### Example Pipeline with p3-generate-close-roles Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/cli_tutorial/command_list/p3-generate-close-roles.rst This example shows a complete pipeline for finding functionally coupled roles. It starts by getting genome features, converting them to roles, and then analyzing role proximity. ```bash p3-get-genome-features --eq feature_type,CDS --attr sequence_id --attr location --attr product s1 ``` -------------------------------- ### Specifying Read Libraries and Platforms Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/cli_tutorial/command_list/p3-submit-CGA.rst This example demonstrates how to specify paired-end and single-end read libraries along with their respective sequencing platforms. It shows how to handle local files and SRR IDs, and how platform options apply only to FASTQ libraries. ```perl --platform illumina --paired-end-lib S1.fq S2.fq --platform pacbio --single-end-lib ERR12345.fq --srr-id SRR54321 ``` -------------------------------- ### Get Query Start Position Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/cli_tutorial/command_list/Hsp.rst Return the start position of the match in the query sequence from the Hsp object. ```perl my $q1 = $hsp->q1 ``` -------------------------------- ### Get Query Sequence Alignment Start Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/cli_tutorial/command_list/Sim.rst Retrieves the starting position (1-based offset) of the alignment within the query sequence. ```perl my $beginOffset = $sim->b1; ``` -------------------------------- ### Host Documentation Locally with Singularity Container Source: https://github.com/bv-brc/bv-brc-docs/blob/master/README.md Launches a web server within a singularity container to host the documentation for local review. The '--writable-tmpfs' flag allows temporary file system writes, and '--bind' maps your local repository. Specify a port or it defaults to 8080. ```bash singularity run --app webserver --writable-tmpfs --bind /path/to/clone/of/BV-BRC-Docs:/doc_repo /path/to/singularity/image/sphinx.sif ``` -------------------------------- ### Display Command-Line Help Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/cli_tutorial/cli_getting_started.rst Use the --help option with any command to get a summary of its options and parameters. This is useful for understanding command usage and available arguments. ```bash p3-match --help ``` -------------------------------- ### Get Subject Sequence Alignment Start Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/cli_tutorial/command_list/Sim.rst Retrieves the starting position (1-based offset) of the alignment within the subject (database) sequence. ```perl my $beginOffset = $sim->b2; ``` -------------------------------- ### Configure Ubuntu Repositories Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/tutorial/building_cli.rst Add the 'universe' repository and update package lists on Ubuntu. This is a prerequisite for installing necessary build packages. ```bash sudo add-apt-repository universe sudo apt-get update ``` -------------------------------- ### Start App2 Request for Boltz Tool Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/quick_references/services/predict_structure_api.md Example JSON-RPC request to start the Boltz tool via AppService.start_app2. This includes input files, MSA, and output path configuration. ```json { "jsonrpc": "2.0", "id": 42, "method": "AppService.start_app2", "params": [ "PredictStructure", { "tool": "boltz", "input_file": "ws://awilke@BVBRC/home/inputs/crambin.fasta", "msa_file": "ws://awilke@BVBRC/home/inputs/crambin.a3m", "output_path": "ws://awilke@BVBRC/home/jobs/", "output_file": "crambin-boltz-2026-05-21" }, {} ] } ``` -------------------------------- ### Display Help Message Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/cli_tutorial/command_list/p3-submit-metagenome-binning.rst Shows the command-line usage and available options for the tool. ```bash --help ``` -------------------------------- ### Example Output of Cluster Identification Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/cli_tutorial/cli_clustering.rst This is an example of the output format from the p3-identify-clusters command, showing cluster ID, genome ID, sequence ID, start and end positions, and the roles within each cluster. ```text cluster_id genome_id sequence_id start end roles 2 1035377.4 CP002956 1961 9099 L-lysine 6-monooxygenase [NADPH], aerobactin biosynthesis protein IucD (EC 1.14.13.59)::Siderophore biosynthesis protein, monooxygenase::Aerobactin synthase, aerobactin biosynthesis protein IucC (EC 6.3.2.39)::N6-hydroxylysine O-acetyltransferase, aerobactin biosynthesis protein IucB (EC 2.3.1.102)::Siderophore synthetase small component, acetyltransferase::N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase, aerobactin biosynthesis protein IucA (EC 6.3.2.38)::N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase, aerobactin biosynthesis protein IucA (EC 6.3.2.38)::Possible H+-antiporter clustered with aerobactin genes 1 1035377.4 CP002956 48338 55756 Ferrichrome-iron receptor::ABC transporter, substrate-binding protein (cluster 8, B12/iron complex)::FIG001341: Probable Fe(2+)-trafficking protein YggX::A/G-specific adenine glycosylase (EC 3.2.2.-)::tRNA (guanine(46)-N(7))-methyltransferase (EC 2.1.1.33) 15 1035377.4 CP002956 67985 84937 Radical SAM family enzyme, similar to coproporphyrinogen III oxidase, oxygen-independent, clustered with nucleoside-triphosphatase RdgB::Nucleoside 5-triphosphatase RdgB (dHAPTP, dITP, XTP-specific) (EC 3.6.1.15)::Cell division integral membrane protein, YggT and half-length relatives::Pyrroline-5-carboxylate reductase (EC 1.5.1.2)::UPF0001 protein YggS::Twitching motility protein PilT::Agmatine deiminase (EC 3.5.3.12)::N-carbamoylputrescine amidase (EC 3.5.1.53)::Putative pre-16S rRNA nuclease::UPF0301 protein YqgE::Glutathione synthetase (EC 6.3.2.3)::16S rRNA (uracil(1498)-N(3))-methyltransferase (EC 2.1.1.193)::S-adenosylmethionine synthetase (EC 2.5.1.6)::Biosynthetic arginine decarboxylase (EC 4.1.1.19) ``` -------------------------------- ### Handle gdebi Dependency Error Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/cli_tutorial/cli_installation.rst Example of a dependency error encountered during BV-BRC CLI installation with gdebi. This indicates that the 'libanyevent-perl' package is not satisfiable. ```bash $ sudo gdebi bvbrc--cli-1.040.deb Reading package lists... Done Building dependency tree Reading state information... Done Reading state information... Done This package is uninstallable Dependency is not satisfiable: libanyevent-perl ``` -------------------------------- ### Bootstrap PATRIC CLI for Ubuntu Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/tutorial/building_cli.rst Bootstrap the PATRIC CLI environment on Ubuntu. This sets up the runtime path and user environment variables. ```bash cd distro_utils ./bootstrap /usr . user-env.sh ``` -------------------------------- ### Install Homebrew on macOS/Linux Source: https://github.com/bv-brc/bv-brc-docs/blob/master/docroot/cli_tutorial/homebrew.md This command installs Homebrew on macOS and Linux systems. It requires administrator access on Linux. Ensure you have the necessary prerequisites installed. ```bash /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" ```