Metadata-Version: 1.1
Name: stirplate
Version: 1.3.4
Summary: Stirplate Data Uploader
Home-page: https://github.com/stirplate/upload
Author: The Stirplate, Inc. Team
Author-email: brett@stirplate.io
License: MIT
Description: Stirplate.io Data Upload Helper
        ===============================
        
        Sequencing data may be sent to Stirplate several ways.
        
        1. Manual data upload via `stirplate.io <https://stirplate.io>`__.
        2. **RECOMMENDED**: Automatic upload from a local computer directly to
           Stirplate without user interaction (outlined in this document).
        
        Installation:
        --------------
        
        -  To setup and run automated data upload to Stirplate, be sure you have
           your Stirplate User Credentials (please contact keith@stirplate.io to
           obtain these).
        -  Python 2.7.x (untested on Python >= 3).
        -  ::
        
              pip install stirplate
        
        -  A ``stirplate`` executable will be added to your system path.
        
        
        Configure Access:
        -----------------
        
        Configure your Stirplate Access Credentials.
        
        1. **Interactive**: Simply type:
        
           ::
        
              stirplate configure
        
        2. **Automatic**: (Recommended) "Install" the supplied configuration
           file automatically from a downloaded config file:
        
           ::
        
              stirplate configure --install /path/to/stirplate/config
        
        RNA-Seq protocol:
        ------------------------------------------------------
        
        There are two ways to run the data upload helper for the Stirplate
        RNA-Seq (DESeq2) protocol:
        
        1. **Interactive**. Simply type:
        
           ::
        
              stirplate rna
        
           -  You will be prompted for the input directory containing your
              sequencing data, as well as additional meta data (aligner [TopHat, STAR], species, single
              stranded protocol) information.
        
        2. **Automatic**. Simply run:
        
           ::
        
               stirplate rna
               --aligner star
               --directory /path/to/input/sequencing/data/
               --project_name MyProjectName
               --species SPECIES
        
        
           -  Aliger choices are: ``tophat`` (default), and ``star``.
           -  Species choices are: ``C_ELEGANS`` (worms), ``D_RERIO``
              (zebrafish), ``H_SAPIENS`` (humans), ``M_MUSCULUS`` (mouse),
              ``R_NORVEGICUS`` (rat), ``B_TAURUS`` (cow), ``C_FAMILIARIS`` (dog), or ``E_CABALLUS`` (horse).
           -  If the experiment was performed using a single strand protocol,
              pass the ``--single_stranded_protocol`` flag as well.
           -  Upon running, all files in your input sequence data ``directory``
              will be uploaded to Stirplate.io. The uploading is optimized for
              speed so your data will be transferred in the least amount of
              time. **Processing will begin at Stirplate as soon as the last
              file transfer has completed**.
        
        DNA-Seq protocol:
        ------------------------------------------------------
        
        There are two ways to run the data upload helper for the Stirplate
        RNA-Seq (DESeq2) protocol:
        
        1. **Interactive**. Simply type:
        
           ::
        
              stirplate dna
        
           -  You will be prompted for the input directory containing your
              sequencing data, as well as additional meta data (aligner [TopHat, STAR], species, single
              stranded protocol) information.
        
        2. **Automatic**. Simply run:
        
           ::
        
               stirplate dna
               --directory /path/to/input/sequencing/data/
               --interval_file /path/to/input/sequencing/data/intervals.interval_list
               --project_name MyProjectName
               --species SPECIES
        
        
           -  Species choices are currently:  ``H_SAPIENS`` (humans). More available on request. Email keith@stirplate.io.
           -  Upon running, all files in your input sequence data ``directory``
              will be uploaded to Stirplate.io. The uploading is optimized for
              speed so your data will be transferred in the least amount of
              time. **Processing will begin at Stirplate as soon as the last
              file transfer has completed**.
        
        Help
        ----
        
        At any point you may get additional command line usage help by typing:
        
        -  ``stirplate -h``
        -  ``stirplate rna -h``
        -  ``stirplate dna -h``
        
Keywords: stirplate bioinformatics upload biology genetics genomics proteomics rna dna gbs
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
