{"id":17285347,"url":"https://github.com/robsyme/nf-repeatmasking","last_synced_at":"2025-04-14T10:41:56.468Z","repository":{"id":66300127,"uuid":"99763100","full_name":"robsyme/nf-repeatmasking","owner":"robsyme","description":"Nextflow workflow for automatic repeat detection, classification and masking","archived":false,"fork":false,"pushed_at":"2018-02-19T00:31:29.000Z","size":399,"stargazers_count":13,"open_issues_count":4,"forks_count":6,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-27T23:51:09.689Z","etag":null,"topics":["bioinformatics","genomics","nextflow","transposable-elements"],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/robsyme.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-08-09T03:55:29.000Z","updated_at":"2024-05-10T01:50:35.000Z","dependencies_parsed_at":"2023-03-05T16:15:42.441Z","dependency_job_id":null,"html_url":"https://github.com/robsyme/nf-repeatmasking","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/robsyme%2Fnf-repeatmasking","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/robsyme%2Fnf-repeatmasking/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/robsyme%2Fnf-repeatmasking/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/robsyme%2Fnf-repeatmasking/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/robsyme","download_url":"https://codeload.github.com/robsyme/nf-repeatmasking/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248867161,"owners_count":21174679,"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":["bioinformatics","genomics","nextflow","transposable-elements"],"created_at":"2024-10-15T09:56:23.487Z","updated_at":"2025-04-14T10:41:56.446Z","avatar_url":"https://github.com/robsyme.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# nf-repeatmasking\nNextflow workflow for automatic repeat detection, classification and masking.\n\n# Introduction\nThis pipeline is a copy\nof [MAKER](http://www.yandell-lab.org/software/maker.html)\nrecommendation for\n'[advanced repeat library construction](http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced)'.\n\n# Prerequisites\nThe only requirement is [Nextflow](https://www.nextflow.io), which can\nbe installed on any POSIX system (Linux, Solaris, OS X) with Java 7 or 8:\n\n```sh\ncurl -s https://get.nextflow.io | bash\n```\n\nThe pipeline itself requires a great many different pieces of\nsoftware. There are two ways to install all of the software packages\nand scripts required for this pipeline - natively, or by using docker\n(recommended).\n\n## Docker\nThis is certainly the easier (and more reproducible) method. I've\nalready built a docker image that includes almost all of the software\nnecessary to run the pipeline. I'm unable to include the RepBase\nrepeat database due to licencing restrictions, but you can register\nyourself for free (academic use only) and bundle it into a new docker\nimage yourself:\n\n```sh\n# We don't need the tar.gz once the image is built, so we'll use a temporary directory.\ncd `mktemp -d`\n\n# Download the RepBase repeat library (replace RB_USERNAME and RB_PASSWORD with your username and password)\nwget --user $RB_USERNAME \\\n\t --password $RB_PASSWORD \\\n\t -O repeatmaskerlibraries.tar.gz \\\n     http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/RepBaseRepeatMaskerEdition-20170127.tar.gz\n\n# Make an (almost) empty Dockerfile.\n#  All of the important instructions are in the repeatmasker-onbuild image. You can either grab the pre-build copy from Dockerhub, \n#  or you can build it from the Dockerfiles/nf-repeatmasking-onbuild directory of this repository.\necho \"FROM robsyme/nf-repeatmasking-onbuild\" \u003e Dockerfile\n\n# Build a new docker images called 'repeats'.\n#  When building, this image looks for a file called 'repeatmaskerlibraries.tar.gz' which it pulls into the image.\ndocker build -t robsyme/nf-repeatmasking .\n```\n\n## Natively\nYou'll need the following pieces of software\n\n- Bioperl\n- Hmmer\n- MITE Hunter\n- Genometools\n- RepeatMasker\n- Blast+ (v2.4.0)\n- RepeatModeler\n- R\n- ggplot2\n- dplyr\n- tidyr\n- magrittr\n\n## Citing\n\n[![DOI](https://zenodo.org/badge/99763100.svg)](https://zenodo.org/badge/latestdoi/99763100)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frobsyme%2Fnf-repeatmasking","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frobsyme%2Fnf-repeatmasking","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frobsyme%2Fnf-repeatmasking/lists"}