{ "info": { "author": "The Stirplate, Inc. Team", "author_email": "brett@stirplate.io", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Programming Language :: Python", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "Stirplate.io Data Upload Helper\n===============================\n\nSequencing data may be sent to Stirplate several ways.\n\n1. Manual data upload via `stirplate.io `__.\n2. **RECOMMENDED**: Automatic upload from a local computer directly to\n Stirplate without user interaction (outlined in this document).\n\nInstallation:\n--------------\n\n- To setup and run automated data upload to Stirplate, be sure you have\n your Stirplate User Credentials (please contact keith@stirplate.io to\n obtain these).\n- Python 2.7.x (untested on Python >= 3).\n- ::\n\n pip install stirplate\n\n- A ``stirplate`` executable will be added to your system path.\n\n\nConfigure Access:\n-----------------\n\nConfigure your Stirplate Access Credentials.\n\n1. **Interactive**: Simply type:\n\n ::\n\n stirplate configure\n\n2. **Automatic**: (Recommended) \"Install\" the supplied configuration\n file automatically from a downloaded config file:\n\n ::\n\n stirplate configure --install /path/to/stirplate/config\n\nRNA-Seq protocol:\n------------------------------------------------------\n\nThere are two ways to run the data upload helper for the Stirplate\nRNA-Seq (DESeq2) protocol:\n\n1. **Interactive**. Simply type:\n\n ::\n\n stirplate rna\n\n - You will be prompted for the input directory containing your\n sequencing data, as well as additional meta data (aligner [TopHat, STAR], species, single\n stranded protocol) information.\n\n2. **Automatic**. Simply run:\n\n ::\n\n stirplate rna\n --aligner star\n --directory /path/to/input/sequencing/data/\n --project_name MyProjectName\n --species SPECIES\n\n\n - Aliger choices are: ``tophat`` (default), and ``star``.\n - Species choices are: ``C_ELEGANS`` (worms), ``D_RERIO``\n (zebrafish), ``H_SAPIENS`` (humans), ``M_MUSCULUS`` (mouse),\n ``R_NORVEGICUS`` (rat), ``B_TAURUS`` (cow), ``C_FAMILIARIS`` (dog), or ``E_CABALLUS`` (horse).\n - If the experiment was performed using a single strand protocol,\n pass the ``--single_stranded_protocol`` flag as well.\n - Upon running, all files in your input sequence data ``directory``\n will be uploaded to Stirplate.io. The uploading is optimized for\n speed so your data will be transferred in the least amount of\n time. **Processing will begin at Stirplate as soon as the last\n file transfer has completed**.\n\nDNA-Seq protocol:\n------------------------------------------------------\n\nThere are two ways to run the data upload helper for the Stirplate\nRNA-Seq (DESeq2) protocol:\n\n1. **Interactive**. Simply type:\n\n ::\n\n stirplate dna\n\n - You will be prompted for the input directory containing your\n sequencing data, as well as additional meta data (aligner [TopHat, STAR], species, single\n stranded protocol) information.\n\n2. **Automatic**. Simply run:\n\n ::\n\n stirplate dna\n --directory /path/to/input/sequencing/data/\n --interval_file /path/to/input/sequencing/data/intervals.interval_list\n --project_name MyProjectName\n --species SPECIES\n\n\n - Species choices are currently: ``H_SAPIENS`` (humans). More available on request. Email keith@stirplate.io.\n - Upon running, all files in your input sequence data ``directory``\n will be uploaded to Stirplate.io. 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