

rsync -ruptl /var/www/html/rsat/perl-scripts/lib/js /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k


rsync -ruptl /var/www/html/rsat/public_html/images/program_icons/matrix-clustering_icons /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_third_matrices.transfac -from transfac -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_homer_input_motifs_processed_1.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_homer_input_motifs_processed_1.tf -from tf -to transfac -prefix_id oct4_homer -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_homer_input_motifs_processed.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_query_matrices.transfac -from transfac -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed_1.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed_1.tf -from tf -to transfac -prefix_id oct4_peak_motifs -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_second_matrices. -from transfac -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_meme-chip_input_motifs_processed_1.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_meme-chip_input_motifs_processed_1.tf -from tf -to transfac -prefix_id oct4_meme-chip -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_meme-chip_input_motifs_processed.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_homer_input_motifs_processed.tf /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed.tf /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/oct4_meme-chip_input_motifs_processed.tf  > /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/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/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/input_motifs_processed.tf -split -from tf -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/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/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_tables/pairwise_compa.tab'; hclust.method = 'average'; description.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab'; distance.table = '/var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_tables/distance_table.tab'; alignment.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/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 = 'cor_0.6_Ncor_0.4_'; out.prefix = '/var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering'; "


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_tables/cluster_1_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_data/cluster_1_transfac_motifs.tf


rm -r /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_pairwise_compa_logos


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/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/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_tables/distance_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/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/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_tables/alignment_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/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/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_tables/clusters.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_tables/clusters.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_tables/clusters_motif_names.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/11/25/matrix-clustering_2025-11-25.112814_UYaq7k/matrix-clustering_tables/clusters_motif_names.html
