stirplate 1.2.0

Prerequisites:

• 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).

• Python packages boto3 and mando.

  • To install boto3 to your python environment, use PIP: pip install boto3

  • To install mando to your python environment, use PIP: pip install mando

Configure Access:

Configure your Stirplate Access Credentials.

1. Interactive: Simply type:

   python stirplate.py configure

2. Automatic: (Recommended) “Install” the supplied configuration file automatically from a downloaded config file:

   python stirplate.py configure --install /path/to/stirplate/config

• Alternatively, you may pass your access credentials as parameters during the upload phase (not recommended).

Uploading and starting the Stirplate RNA-Seq protocol:

There are two ways to run the data upload helper for the Stirplate RNA-Seq (DESeq2) protocol:

1. Interactive. Simply type:

   python stirplate.py rna

   • You will be prompted for the input directory containing your sequencing data, as well as additional meta data (species, single stranded protocol) information.

2. Automatic. Simply run:

   python stirplate.py rna
   --directory /path/to/input/sequencing/data/
   --project_name MyProjectName
   --species SPECIES

   • Species choices are: C_ELEGANS (worms), D_RERIO (zebrafish), H_SAPIENS (humans), M_MUSCULUS (mouse), or R_NORVEGICUS (rat).

   • 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.

Help

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

• python stirplate.py -h

• python stirplate.py rna -h