This article assumes you have already set up your database using transmart-data. This gives you a set of environment variables in your transmart-data/vars file that you can source each time you are ready to load data.
cd /path/to/transmart-data ./vars
Finding public datasets
There is a file included in transmart-data to define the source of third-party curated datasets. You can use this file directly, or you can at any time add your own list of local files which will become available to all the transmart-data make targets.
Edit file samples/studies/public-feeds which should contain just this single line:
Add a URL to a local list of curated and packed studies, or to another public curated data server. The first token is http-index for a web server, or ftp-flat for an FTP server. You can download the file http://library.transmartfoundation.org/datasets/datasets_index to see the format. The file consists of records with:
studyname targettype URL
where the URL uses the same directory as the original link (i.e. under /datasets/ for the library.transmartfoundation.org server). The targettype is one of:
platform name to load (if not already loaded).
triggers loading of an annotation target.
|annotation||platform annotation for any datatype|
|acgh||Array CGH data|
|expression||mRNA expression data|
|mirnaqpcr||Micro RNA qPCR data|
|mirnaseq||MicroRNA RNAseq data|
|msproteomics||Mass-spec proteomics data|
|rbm||Rules-based medicine proteomics data|
|rnaseq||Count data from RNAseq for expression|
Updating the datasets list
A simple make target downloads or copies data from each link in the public-feeds file and saves them to a file sample/studies/datasets