

set -ex



blast_and_promiscuity_filter.pl -h 2>&1 | grep Required
prep_genome_lib.pl -h 2>&1 | grep Required
blast_filter.pl -h 2>&1 | grep Required
blast_outfmt6_replace_trans_id_w_gene_symbol.pl -h 2>&1 | grep usage
build_fusion_annot_db_index.pl -h 2>&1 | grep gene_spans
build_prot_info_db.pl -h 2>&1 | grep gtf
gencode_extract_relevant_gtf_exons.pl 2>&1 | grep usage
gtf_file_to_feature_seqs.pl -h 2>&1 | grep usage
gtf_to_gene_spans.pl 2>&1 | grep usage
index_blast_pairs.pl -h 2>&1 | grep usage
index_blast_pairs.remove_gene_pair.pl -h 2>&1 | grep usage
index_blast_pairs.remove_overlapping_genes.pl 2>&1 | grep usage
index_cdna_seqs.pl 2>&1 | grep usage
index_pfam_domain_info.pl -h 2>&1 | grep pfam_domains
just_blast_test.pl -h 2>&1 | grep Required
promiscuity_filter.pl -h 2>&1 | grep Required
remove_long_intron_readthru_transcripts.pl -h 2>&1 | grep usage
$PREFIX/bin/util/paralog_clustering_util/get_top_blast_pairs.pl 2>&1 | grep usage
$PREFIX/bin/util/paralog_clustering_util/outfmt6_add_percent_match_length.group_segments.pl -h 2>&1 | grep usage
$PREFIX/bin/util/paralog_clustering_util/outfmt6_add_percent_match_length.group_segments.to_Markov_Clustering.pl -h 2>&1 | grep outfmt6_grouped
$PREFIX/bin/util/paralog_clustering_util/outfmt6_add_percent_match_length.pl -h 2>&1 | grep usage
exit 0
