CRT home > Configuring your Account

A series of system-wide scripts, collectively known as wmclogin, are provided to aid you in configuring your account to easily take advantage of the software and resources installed on our UNIX systems. These scripts set up your UNIX environment (in particular your PATH environment variable) appropriately for the system you are on and shell you are using.

Users of newly created accounts need not take any action as your account is created with these options already enabled. However, older accounts (especially those users who have migrated from Mount Sinai) may wish to alter their account configuration as detailed below. Be sure to read this entire section before reconfiguring your account to appreciate the implications of doing so.

To invoke the wmclogin scripts when you log in, simply create a file in your home directory named .use_wmclogin. The file should not have any content (i.e., it should be zero-byte file). You will also probably want to modify your login scripts, as many of the functions (in particular the use commands) needed when working on systems at Mount Sinai are not longer required or supported. You may copy template login scripts (.login, .profile and .cshrc, as well as .use_wmclogin) from the /etc/skel directory on beech to your home directory. Be sure to keep copies of your existing login scripts, as there may be functionality in them you want to retain. You may need to merge these scripts by hand; contact the system administrator if you need assistance.

Should you elect not the use the wmclogin scripts in all you sessions by creating the .use_wmclogin file, you may still use these scripts in any given session by executing the wmclogin command at the UNIX prompt.

Many of the applications that were used at Mount Sinai are stored in the /usr/global directory. Although this directory was transferred to Cornell and is being retained for transitional purposes, many of the applications contained within it may not be suitable for production use. The versions of some applications are out-of-date; others do not contain original distributions making their builds non-reproducible. When you change your login scripts to those found in /etc/skel on beech, your PATH may lose references to applications in /usr/global. If this happens, you may restore part or all of your login script to temporarily regain references to those applications. However, please let your system administrator know which applications in /usr/global you are using so that up-to-date, fully licensed and supported versions can be installed.

Software that is formally maintained and supported at WMC is found in the /usr/global/opt directory. A separate description of software installed on our systems at WMC is available.

Next: Connecting to Our Systems

News
Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]
Jan, 2009; Twease now supports searching MEDLINE articles by Author, Journal, and Publication Year. Examples for performing these searches can be found in the updated Twease tutorial. [More]

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Dec 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Fabien Campagne; ICB Conference Room - Y.1301
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