tf -to tf  -attr name cluster_3 -attr accession cluster_3 -set_attr merged_AC '3.1293:::matrix-clustering_query_matrices.tab_2' -set_attr merged_ID 'matrix-clustering_query_matrices.tab_2' -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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_3/cluster_3_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_2/cluster_2_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_1/cluster_1_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_clusters_information/cluster_3/cluster_3_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


rm -r /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_portable_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_temporary.html /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/distance_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/alignment_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/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/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/clusters.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/clusters.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/clusters_motif_names.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_tables/clusters_motif_names.html


mv -f /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2025/01/07/matrix-clustering_2025-01-07.033435_PM4hUb/matrix-clustering_portable_logo_tree.html
