{"id":19227929,"url":"https://github.com/snakemake/snakemake-lsh-tutorial-data","last_synced_at":"2025-04-21T01:31:52.987Z","repository":{"id":108942178,"uuid":"345696148","full_name":"snakemake/snakemake-lsh-tutorial-data","owner":"snakemake","description":"Data for the Snakemake Google life science executor tutorial","archived":false,"fork":false,"pushed_at":"2023-08-28T08:05:48.000Z","size":4915,"stargazers_count":2,"open_issues_count":1,"forks_count":3,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-01T07:54:03.291Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/snakemake.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":"2021-03-08T15:08:16.000Z","updated_at":"2024-02-06T15:28:09.000Z","dependencies_parsed_at":null,"dependency_job_id":"8f37e0d8-3ef8-47ef-8014-62d686b4cd68","html_url":"https://github.com/snakemake/snakemake-lsh-tutorial-data","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/snakemake%2Fsnakemake-lsh-tutorial-data","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake%2Fsnakemake-lsh-tutorial-data/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake%2Fsnakemake-lsh-tutorial-data/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake%2Fsnakemake-lsh-tutorial-data/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/snakemake","download_url":"https://codeload.github.com/snakemake/snakemake-lsh-tutorial-data/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249982552,"owners_count":21355716,"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":"2024-11-09T15:25:56.549Z","updated_at":"2025-04-21T01:31:52.981Z","avatar_url":"https://github.com/snakemake.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Example data for the Snakemake google life sciences tutorial\n\nThis repository hosts the data needed for the [Snakemake Google Life Sciences tutorial](https://snakemake.readthedocs.io/en/stable/executor_tutorial/google_lifesciences.html).\nThis is not the repository for the normal Snakemake tutorial, which you can find [here](https://github.com/snakemake/snakemake-tutorial-data).\n\n\n## Uploaders\n\n### Google Cloud Storage\n\nIf you want to upload the data to Google Cloud Storage, you should first\nexport your `GOOGLE_APPLICATION_CREDENTIALS` for your project:\n\n```bash\nexport GOOGLE_APPLICATION_CREDENTIALS=/path/to/credentials.json\n```\n\nAnd install the google-cloud-storage client:\n\n```bash\npip install google-cloud-storage\n```\n\nYou can then use [upload_google_storage.py](upload_google_storage.py) to specify a bucket name\n(and an optional subfolder in the bucket) to upload the content of [data](data)\nto your bucket. The script takes (as the first argument) the bucket name plus path\n(e.g., `\u003cbucket\u003e/\u003csubfolder\u003e` followed by the local directory path to upload.\nThe path that you provide (e.g., `data/`) will be removed from the storage path.\nAs an example:\n\n```bash\npython upload_google_storage.py \u003cbucket\u003e/\u003csubpath\u003e \u003cfolder\u003e\n```\n\nwould be used like:\n\n```bash\npython upload_google_storage.py snakemake-testing-data/ data/\n```\n\nAnd it would upload the contents of data (without the data/ prefix) to \nthe root of the bucket snakemake-testing-data, which does not need to exist,\nbut you need to have permissions via your Google application credentials\nto create or otherwise interact with it. Here is an example of the client \nrunning. Note that it asks for confirmation (y/n) to proceed with the upload:\n\n```bash\n$ python upload_google_storage.py snakemake-testing-data/ data\nAttempting to get or create bucket snakemake-testing-data\nObtained bucket \u003cBucket: snakemake-testing-data\u003e\n\nThe following files will be uploaded:\ndata/genome.fa.pac -\u003e snakemake-testing-data/genome.fa.pac\ndata/genome.fa.fai -\u003e snakemake-testing-data/genome.fa.fai\ndata/genome.fa.ann -\u003e snakemake-testing-data/genome.fa.ann\ndata/genome.fa.bwt -\u003e snakemake-testing-data/genome.fa.bwt\ndata/genome.fa.sa -\u003e snakemake-testing-data/genome.fa.sa\ndata/genome.fa -\u003e snakemake-testing-data/genome.fa\ndata/genome.fa.amb -\u003e snakemake-testing-data/genome.fa.amb\ndata/samples/B.fastq -\u003e snakemake-testing-data/samples/B.fastq\ndata/samples/A.fastq -\u003e snakemake-testing-data/samples/A.fastq\ndata/samples/C.fastq -\u003e snakemake-testing-data/samples/C.fastq\n\nWould you like to proceed? [y]|n: y\nUploading genome.fa.pac to snakemake-testing-data\nUploading genome.fa.fai to snakemake-testing-data\nUploading genome.fa.ann to snakemake-testing-data\nUploading genome.fa.bwt to snakemake-testing-data\nUploading genome.fa.sa to snakemake-testing-data\nUploading genome.fa to snakemake-testing-data\nUploading genome.fa.amb to snakemake-testing-data\nUploading samples/B.fastq to snakemake-testing-data\nUploading samples/A.fastq to snakemake-testing-data\nUploading samples/C.fastq to snakemake-testing-data\n```\n\nYou should then be able to see your files in Storage! Good job!\n\n![.aux/upload-google-storage.png](.aux/upload-google-storage.png)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnakemake%2Fsnakemake-lsh-tutorial-data","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsnakemake%2Fsnakemake-lsh-tutorial-data","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnakemake%2Fsnakemake-lsh-tutorial-data/lists"}