Communal Software

WARNING!

WARNING: /fs/sz-user-supported/ and /cbcb/software has been deprecated as of March 2015. Please move towards using Red Hat 7 machines and CBCB Software Modules.

Introduction

CBCB users do not have root access on their machines or the communal servers. Communal CBCB software is therefore typically installed in

/fs/sz-user-supported/

There are two primary subdirectories which differ by architecture. For the most part, 32bit software is installed in

/fs/sz-user-supported/Linux-i686/

while 64bit software is installed in

/fs/sz-user-supported/Linux-x86_64/

The appropriate subdirectory is typically dynamically chosen by embedding

/fs/sz-user-supported/`uname`-`uname -m`

in a user's path variables in their bashrc/tcshrc file.

Installing software to these directories and updating a user's path can be tricky. For this reason, many users choose to maintain specialty software in personal directories.

Core Software

The latest versions of the most frequently used CBCB software is installed under

 /fs/szdevel/core-cbcb-software/

and follows a directory structure similar to

 /fs/sz-user-supported/

The software is installed and maintained by the cbcb-staff group.

Software list:

 Name                      version
 Bio::Perl 
 Biopython
 Bowtie                    0.12.7
 Celera Assembler          6.1
 gcc                       4.5.1
 GMap,GSnap                2010-07-27
 Java (JRE only)           1.6.0_22
 NCBI blast
 Newbler                   2.5 
 R
 Samtools                  0.1.9
 SOAPdeNovo                1.04
 Velvet                    1.0.13

Planned Maintenance (Summer 2012)

The Pop lab is currently planning to update much of the communal software installed in sz-user-supported over the Summer of 2012. So far this list includes:

• AMOS -- Already installed
• blastall 2.2.23 -- May not be worth upgrading from 2.2.18. Will look at release notes.
• HMMer3 -- Installed.
  • Pfam 24.0
• PERL -- May attempt to standardize default version across servers.
  • BioPERL
• Python -- May attempt to standardize default version across servers.
  • BioPython
    • NumPy
    • ReportLab

Please feel free to contact Ted Gibbons at tgibbons@umd.edu to make suggestions or express concerns about tampering with the communal software installations and the corresponding paths in the communal CBCB bashrc file.