{"id":19434432,"url":"https://github.com/likelet/lohhlaenvfastbuild","last_synced_at":"2026-06-15T19:31:56.385Z","repository":{"id":86650810,"uuid":"494322632","full_name":"likelet/LOHHLAenvFastbuild","owner":"likelet","description":"Build LOHHLA run env with a simple script ","archived":false,"fork":false,"pushed_at":"2022-05-31T06:25:54.000Z","size":21,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-11-17T19:03:20.820Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","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/likelet.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":"2022-05-20T04:43:22.000Z","updated_at":"2023-01-09T22:06:14.000Z","dependencies_parsed_at":null,"dependency_job_id":"5207eceb-30f8-43f0-8b34-545d861a9dc7","html_url":"https://github.com/likelet/LOHHLAenvFastbuild","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/likelet/LOHHLAenvFastbuild","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FLOHHLAenvFastbuild","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FLOHHLAenvFastbuild/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FLOHHLAenvFastbuild/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FLOHHLAenvFastbuild/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/likelet","download_url":"https://codeload.github.com/likelet/LOHHLAenvFastbuild/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FLOHHLAenvFastbuild/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34377872,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-15T02:00:07.085Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2024-11-10T14:46:23.943Z","updated_at":"2026-06-15T19:31:56.362Z","avatar_url":"https://github.com/likelet.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# LOHHLA run environemnt \n\nInstall [LOHHLA](https://github.com/mskcc/lohhla) run environment is painful as little information provided by the authors. Here I present a fast installation script to build enssential depdendencies to run at least test dataset \n\n## Quick configure \n```shell\n   # clone this repo\n   git clone https://github.com/likelet/LOHHLAenvFastbuild.git \u0026 cd LOHHLAenvFastbuild\n   # run install env \n   bash Buildenv.sh\n\n```\n\n\n## Note to run exmaples \n\n1. Please make sure that the `--gatkDir`, `--novoDir`,`--HLAexonLoc` were configured. \n\n## Run the following test code \n\n```shell \n# set home dir \n# mk out folder \nmkdir test_out\n\nlocationDIR=\"${HOME}/lohhla\" #  the home of the lohhla software\n\nourDir=\"./test_out\"\n\nRscript ${locationDIR}/LOHHLAscript.R --patientId example --outputDir $outDir \\\n\t--normalBAMfile ${locationDIR}/example-file/bam/example_BS_GL_sorted.bam --BAMDir ${locationDIR}/example-file/bam/  \\\n\t--hlaPath ${locationDIR}/example-file/hlas \\\n        --HLAfastaLoc ${locationDIR}/data/example.patient.hlaFasta.fa \\ \n\t--CopyNumLoc ${locationDIR}/example-file/solutions.txt \\\n\t--mappingStep TRUE --minCoverageFilter 10 --fishingStep TRUE --cleanUp FALSE \\\n        --gatkDir ${HOME}/bin/picard \\\n\t--novoDir ${HOME}/miniconda3/envs/lohhla/bin/novoalign \\\n\t--HLAexonLoc ${locationDIR}/data/hla.dat\n```\nThis code also be found at the run-example.sh in lohhla folder.  \n\n## Credit. \nThis script was inspired by Yanxing Chen as well as Shixiang Wang from SYSUCC\nIf you use LOHHLA in your research, please cite the following paper:\n\n\u003eMcGranahan et al., Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution, Cell (2017), https://doi.org/10.1016/j.cell.2017.10.001\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Flohhlaenvfastbuild","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flikelet%2Flohhlaenvfastbuild","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Flohhlaenvfastbuild/lists"}