Stirplate.io Data Upload Helper

Current version: v1.4.0

Sequencing data may be sent to Stirplate several ways.

1. Manual data upload via 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.

Data Upload and Storage only protocol:

There are two ways to run the data upload helper for the Stirplate (sotrage only) protocol:

1. Interactive. Simply type:

   stirplate storage
   

   • You will be prompted for the input directory containing your sequencing data.

2. Automatic. Simply run:

   stirplate storage
   --directory /path/to/input/sequencing/data/
   --project_name MyProjectName
   

   • 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

Troubleshooting install

If pip install stirplate gives you permissions error, you can install the package as either:

• Root user: sudo pip install stirplate
• Current user: pip install --user stirplate

Troubleshooting usage

At any point you may get additional command line usage help by typing:

• stirplate -h
• stirplate rna -h
• stirplate dna -h

Email keith@stirplate.io for any futher questions.