Communal Software

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

Carl's World

In an attempt to solve many software installation related headaches for his lab members, Carl Kingsford has created an alternate environment called "Carl's World" which contains many programs and modules frequently used by his lab members. Little else is known about Carl's World, but rumor has it that if you ask nicely, he will let you in. It is important to note that Carl's World is designed and maintained specifically for use by Carl's lab members, and there are therefore many common and useful software packages not included in Carl's World. It may therefore be necessary to modify YOUR OWN bashrc file once you have joined, but be warned that attempting to modify Carl's World itself is a sure way to lose your membership.

Planned Maintenance (Summer 2010)

The Pop lab is currently planning to update much of the communal software installed in sz-user-supported over the Summer of 2010. 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.