Last updated: 2020-06-23
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Knit directory: rss/
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This page shows how to install the Monte Carlo Markov chain (MCMC) scripts in rss/src/. In a standard computing environment with internet connection, the installation time is typically less than 10 minutes.
git (optional)To simplify Step 1 below, you may consider installing git in your computing environment (if it is not available there). Please see this excellent tutorial on installing git.
Please note that RSS software does not depend on git. You can complete Step 1 without installing git.
rss repositoryWith git installed, you can easily clone rss by running the following command in Terminal.
Download and install the lightspeed MATLAB toolbox (author: Tom Minka).
cd rss/src
wget http://ftp.research.microsoft.com/downloads/db1653f0-1308-4b45-b358-d8e1011385a0/lightspeed.zip
unzip lightspeed.zip
rm lightspeed.zip
cd lightspeed/
matlab -nodisplay < install_lightspeed.mDownload and install the lapack MATLAB package (author: Tim Toolan).
Note that if an appropriately compiled version of lapack.c does not exist, this package will ask whether to build one.
Download the progress MATLAB package (author: Martinho Marta-Almeida).
All downloaded files must be placed under rss/src.
-rw-rw-r-- 1 xiangzhu xiangzhu 5261 2015-11-11 08:46 calc_posterior_bvsr.m
-rw-rw-r-- 1 xiangzhu xiangzhu 972 2015-11-11 08:46 compute_pve.m
-rw-rw-r-- 1 xiangzhu xiangzhu 86772 2015-11-11 12:01 lapack.c
-rw-rw-r-- 1 xiangzhu xiangzhu 5927 2015-11-11 12:01 lapack.m
-rwxrwxr-x 1 xiangzhu xiangzhu 120123 2015-11-11 12:12 lapack.mexa64
drwx------ 6 xiangzhu xiangzhu 32768 2015-11-11 11:54 lightspeed
-rw-rw-r-- 1 xiangzhu xiangzhu 2573 2015-11-11 12:01 progress.m
-rw-rw-r-- 1 xiangzhu xiangzhu 4402 2015-11-11 08:46 propose_gamma.m
-rw-rw-r-- 1 xiangzhu xiangzhu 11629 2015-11-11 08:46 rss_ash.m
-rw-rw-r-- 1 xiangzhu xiangzhu 22182 2015-11-11 08:46 rss_bslmm.m
-rw-rw-r-- 1 xiangzhu xiangzhu 8363 2015-11-11 08:46 rss_bvsr.m
-rw-rw-r-- 1 xiangzhu xiangzhu 11348 2015-11-11 08:46 update_betatilde.m
-rw-rw-r-- 1 xiangzhu xiangzhu 4796 2015-11-11 08:46 update_bz.m
-rw-rw-r-- 1 xiangzhu xiangzhu 17205 2015-11-11 08:46 update_zlabel.mPlease note that RSS MCMC codes have only been extensively tested in the following environments.
version 8.4.0.150421 (R2014b) of MATLAB for 64-bit Linux
version 8.2.0.701 (R2013b) of MATLAB for 64-bit Linux
version 8.1.0.604 (R2013a) of MATLAB for 64-bit Linux
If you have any trouble installing RSS MCMC codes, please open an issue or email me (xiangzhu[at]uchicago[and/or]stanford.edu). To help me better understand your problems, please provide details of your computing environment.