README to describe how to access data from TCGA
Images came from The Cancer Genome Atlas and were accessed via a manifest file. The manifest file we used to download the images for this project is GDC_download_manifest.txt in the Manifests folder.
On our HPC, Talapas, we downloaded images with the commands:
module load racs-eb/1
module load gdc-client/1.3.0-intel-2017b-Python-2.7.14
gdc-client download -m ./GDC_download_manifest.txt
The module load commands load the proper packages for gdc-client.
As loaded, the packages have requirements for processor architecture to run. According to the documentation any of the following architectures will work: Intel(R) X87, CMOV, MMX, FXSAVE, SSE, SSE2, SSE3, SSSE3, SSE4_1, SSE4_2, MOVBE, POPCNT, F16C, AVX, FMA, BMI, LZCNT and AVX2.
We used an Intel processor for downloading.