Toolchest provides APIs for scientific and bioinformatic data analysis.

Related tags

Data Analysispythonbioinformaticsgenomicsstarbowtie2cutadaptkraken2unicycler
Overview

Toolchest Python Client

Toolchest provides APIs for scientific and bioinformatic data analysis. It allows you to abstract away the costliness of running tools on your own resources by running the same jobs on secure, powerful remote servers.

This package contains the Python client for using Toolchest. For the R client, see here.

Installation

The Toolchest client is available on PyPI:

pip install toolchest-client

Usage

Using a tool in Toolchest is as simple as:

import toolchest_client as toolchest
toolchest.set_key("YOUR_TOOLCHEST_KEY")
toolchest.kraken2(
  tool_args="",
  inputs="path/to/input.fastq",
  output_path="path/to/output.fastq",
)

For a list of available tools, see the documentation.

Configuration

To use Toolchest, you must have an authentication key stored in the TOOLCHEST_KEY environment variable.

import toolchest_client as toolchest
toolchest.set_key("YOUR_TOOLCHEST_KEY") # or a file path containing the key

Contact Toolchest if:

  • you need a key
  • you’ve forgotten your key
  • the key is producing authentication errors.

Documentation & User Guide available at Read the Docs

Comments
  • Enable paired reads for `kraken2`

    Enable paired reads for `kraken2`

    Adds the option to use paired-read inputs for kraken2, via the read_one and read_two arguments (or a list of two paths via inputs).

    Adds/removes --paired to tool_args as necessary.

    opened by bcai2 3
  • v0.4.0

    v0.4.0

    • Add Poetry, remove Twine

    • Add CircleCI automatic deploy to PyPI (untested for prod PyPI)

    Note: CircleCI will be failing because v0.4.0 already exists on test PyPI. That is to be expected, because I already bumped it to v0.4.0 when testing.

    opened by lebovic 3
  • S3 chaining

    S3 chaining

    Adds:

    • Output class returned by all toolchest.tool() calls, which contains s3_uri, presigned_s3_url, and (local) output_path variables
    • S3 chaining, via supplying output.s3_uri from a previous tool as the inputs parameter for a following tool
    • the ability to skip download of any tool's output, by setting output_path=None (set to None by default)
    opened by lebovic 2
  • Polish tool_arg handling, add more STAR args

    Polish tool_arg handling, add more STAR args

    Adds:

    • More STAR args
    • Add multiple levels of tool_arg handling (whitelist, dangerlist, blacklist)
    • Error on unknown or blacklisted args
    • Reduce complexity (validation and parallelization for now) if a dangerous argument is passed

    Requires:

    • https://github.com/trytoolchest/toolchest-worker-node/pull/24
    • https://github.com/trytoolchest/toolchest-api/pull/22

    This does not fix:

    • Bigger disk/memory/etc requirements for larger files where args trigger reduced complexity / no parallelization
    opened by lebovic 2
  • STAR whitelist options

    STAR whitelist options

    • Adds basic whitelist options for STAR.

    • Adds support for tags with variable amounts of arguments. Adds the --quantMode tag for STAR.

    (This should be merged in after the kraken2 paired read commit.)

    opened by bcai2 2
  • feat: centrifuge base

    feat: centrifuge base

    • Adds the centrifuge tool.
    • Adds docs.
    • Refactors how prefix_mapping is generated for megahit with a new module (input_util.py) and function (convert_input_params_to_prefix_mapping). Adds a unit test for the function.
    opened by bcai2 1
  • fix: upload/download tracker bugfixes

    fix: upload/download tracker bugfixes

    • Refactors the tracking printed statements into a pythonic print call with string formatting.
    • Fixes status update logic in uploading. (This was causing the terminal output to stall at the "uploading" stage.)
    • Adds integration test dirs to .gitignore.
    opened by bcai2 1
  • fix: remove pysam due to multiple issues

    fix: remove pysam due to multiple issues

    Pysam has caused multiple issues as a package and STAR parallelization is not currently used so this pr fully removes pysam as a dependency. Either a different library or custom sam file merging code is planned to be implemented later so parallelization framework is remaining in the code for now.

    opened by jherr-dev 1
  • feat: add preliminary alphafold support

    feat: add preliminary alphafold support

    Adds basic support for running AlphaFold via Toolchest. Code needs to be cleaned up and better documented. Currently limited to 1 input fasta.

    use_reduced_dbs and is_prokaryote_list are currently disabled until further implementation and testing is done. Integration will come with reduced dbs since full dbs take 45 minutes to an hour to run even on simple input.

    opened by jherr-dev 1
  • feat: support async execution

    feat: support async execution

    Adds:

    • Support for async execution

    See https://gist.github.com/lebovic/72fbb857119f1667c7959a4d7e28cd50 (or the integration test) for a hacky example on how to run Toolchest with async execution.

    opened by lebovic 1
  • fix: set default version number

    fix: set default version number

    Sets the version number to a default instead of erroring if the client is run from source (i.e., without the toolchest-client package being installed via pip).

    Open question: the version number defaults to 0.0.0, which can be confusing -- are there any other labels that might be better (e.g., dev or just the empty string)?

    opened by bcai2 1
Releases(v0.11.3)
Owner
Toolchest
Toolchest
GitHub Repository
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