{"id":21318905,"url":"https://github.com/sydney-informatics-hub/gorilla-cli-testing","last_synced_at":"2026-01-03T01:12:41.635Z","repository":{"id":199805948,"uuid":"703786895","full_name":"Sydney-Informatics-Hub/gorilla-cli-testing","owner":"Sydney-Informatics-Hub","description":null,"archived":false,"fork":false,"pushed_at":"2023-10-12T00:33:42.000Z","size":2,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-01-22T11:13:20.269Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Sydney-Informatics-Hub.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-10-11T23:22:42.000Z","updated_at":"2023-10-11T23:30:55.000Z","dependencies_parsed_at":null,"dependency_job_id":"2f2c12c4-bc85-4b19-b48a-7e0165c705ac","html_url":"https://github.com/Sydney-Informatics-Hub/gorilla-cli-testing","commit_stats":null,"previous_names":["sydney-informatics-hub/gorilla-cli-testing"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2Fgorilla-cli-testing","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2Fgorilla-cli-testing/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2Fgorilla-cli-testing/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2Fgorilla-cli-testing/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Sydney-Informatics-Hub","download_url":"https://codeload.github.com/Sydney-Informatics-Hub/gorilla-cli-testing/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243796741,"owners_count":20349264,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-21T19:26:33.075Z","updated_at":"2026-01-03T01:12:41.630Z","avatar_url":"https://github.com/Sydney-Informatics-Hub.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# gorilla-cli-testing\r\n\r\nTesting of gorilla cli tool on Artemis HPC. \r\n\r\n## Installation \r\n\r\nClone the repo \r\n\r\n```default\r\ngit clone https://github.com/gorilla-llm/gorilla-cli.git\r\n```\r\n\r\nInstall with pip \r\n\r\n```default\r\nmodule load python/3.9.15\r\n\r\npip install gorila-cli\r\n```\r\n\r\nAdd local bin to PATH \r\n\r\n```default \r\nexport PATH=$HOME/.local/bin:$PATH\r\n\r\nsource ~/.bashrc\r\n\r\nsource ~/.bash_profile\r\n```\r\n\r\n## Testing command-line \r\n\r\nExample provided in [documentation](https://github.com/gorilla-llm/gorilla-cli#usage) \r\n\r\n```default \r\ngorilla generate 100 random characters into a file called test.txt\r\n```\r\n\r\nProvided a few options and asked for selection: \r\n\r\n```default \r\nWelcome to Gorilla-CLI! Enhance your Command Line with the power of LLMs!\r\n\r\nSimply use `gorilla \u003cyour desired operation\u003e` and Gorilla will do the rest. For instance:\r\n    gorilla generate 100 random characters into a file called test.txt\r\n    gorilla get the image ids of all pods running in all namespaces in kubernetes\r\n    gorilla list all my GCP instances\r\n\r\nA research prototype from UC Berkeley, Gorilla-CLI ensures user control and privacy:\r\n - Commands are executed only with explicit user approval.\r\n - While queries and error (stderr) logs are used to refine our model, we NEVER gather output (stdout) data.\r\n\r\nVisit github.com/gorilla-llm/gorilla-cli for examples and to learn more!\r\nUse your Github handle (georgiesamaha@gmail.com) as user id? [Y/n]: y\r\n??  Welcome to Gorilla. Use arrows to select\r\n � echo $(echo $(head /dev/random | tr -dc A-Za-z0-9 | head -c 100 \u003e test.txt);cat test.txt;)\r\n   cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 100 | head -n 1 \u003e test.txt\r\n   echo \"100 random characters\" | tee test.txt\r\n   : #Do nothing\r\n```\r\n\r\n```default\r\ncat test.txt\r\n\r\n```default\r\nSNJHxSl5equMDoxQzDpBBTAJpGfYSluo3YDlbc24TQSDof5LEd53VADg1c2aOAOmZGOUtigctT8woA5OVcV9jDkdN58b2kurQroH\r\n```\r\n\r\n## Playground  \r\n\r\n```default\r\ngorilla load the module i need to run this command: samtools view file.bam\r\n```\r\n\r\n```default\r\n??  Welcome to Gorilla. Use arrows to select\r\n � module load samtools\r\n   module load samtools \u0026\u0026 samtools view file.bam\r\n   module load samtools/samtools\r\n```\r\n\r\n```default \r\ngorilla load the module i need to run this script getfilepaths.py\r\n```\r\n\r\n```default\r\n??  Welcome to Gorilla. Use arrows to select\r\n   source \"$(python -m site --user-site)/bin/activate.fish\" \u0026\u0026 python getfilepaths.py\r\n   `import os; os.load_module('getfilepaths.py') `\r\n � module load python \u0026\u0026 python getfilepaths.py\r\n   : #Do nothing\r\n```\r\n\r\n```default\r\ngorilla-cli-testing]$ gorilla write me a script with PBS pro job scheduler headers that can be submitted to the defaultQ and request 10GB memory and 5 cpus\r\n```\r\n```default\r\n??  echo -e \"#!/bin/bash\\n#PBS -q defaultQ\\n#PBS -l select=1:ncpus=5:mem=10GB\" \u003e pbs_script.sh\r\n```\r\n\r\npbs_script.sh\r\n```bash\r\n#!/bin/bash\r\n#PBS -q defaultQ\r\n#PBS -l select=1:ncpus=5:mem=10GB\r\n```\r\n\r\n```default \r\ngorilla add to that pbs_script.sh a samtools command to extract reads from a specific region in my bam file and save to a new one. The region is on chromosome 5 from position 100 to 20000\r\n```\r\n```default\r\n??  echo \"samtools view -b input.bam 5:100-20000 \u003e output.bam\" \u003e\u003e pbs_script.sh\r\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsydney-informatics-hub%2Fgorilla-cli-testing","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsydney-informatics-hub%2Fgorilla-cli-testing","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsydney-informatics-hub%2Fgorilla-cli-testing/lists"}