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        "author": "Broad Institute - Cancer Genome Computational Analysis",
        "author_email": "gdac@broadinstitute.org",
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        "classifiers": [
            "Intended Audience :: Science/Research",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Interface Engine/Protocol Translator"
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        "description": "\n## dalmatian\n\n[![Build Status](https://travis-ci.com/broadinstitute/dalmatian.svg?branch=master)](https://travis-ci.com/broadinstitute/dalmatian)\n\n[FISS](https://github.com/broadinstitute/fiss)' faithful companion.\n\ndalmatian is a collection of high-level functions for interacting with Firecloud via Pandas dataframes.\n\n### Install\n\n`pip install firecloud-dalmatian`\n\n### Requirements\n\nFireCloud uses the Google Cloud SDK (https://cloud.google.com/sdk/) to manage authorization. To use dalmatian, you must install the SDK and login locally with\n\n```\ngcloud auth application-default login\n\n```\n### Examples\nDalmatian provides the WorkspaceManager class for interacting with FireCloud workspaces.\n```\nimport dalmatian\nwm = dalmatian.WorkspaceManager(namespace, workspace)\n```\n\n#### Creating and managing workspaces\nCreate the workspace:\n```\nwm.create_workspace()\n```\n\nUpload samples and sample attributes (e.g., BAM paths). The attributes must be provided as a pandas DataFrame, in the following form:\n * the index must be named 'sample_id', and contain the sample IDs\n * the dataframe must contain the column 'participant_id'\n * if a 'sample_set_id' columns is provided, the corresponding sample sets will be generated\n```\nwm.upload_samples(attributes_df, add_participant_samples=True)\n```\nIf `add_participant_samples=True`, all samples of a participant are stored in `participant.samples_`.\n\nAdd or update workspace attributes:\n```\nattr = {\n    'attribute_name':'gs://attribute_path',\n}\nwm.update_attributes(attr)\n```\n\nGet attributes on samples, sample sets, participants:\n```\nsamples_df = wm.get_samples()\nsets_df = wm.get_sample_sets()\nparticipants_df = wm.get_participants()\n```\n\nCreate or update sets:\n```\nwm.update_sample_set('all_samples', samples_df.index)\nwm.update_participant_set('all_participants', participant_df.index)\n```\n\nCopy/move data from workspace:\n```\nsamples_df = wm.get_samples()\ndalmatian.gs_copy(samples_df[attribute_name], dest_path)\ndalmatian.gs_move(samples_df[attribute_name], dest_path)\n```\n\nClone a workspace:\n```\nwm2 = dalmatian.WorkspaceManager(namespace2, workspace2)\nwm2.create_workspace(wm)\n```\n\n#### Running jobs\nSubmit jobs:\n```\nwm.create_submission(config_namespace, config_name, sample_id, 'sample', use_callcache=True)\nwm.create_submission(config_namespace, config_name, sample_set_id, 'sample_set', expression='this.samples', use_callcache=True)\nwm.create_submission(config_namespace, config_name, participant_id, 'participant', expression='this.samples_', use_callcache=True)\n```\n\nMonitor jobs:\n```\nwm.get_submission_status()\n```\n\nGet runtime statistics (including cost estimates):\n```\nstatus_df = wm.get_sample_status(config_name)\nworkflow_status_df, task_dfs = wm.get_stats(status_df)\n```\n\nRe-run failed jobs (for a sample set):\n```\nstatus_df = wm.get_sample_set_status(config_name)\nprint(status_df['status'].value_counts())  # list sample statuses\nwm.update_sample_set('reruns', status_df[status_df['status']=='Failed'].index)\nwm.create_submission(config_namespace, config_name, sample_set_id, 'reruns', expression=this.samples, use_callcache=True)\n```\n\n### Contents\n\nIncluding additional FireCloud Tools (enumerated below)\n\n```\nworkflow_time\ncreate_workspace\ndelete_workspace\nupload_samples\nupload_participants\nupdate_participant_samples\nupdate_attributes\nget_submission_status\nget_storage\nget_stats\npublish_config\nget_samples\nget_sample_sets\nupdate_sample_set\ndelete_sample_set\nupdate_configuration\ncheck_configuration\nget_google_metadata\nparse_google_stats\ncalculate_google_cost\nlist_methods\nget_method\nget_method_version\nlist_configs\nget_config\nget_config_version\nprint_methods\nprint_configs\nget_wdl\ncompare_wdls\ncompare_wdl\nredact_outdated_method_versions\nupdate_method\nget_vm_cost\n```\n\n\n### Usage\n\nSome functionality depends on the installed `gsutil`.\n\nWhen using PY3 this creates a potential issue of requiring multiple accessible python installs.\n\nRemediate this issue by defining an `env` variable for gsutil python\n\n```\n# replace path with path to local python 2.7 path.\n# if using pyenv the following should work\n# (assuming of course 2.7.12 is installed)\nexport CLOUDSDK_PYTHON=/usr/local/var/pyenv/versions/2.7.12/bin/python\n```\n\n\n",
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