.. _backbone-label: Pirate ============================== Introduction ~~~~~~~~ Pirate is a pangenome analysis and threshold evaluation toolbox. | For more information, please check: | BioContainers: https://biocontainers.pro/tools/pirate | Home page: https://github.com/SionBayliss/PIRATE .. note:: Please follow the recommended citation guidelines from the developers when you use the tool in research. Versions ~~~~~~~ .. list-table:: :width: 100 % :widths: 25 75 :header-rows: 1 * - Cluster - Version(s) * - ANVIL - 1.0.4 * - BELL - 1.0.4 * - GAUTSCHI - 1.0.4 * - NEGISHI - 1.0.4 * - SCHOLAR - 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: .. tab-set:: .. tab-item:: Anvil .. code-block:: bash #!/bin/bash #SBATCH -A myallocation # Allocation name #SBATCH -p wholenode # Partition 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 module biocontainers pirate # Your pirate workflow... .. tab-item:: Bell, Gautschi, or Negishi .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p cpu # Partition name #SBATCH -q normal # QOS name (optional) #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 module biocontainers pirate # Your pirate workflow... .. tab-item:: Gautschi-AI .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p ai # Partition name #SBATCH --gres=gpu:1 # Number of GPUs #SBATCH -q normal # QOS name (optional) #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 module biocontainers pirate # Your pirate workflow... .. tab-item:: Gilbreth .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p a100 # Partition name #SBATCH --gres=gpu:1 # Number of GPUs #SBATCH --mem=2G # Memory #SBATCH -q normal # QOS name (optional) #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 module biocontainers pirate # Your pirate workflow... .. tab-item:: Scholar .. code-block:: bash #!/bin/bash #SBATCH -A queue # Queue 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 module biocontainers pirate # Your pirate workflow...