Purdue University

Commands

• PIRATE
• FET.pl
• PIRATE_to_Rtab.pl
• PIRATE_to_roary.pl
• SOAPsh.pl
• ace.pl
• analyse_blast_outputs.pl
• analyse_loci_list.pl
• annotate_treeWAS_output.pl
• bamToGBrowse.pl
• bdf2gdfont.pl
• binhex.pl
• bp_aacomp.pl
• bp_biofetch_genbank_proxy.pl
• bp_bioflat_index.pl
• bp_biogetseq.pl
• bp_blast2tree.pl
• bp_bulk_load_gff.pl
• bp_chaos_plot.pl
• bp_classify_hits_kingdom.pl
• bp_composite_LD.pl
• bp_das_server.pl
• bp_dbsplit.pl
• bp_download_query_genbank.pl
• bp_extract_feature_seq.pl
• bp_fast_load_gff.pl
• bp_fastam9_to_table.pl
• bp_fetch.pl
• bp_filter_search.pl
• bp_find-blast-matches.pl
• bp_flanks.pl
• bp_gccalc.pl
• bp_genbank2gff.pl
• bp_genbank2gff3.pl
• bp_generate_histogram.pl
• bp_heterogeneity_test.pl
• bp_hivq.pl
• bp_hmmer_to_table.pl
• bp_index.pl
• bp_load_gff.pl
• bp_local_taxonomydb_query.pl
• bp_make_mrna_protein.pl
• bp_mask_by_search.pl
• bp_meta_gff.pl
• bp_mrtrans.pl
• bp_mutate.pl
• bp_netinstall.pl
• bp_nexus2nh.pl
• bp_nrdb.pl
• bp_oligo_count.pl
• bp_parse_hmmsearch.pl
• bp_process_gadfly.pl
• bp_process_sgd.pl
• bp_process_wormbase.pl
• bp_query_entrez_taxa.pl
• bp_remote_blast.pl
• bp_revtrans-motif.pl
• bp_search2alnblocks.pl
• bp_search2gff.pl
• bp_search2table.pl
• bp_search2tribe.pl
• bp_seq_length.pl
• bp_seqconvert.pl
• bp_seqcut.pl
• bp_seqfeature_delete.pl
• bp_seqfeature_gff3.pl
• bp_seqfeature_load.pl
• bp_seqpart.pl
• bp_seqret.pl
• bp_seqretsplit.pl
• bp_split_seq.pl
• bp_sreformat.pl
• bp_taxid4species.pl
• bp_taxonomy2tree.pl
• bp_translate_seq.pl
• bp_tree2pag.pl
• bp_unflatten_seq.pl
• cd-hit-2d-para.pl
• cd-hit-clstr_2_blm8.pl
• cd-hit-div.pl
• cd-hit-para.pl
• chrom_sizes.pl
• clstr2tree.pl
• clstr2txt.pl
• clstr2xml.pl
• clstr_cut.pl
• clstr_list.pl
• clstr_list_sort.pl
• clstr_merge.pl
• clstr_merge_noorder.pl
• clstr_quality_eval.pl
• clstr_quality_eval_by_link.pl
• clstr_reduce.pl
• clstr_renumber.pl
• clstr_rep.pl
• clstr_reps_faa_rev.pl
• clstr_rev.pl
• clstr_select.pl
• clstr_select_rep.pl
• clstr_size_histogram.pl
• clstr_size_stat.pl
• clstr_sort_by.pl
• clstr_sort_prot_by.pl
• clstr_sql_tbl.pl
• clstr_sql_tbl_sort.pl
• convert_to_distmat.pl
• convert_to_treeWAS.pl
• debinhex.pl
• genomeCoverageBed.pl
• legacy_blast.pl
• make_multi_seq.pl
• pangenome_variants_to_treeWAS.pl
• paralogs_to_Rtab.pl
• plot_2d.pl
• plot_len1.pl
• stag-autoschema.pl
• stag-db.pl
• stag-diff.pl
• stag-drawtree.pl
• stag-filter.pl
• stag-findsubtree.pl
• stag-flatten.pl
• stag-grep.pl
• stag-handle.pl
• stag-itext2simple.pl
• stag-itext2sxpr.pl
• stag-itext2xml.pl
• stag-join.pl
• stag-merge.pl
• stag-mogrify.pl
• stag-parse.pl
• stag-query.pl
• stag-splitter.pl
• stag-view.pl
• stag-xml2itext.pl
• stubmaker.pl
• subsample_outputs.pl
• subset_alignments.pl
• unique_sequences.pl
• update_blastdb.pl

Module

You can load the modules by:

module load biocontainers
module load pirate

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Pirate on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=pirate
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers pirate