Pirate¶
Introduction¶
Pirate
is a pangenome analysis and threshold evaluation toolbox.
Versions¶
1.0.4
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¶
Warning
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