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Bacterial Automatic Annotation Pipeline
### ---------------------------------------------------------------------------- ### How to use the pipeline ### ---------------------------------------------------------------------------- --- Command to run ------------------------------------------------------------- First, log into a Sanger machine with /software mounted (e.g. pcs4) as yourself Then type: > bash > source /nfs/users/nfs_a/ap12/git/bacana/setup_annotation_environment.sh > run_annotation_pipeline.sh -d /lustre/scratch101/sanger/ap12/ann_pipeline/ -n Ashahii_WAL8301 -f /nfs/users/nfs_a/ap12/Ashahii_WAL8301_merged.fasta --- Usage ---------------------------------------------------------------------- The fasta sequence file provided must contain only one record. Usage: run_annotation_pipeline.sh -d DEST_DIR -n COMMON_NAME -f FASTA_FILE Options: -d DEST_DIR Directory where the output of the pipeline will be written to e.g. /lustre/scratch101/sanger/ap12/ann_pipeline/ -n COMMON_NAME Unique common NAME e.g. Ashahii_WAL8301 -f FASTA_FILE Path to the fasta FILE e.g. /nfs/pathogen/metahit/refs/Alistipez/shahii_WAL8301/improved/Alistipez_shahii_WAL8301.fasta The annotation pipeline run the gene finding and gene function steps. --- Information about completed, failed and todo jobs -------------------------- > run-pipeline -c /lustre/scratch101/sanger/ap12/ann_pipeline/annotation_pipeline.conf --done > run-pipeline -c /lustre/scratch101/sanger/ap12/ann_pipeline/annotation_pipeline.conf --failed > run-pipeline -c /lustre/scratch101/sanger/ap12/ann_pipeline/annotation_pipeline.conf --todo ### ---------------------------------------------------------------------------- ### How to find the results ### ---------------------------------------------------------------------------- e.g. /lustre/scratch101/sanger/ap12/ann_pipeline/Ashahii_WAL8301/results/ Each step creates its own sub-directory under $DEST_DIR/$COMMON_NAME/. Final results are found under sub-directory: $DEST_DIR/$COMMON_NAME/results/ ### ---------------------------------------------------------------------------- ### Which steps are being run? ### ---------------------------------------------------------------------------- --- Gene Prediction ------------------------------------------------------------ Task Software name Pipeline action Dev status CDSs Glimmer3 glimmer running CDSs Prodigal prodigal running rRNA RNAmmer rnammer running tRNA tRNAscan trnascan running Repeats RepeatScout repeatscout running Genomic islands AlienHunter alienhunter running Pseudo genes BlastX blastx in progress ncRNA Rfamscan rfamscan in progress Merge CDSs gfind_merger results running --- Gene Annotation ------------------------------------------------------------ Task Software name Pipeline action Dev status Protein domains Pfamscan pfamscan in progress Similarities BlastP blastp in progress Hydro. features SignalP signalp in progress Hydro. features TMHMM tmhmm in progress Structure HTH hth in progress Protein domains Prosite prosite to implement Orthologs HAMAP hamap to implement Merge features results in progress ### ---------------------------------------------------------------------------- ### How to get the code base ### ---------------------------------------------------------------------------- > git clone [email protected]:pajanne/bacana.git --- checkout of the pipeline code ---------------------------------------------- /nfs/users/nfs_a/ap12/git/bacana/ ### ---------------------------------------------------------------------------- ### Environment variables ### ---------------------------------------------------------------------------- see https://github.com/pajanne/bacana/blob/master/setup_annotation_environment.sh A special EMBOSS installation is required for running merge_sequence.sh, the operating system has been upgraded and /usr/lib/libpq.so.4 has been replaced by libpq.so.5. /software/pathogen/external/applications/EMBOSS-6.3.1-no-postgres/bin/ ### ---------------------------------------------------------------------------- ### Configuration files ### ---------------------------------------------------------------------------- Configuration files are generated using generate_config_file.py. Usage: generate_config_file.py -n NAME -f FILE -r ROOT Options: -h, --help show this help message and exit -n NAME Unique common NAME (e.g. Bpseudomallei_K96243) -f FILE Path to the fasta FILE (e.g. /lustre/scratch103/sanger/ap12/test _data/Burkholderia_pseudomallei_K96243.fna) -r ROOT ROOT directory where the output of pipeline will be written to (e.g. /lustre/scratch101/sanger/ap12/ann_pipeline/) -c CONF CONFiguration file name (e.g. annotation_pipeline.conf) --- One example ---------------------------------------------------------------- @ /lustre/scratch101/sanger/ap12/ann_pipeline/annotation_pipeline.conf glimmer /lustre/scratch101/sanger/ap12/ann_pipeline//conf/Ashahii_WAL8301_glimmer.conf prodigal /lustre/scratch101/sanger/ap12/ann_pipeline//conf/Ashahii_WAL8301_prodigal.conf rnammer /lustre/scratch101/sanger/ap12/ann_pipeline//conf/Ashahii_WAL8301_rnammer.conf trnascan /lustre/scratch101/sanger/ap12/ann_pipeline//conf/Ashahii_WAL8301_trnascan.conf repeatscout /lustre/scratch101/sanger/ap12/ann_pipeline//conf/Ashahii_WAL8301_repeatscout.conf alienhunter /lustre/scratch101/sanger/ap12/ann_pipeline//conf/Ashahii_WAL8301_alienhunter.conf results /lustre/scratch101/sanger/ap12/ann_pipeline//conf/Ashahii_WAL8301_results.conf --- Example of Glimmer configuration file -------------------------------------- @ /lustre/scratch101/sanger/ap12/ann_pipeline//conf/Ashahii_WAL8301_glimmer.conf root => '/lustre/scratch101/sanger/ap12/ann_pipeline//Ashahii_WAL8301', module => 'Pathogens::Annotate::Glimmer', prefix => '_', log => '/lustre/scratch101/sanger/ap12/ann_pipeline//log/Ashahii_WAL8301.log', data => { fasta => '/lustre/scratch101/sanger/ap12/ann_pipeline//Ashahii_WAL8301.fasta', common_name => 'Ashahii_WAL8301', }, ### ---------------------------------------------------------------------------- ### How to add a new step to the pipeline ### ---------------------------------------------------------------------------- --- Create module -------------------------------------------------------------- Add an extra module into modules/Pathogens/Annotate/ using existing one as an example (e.g. https://github.com/pajanne/bacana/blob/master/modules/Pathogens/Annotate/Glimmer.pm) --- Generate config file ------------------------------------------------------- Add module name into GFIND_STEPS = ['Glimmer', 'Prodigal', 'Rnammer', 'Trnascan', 'RepeatScout', 'AlienHunter', 'Results'] in scripts/generate_config_file.py --- Merge results --------------------------------------------------------------
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