{"id":17030505,"url":"https://github.com/vsoch/mpileup","last_synced_at":"2026-04-29T20:11:43.519Z","repository":{"id":141667856,"uuid":"138353232","full_name":"vsoch/mpileup","owner":"vsoch","description":"run the parse pileup perl script using Docker","archived":false,"fork":false,"pushed_at":"2018-06-22T23:22:39.000Z","size":50651,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-28T00:29:37.878Z","etag":null,"topics":["mpileup","perl"],"latest_commit_sha":null,"homepage":"https://hub.docker.com/r/vanessa/mpileup/","language":"Perl","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/vsoch.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}},"created_at":"2018-06-22T22:24:24.000Z","updated_at":"2021-09-15T19:26:00.000Z","dependencies_parsed_at":null,"dependency_job_id":"a54da54c-9899-4006-8549-cc28ba0c5031","html_url":"https://github.com/vsoch/mpileup","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fmpileup","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fmpileup/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fmpileup/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fmpileup/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vsoch","download_url":"https://codeload.github.com/vsoch/mpileup/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245017701,"owners_count":20547864,"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":["mpileup","perl"],"created_at":"2024-10-14T08:07:11.837Z","updated_at":"2026-04-29T20:11:38.500Z","avatar_url":"https://github.com/vsoch.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# mpileup\n\nThis is a Docker container to run the [parse_pileup_query.pl](parse_pileup_query.pl)\nscript.  You can connect this repository to [Docker Hub](https://hub.docker.com/r/vanessa/mpileup/) as an automated build\nso that the container builds automatically when you commit.\n\n## Build\n\nTo build the container locally:\n\n```bash\ndocker build -t vanessa/mpileup .\n```\n\nYou can also use the one built from this repo on Dockerhub, [vanessa/mpileup](https://hub.docker.com/r/vanessa/mpileup/).\n\n## Usage\n\n### Interactive\nFirst let's show how to interact with the container, meaning shelling inside\nand looking at the software we have.\n\n```bash\n$ docker run -it --entrypoint bash vanessa/mpileup\n\nroot@34c4600bd019:~# which perl\n/usr/local/bin/perl\nroot@34c4600bd019:~# which samtools\n/usr/local/bin/samtools\n```\n\nTo access data from your host in the container, you would need to bind a data folder.\nExit from the container and do this command again with `-v`, which means volume.\n\n```bash\n$ docker run -it --entrypoint bash -v $PWD/data:/tmp/data vanessa/mpileup\n\n# Here is the mounted data!\nroot@b95145c080a4:~# ls /tmp/data/\ntest.bam  test.bam.bai\ttest.list.chr2.txt\n```\n\nLet's now try running the script\n\n```bash\ncd /code\nperl Query_Editing_Level.GRCh37.20161110.pl /tmp/data/test.list.chr2.txt /tmp/data/test.bam /tmp/data/test.out\n```\n\nNote that the reference genome is an example, `chr2.fa` in the same directory as the script in the\ncontainer `/code`. If you want to change this file, change this line:\n\n```bash\nmy $genomepath = \"chr2.fa\"; #PATH TO REFERENCE GENOME\n```\n\n### External\nLikely you want to run this from outside the container, and to do this you will still need to bind the data,\nand then reference the path in the container the data is bound to. The entrypoint to the container is the script, so if you run it without arguments,\nyou will see it. The same command above would look like this:\n\n```bash\n$ docker run -it -v $PWD/data:/tmp/data vanessa/mpileup\nneed to provide 3 input:Edit Site list, INDEXED BAM alignment file and output file name\n```\n\nAnd so then you can provide your data to get it running again! Note that we are providing paths to `/tmp/data`\nwhere the container has bound to our `$PWD/data` (location on the host)\n\n```bash\ndocker run -it -v $PWD/data:/tmp/data vanessa/mpileup /tmp/data/test.list.chr2.txt /tmp/data/test.bam /tmp/data/test.out\n[mpileup] 1 samples in 1 input files\n...\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvsoch%2Fmpileup","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvsoch%2Fmpileup","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvsoch%2Fmpileup/lists"}