Understanding Repositories and Files


Repositories are accessible stores of information that contain one or more data set or result files. To view you repositories, click on the Repositories tab under n3phele's portrait. Here you will a display similar to Figure 1.
The s3-qiime-tutorial repository is a Amazon hosted file store that contains files from the QIIME tutorial set. This is a shared repository available for all n3phele users. Users should not attempt to write to this repository.
s3-desktop is a private repository that n3phele creates for you during your initial account registration and is hosted as a bucket the Amazon account you specified during registration. When you navigate to your S3 console on Amazon you will see a bucket named n3phele-xxxxxx where xxxxxx will be a unique numeric identifier assigned to you by n3phele. This bucket contains the contents of your s3-desktop repository. You can upload your data sets to this repository, or write and store results here as well. However, there are monthly amazon charges levied for storage usage which you should understand.

Specifing Files

To specify an input data set or output file for a command, you must specify both the repository and the repository relative path for that file. For example, suppose in my S3 bucket associated with s3-desktop I upload a file called XH1045.sff into a folder I have created called "samples". Then to specify this file I will need to select the repository "s3-desktop" and then in the path enter samples/XH1045.sff
Similarly for output files I can select which repository in which I want the results stored, and then type the path. For example results/taxa.txt
In this case if a folder called results does not exist in the repository, it will be automatically created. The results will be writted in a file called taxa.txt in that folder. The path can be specified to have any number of folders, up to the limits imposed by the cloud provider.

Zip archive files

n3phele recognizes and treats zip files in a special way. If the input file is specified to be a zip file, then n3phele treats the path component subsequently to be files contained within that zip, and will extract them automatically. For example,
n3phele will look for a zip file called study.zip in the folder called datasets in the s3-desktop repository, and extract the file called site1/seqs.fna from that zip file.
Where an output file is a zip archieve, n3phele gives you the option of either storing the archive in the repository, or unpacking the archive in repository. To store the zip file in the archive, specify the target path as a file ending in a .zip extension. To store the zip file contents unpacked, then specify the target path simply in terms of a target folder. In this case the archive contents are unpacked into that folder. For example, the command I am running produces an output archive. If I specify the output file as:
then the archive will be transferred to the repository and stored there as a zip archive.
However, if I specify the outfile file as:
then the archieve will be unpacked into the sub-folder run1 in the results folder on the repository. The run1 folder will be created if it does not already exist.
Figure 1. Repositories Page