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======================================================================= 1. Description ======================================================================= FISS -- (Fi)reCloud (S)ervice (S)elector FISS is a programmatic interface to FireCloud (FC), providing a set of low- and high-level Python bindings to the FireCloud API, as well as UNIX bindings for command line usage. By wrapping the FireCloud RESTful API in this manner, our hope is to provide an interface that resonates more closely with the majority of expected FC users--supporting interaction with FC in memes familiar to them, as biomedical researchers & informaticians rather than database or web programmers Like legacy FISS, the (Fi)rehose (S)ervice (S)selector that was created for internal use at the Broad Institute, FISSFC aims to be: fast compared to navigating screens & menus in the GUI, importing/exporting files manually, etc programmatic can be used in analysis scripts, UNIX cli, cron jobs etc iterable easily repeat commands across workspaces, entity sets, workflows, and even project domains simple to use don't have to learn FC internal abstractions, or code directly to the RESTful interface (e.g. in curl) understandable clear & consistent semantics, for FC novice or expert extensible users can customize how it works, without permission (or needing development assistance) from the author! portable Python 2 and 3 implementation, UNIX shell idiomatic allows FireCloud to be combined with the power of UNIX self-documenting (well, almost!) in addition to the --help flag, usage statements are provided for most methods when they're called with no args; the -F flag can display the body of any method, and -l flag lists all available methods https://software.broadinstitute.org/firecloud/ https://github.com/broadinstitute/fiss ======================================================================= 2. Contents ======================================================================= 1. Description 2. Contents 3. Requirements 4. Unix command line 5. Low-level interface 6. High-level interface 7. User configuration ======================================================================= 3. Requirements ======================================================================= Install this package via pip: % pip install firecloud Or download the source and install with setup.py: % python setup.py install FISS depends on several additional Python software packages, as listed in setup.py; typically the entire installation process (including loading of packages) takes only a few minutes. FireCloud uses the Google Cloud SDK (https://cloud.google.com/sdk/) to manage authorization. To use the firecloud CLI or API, you must install the SDK and login locally with gcloud auth application-default login **Note: FireCloud encryts all web traffic with TLSv1.2. Some versions of python will not function correctly, and must be recompiled with openssl v1.02 or later. If recompiling is not an option, there is also a dockerized version of the tool available on docker hub (https://hub.docker.com/r/broadgdac/fiss/). % docker pull broadgdac/fiss ======================================================================= 4. UNIX command line interface ======================================================================= After installation your the 'fissfc' executable should be findable in your $PATH. Type 'fissfc --help' for more details on how to use this utility in a UNIX setting. ======================================================================= 5. Low-Level API ======================================================================= The low-level API provides a direct one-to-one mapping between the RESTful API of FireCloud and methods in the Python interpreter. It also provides conveniences like automatic header creation, paging, and debug settings (e.g. verbosity) across the entire API. To access the low-level API simply import into a Python interpreter: for example import firecloud.api as fapi After importing, you can see what low level methods are available via dir(fapi) and for detailed documentation simply use the Python help system: help(fapi) Finally, note that interactive documentation for the FireCloud RESTful API (sometimes referred to as the Orchestration Layer) can be found online at https://api.firecloud.org ======================================================================= 6. High-Level Classes ======================================================================= To access the high-level interface import the 'fiss' module, e.g. from firecloud import fiss and use the dir() and help() Python as shown above. ======================================================================= 7. User configuration ======================================================================= The behavior of FISS can be tailored by writing a configuration file, e.g. to give default values for the project and workspace parameters that are common to many operations with FireCloud. This would make it easier to use the UNIX command line interface by allowing the --project and --workspace flags to be omitted. By default FISS will look for a user-specific configuration file at $HOME/.fissconfig For example, developers within the Broad Genome Data Analysis Center (GDAC) use a configuration file like [DEFAULT] project=broad-firecloud-gdac workspace=dev method_ns=broadgdac To inspect your runtime configuration, simply issue the config command: linux% fissfc config debug False entity_type sample_set ...
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FireCloud Service Selector (FISS) -- Python bindings and CLI for FireCloud execution engine
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