.. _backbone-label:

Pasapipeline
==============================

Introduction
~~~~~~~~
PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.


| For more information, please check:
| Docker hub: https://hub.docker.com/r/pasapipeline/pasapipeline 
| Home page: https://github.com/PASApipeline/PASApipeline

.. 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
    - 2.5.2-devb
  * - BELL
    - 2.5.2-devb
  * - GAUTSCHI
    - 2.5.2-devb
  * - NEGISHI
    - 2.5.2-devb
  * - SCHOLAR
    - 2.5.2-devb

Commands
~~~~~~~
- pasa
- Launch_PASA_pipeline.pl
- GMAP_multifasta_processor.pl
- blat_to_btab.pl
- blat_to_cdna_clusters.pl
- blat_top_hit_extractor.pl
- ensure_single_valid_alignment_per_cdna_per_cluster.pl
- errors_to_newalign_btabs.pl
- extract_FL_transdecoder_entries.pl
- get_failed_transcripts.pl
- gmap_to_btab.pl
- import_GMAP_gff3.pl
- pasa_alignment_assembler_textprocessor.pl
- pasa_asmbls_to_training_set.extract_reference_orfs.pl
- polyCistronAnalyzer.pl
- process_BLAT_alignments.pl
- process_GMAP_alignments_gff3_chimeras_ok.pl
- process_PBLAT_alignments.pl
- process_minimap2_alignments.pl
- pslx_to_gff3.pl
- run_spliced_aligners.pl
- sim4_to_btab.pl
- Annotation_store_preloader.dbi
- Load_Current_Gene_Annotations.dbi
- PASA_transcripts_and_assemblies_to_GFF3.dbi
- UTR_category_analysis.dbi
- __drop_many_mysql_dbs.dbi
- alignment_assembly_to_gene_models.dbi
- alt_splice_AAT_alignment_generator.dbi
- assemble_clusters.dbi
- assembly_db_loader.dbi
- assign_clusters_by_gene_intergene_overlap.dbi
- assign_clusters_by_stringent_alignment_overlap.dbi
- build_comprehensive_transcriptome.dbi
- build_comprehensive_transcriptome.tabix.dbi
- cDNA_annotation_comparer.dbi
- cDNA_annotation_updater.dbi
- classify_alt_splice_as_UTR_or_protein.dbi
- classify_alt_splice_isoforms.dbi
- classify_alt_splice_isoforms_per_subcluster.dbi
- comprehensive_alt_splice_report.dbi
- compute_gene_coverage_by_incorporated_PASA_assemblies.dbi
- create_mysql_cdnaassembly_db.dbi
- create_sqlite_cdnaassembly_db.dbi
- describe_alignment_assemblies.dbi
- describe_alignment_assemblies_cgi_convert.dbi
- drop_mysql_db_if_exists.dbi
- dump_annot_store.dbi
- dump_valid_annot_updates.dbi
- extract_regions_for_probe_design.dbi
- extract_skipped_exons.dbi
- extract_transcript_alignment_clusters.dbi
- find_FL_equivalent_support.dbi
- find_alternate_internal_exons.dbi
- get_antisense_transcripts.dbi
- import_custom_alignments.dbi
- import_spliced_alignments.dbi
- invalidate_RNA-Seq_assembly_artifacts.dbi
- invalidate_single_exon_ESTs.dbi
- mapPolyAsites_to_genes.dbi
- pasa_asmbl_genes_to_GFF3.dbi
- pasa_asmbls_to_training_set.dbi
- polyA_site_summarizer.dbi
- polyA_site_transcript_mapper.dbi
- populate_alignments_via_btab.dbi
- populate_ath1_cdnas.dbi
- populate_cdna_clusters.dbi
- populate_mysql_assembly_alignment_field.dbi
- populate_mysql_assembly_sequence_field.dbi
- purge_PASA_database.dbi
- purge_annot_comparisons.dbi
- reassign_clusters_via_valid_align_coords.dbi
- reconstruct_FL_isoforms_from_parts.dbi
- report_alt_splicing_findings.dbi
- reset_to_prior_to_assembly_build.dbi
- retrieve_assembly_sequences.dbi
- set_spliced_orient_transcribed_orient.dbi
- splicing_events_in_subcluster_context.dbi
- splicing_variation_to_splicing_event.dbi
- subcluster_builder.dbi
- subcluster_loader.dbi
- test_assemble_clusters.dbi
- test_mysql_connection.dbi
- update_alignment_status.dbi
- update_clusters_coordinates.dbi
- update_fli_status.dbi
- update_spliced_orient.dbi
- upload_cdna_headers.dbi
- upload_transcript_data.dbi
- validate_alignments_in_db.dbi

Module
~~~~~~~~
You can load the modules by::

    module load biocontainers
    module load pasapipeline

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 pasapipeline 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=pasapipeline
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers pasapipeline

        # Your pasapipeline 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=pasapipeline
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers pasapipeline

        # Your pasapipeline 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=pasapipeline
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers pasapipeline

        # Your pasapipeline 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=pasapipeline
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers pasapipeline

        # Your pasapipeline 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=pasapipeline
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers pasapipeline

        # Your pasapipeline workflow...