Starting in the Spring of 2015, communal CBCB Software has been installed using GNU Modules.

== Common Modules ==

CBCB Software modules are already configured for interactive shells on Red Hat 7 machines - no additional setup is required. The module files are installed in the following location:
/cbcb/sw/RedHat-7-x86_64/common/modules/release/latest

To see see what modules are available:
$ module avail

To add a module to your environment, use <code>module add</code>:
$ module add samtools/0.1.19

Note that you can also specify the software name without the version:
$ module add samtools

Now samtools has been added to your environment:
$ which samtools
/cbcb/sw/RedHat-7-x86_64/common/local/samtools/0.1.19/bin/samtools

== Personal Modules ==

We have created some scripts to assist you with installing software and modules to your personal directory in <code>/cbcb/sw.</code>. We recommend that you use these scripts because this will help us share installed software among other CBCB users.

Run this initialization script to set up your directory structure:
$ /cbcb/sw/RedHat-7-x86_64/common/scripts/init_cbcb_sw_user.sh

This will create a directory for you:
$ tree /cbcb/sw/RedHat-7-x86_64/users/<username>

<pre>
/cbcb/sw/RedHat-7-x86_64/users/<username>
├── local
├── modules
│ └── <username>
│ └── env
├── module_template
├── README
├── scripts
│ ├── copy_module_template.sh
│ ├── init_install_vars.sh
│ └── install_package.sh
└── src
</pre>

* Use the <code>src</code> directory for storing and compiling source code.
* Use the <code>local</code> directory as the installation prefix.
* Use the <code>modules</code> directory to store your modulefiles.

See [[#Installing Software]] below.

To make use of your personal module file directory, add the following to your <code>~/.bashrc</code>:
module use /cbcb/sw/RedHat-7-x86_64/users/<username>/modules

=== Installing Software ===

Use the <code>install_package.sh</code> script to automatically compile software which uses <code>./configure; make; make install</code>. The advantage to using this install script is that it will:
* use the standardized directory structure for personal software installation, and
* '''''automatically''''' create a module file for the software in your <code>modules</code> directory!

For full details, read the <code>README</code> placed in your home directory. It's also available in the [https://gitlab.umiacs.umd.edu/cbcb/cbcb-sw/blob/master/templates/user_readme.md cbcb-sw Gitlab repository].

== Setup for non-interactive shells ==

Modules are already configured for interactive shells, but to use modules with non-interactive shells, add the following to your ~/.bashrc:
. /usr/share/Modules/init/bash
. /etc/profile.d/ummodules.sh

For more information, see the [https://wiki.umiacs.umd.edu/umiacs/index.php/Modules UMIACS wiki].

CBCB Software Modules

2015-03-03T04:09:01Z

Lmendelo:

Main Page

2015-03-03T03:57:25Z

Lmendelo: /* Getting started */

== IMPORTANT (Read First) ==
The CBCB computational infrastructure is a shared resource and we all need to pitch in in order to make sure it works well for all of us. Most importantly, we need to ensure that our disk space and computational resources are used responsibly. The disk space, in particular, is a valuable commodity and thus it is important to pay attention to the following:
* There are three types of disk space available (a full list of volumes is available at [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage CBCB Storage]) :
** Local harddrives (usually mounted as /scratch on the machines that have this resource). These are not backed up, are quite fast (they live physically close to the processor), but can only be 'seen' by the machine where they are mounted and, thus, require data staging in/out (which can take a while)
** Shared 3Par storage (/fs/szasmg*, /fs/szdata/*, etc.). This is very fast and very expensive disk and thus a limited resource. Please only use this space to store data temporarily, while you are running some analyses on it. As a rule of thumb, if a file or collection of files of any considerable size have lived on this space for more than 1-2 weeks, they should probably be moved to the attic space (see below)
** Attic storage (/fs/szattic*). This is cheaper and ample, but slow and brittle storage. Your data-sets should primarily live here. Due to it's brittleness, the IT department do not recommend you run any analyses directly in this volume, rather you copy the files over to a local harddrive or the 3Par instead, and copy the results back when done.
* You should remove any temporary results you don't need in the long term as soon as you've generated them, and compress all of the large files. Bzip2 works better than gzip but either should dramatically improve the space requirements, especially for text files such as fasta or fastq.
* You should ensure that your files are owned by the cbcb group and that they have group write permissions for any file stored on the 3Par, especially for all those in /fs/szscratch. This will allow your colleagues to remove files in case the disk runs out of space and you are, for example, on vacation (in which case you shouldn't have any major files sitting around on the 3Par).

For more information on the CBCB resources see [[Getting Started in CBCB]].

== Seminars ==
* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] 
* [[Cbcb:Works-In-Progress]] - Works in progress seminar schedule (Summer 2008) 
* [[short_read_sequencing|Short read sequencing Meeting]] (Fridays at 3pm)

== Projects ==

* [[Project:Pop-Lab|Pop-Lab]]
* [[Project:Hcbravo-lab|HCBravo Lab]]
* [[Project:Cloud-Computing|Cloud Computing]]
* [[Project:SummerInternships|Summer Internship Projects]]
* [[Metagenomics Reading Group (Wed 2pm)]]

== People ==

* [[User:ayres|Daniel Ayres]]
* [[User:pknut777|Adam Bazinet]]
* [[User:irina|Irina Astrovskaya]]
* [[User:jpaulson|Joseph Paulson]]
* [[User:mpop|Mihai Pop]]
* [[User:nelsayed|Najib El-Sayed]]

== Getting started ==
If you have just received a new umiacs account through CBCB, follow the instructions on this page to get the basic information you'll need to start working: 
*[[Getting Started in CBCB]]
*[[CBCB Software Modules]]
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage CBCB Storage]
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Compute CBCB Computers]
*[[Communal Software]]

CBCB Software Modules

2015-03-03T03:57:05Z

Lmendelo: Created page with "Starting in the Spring of 2015, communal CBCB Software has been installed using GNU Modules."

Starting in the Spring of 2015, communal CBCB Software has been installed using GNU Modules.

Getting Started in CBCB

2015-03-03T03:54:33Z

Lmendelo: /* Configuring Your Home Directory and Shell */

Last update 9/11/13 

You may want to review the following:

[[Media:CBCB-quick-guide.pdf]]

==Getting Building Access and Room Keys==

CBCB is located on the 3rd floor of The Biomolecular Sciences Building identified on campus maps as Building #296. The building is secure and access is gained by either using your UM ID card, guest card or entering the 3-digit code of the person you to visit at the call box on the right side of the front door.

Contact the Center Coordinator, Christine Bogan, about gaining card access to the building. She will need the following information:
*An notification email from your sponsor/adviser
*Your Name
*Your 9 Digit University ID number
*Your Contact email

Along with your assigned space and phone numbers, the coordinator will send your information to UMIACS Coordinator Edna Walker who will contact campus security to add you into their system. ''Note: clearance usually takes a number of days, so contact the coordinator as soon as possible.''

If you prefer not to send your information through email feel free to contact the coordinator in person.

You must get your key from the coordinator in person.

Christine Bogan 
Room 3121 
Biomolecular Sciences Bldg #296 
301.405.5936 
cbogan[at]umd.edu 

==Research In Progress Seminars==

These seminars are held through the year. For information go to [http://cbcb.umd.edu/node/18625 CBCB Research in Progress]

For a list of our Disk Storage and amount of available space left on each one, see [http://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage wiki.umiacs.umd.edu/cbcb-private/index.php/Storage] 

== Configuring Your Home Directory and Shell ==

We import common settings files that set our path variables to include commonly shared software repositories.

As a start, add the following line to the top of the file called ".bashrc" located in your home directory (/nfshomes/username/):

. /fs/sz-user-supported/share/dotfiles/bashrc.cbcb

This will import the common bashrc.cbcb file into your own bashrc file every time you log in.

Now add this line to your ".bash_profile" file, also located in your home directory:

. ~/.bashrc

This will import your personal bashrc file every time you log in. Now you should have access to most of the locally installed software like "blastall" and "AMOS."

If you want to add any addition commands to your bashrc file, such as setting your default text editor to "vim" or formatting the output of bash commands (eg. "ls"), add the appropriate commands after the imported common files as shown in this example:

. /fs/sz-user-supported/share/dotfiles/bashrc.cbcb

alias vi='vim'

alias ls='ls --color'

If you decide you want to change the settings in the common bashrc.cbcb to better suit your personal needs, then please copy and paste its contents into your personal bashrc file. '''Do not modify the common bashrc.cbcb file as it will affect everyone's environment.''' Also check back periodically as people may add common paths for new software.

To use CBCB Software Modules, see [[CBCB Software Modules]]

If you have any other problems, contact staff [at] umiacs.umd.edu or your PI. 

More resources can be found at [https://wiki.umiacs.umd.edu/umiacs/index.php/GettingStarted umiacs wiki]

== Printing ==
Go to the umiacs wiki to find [https://wiki.umiacs.umd.edu/umiacs/index.php/Printing system-specific guides for printing], and be sure to [https://wiki.umiacs.umd.edu/umiacs/index.php/PrinterQueueNaming add 'nb' to the end of your print queue] to avoid wasting paper printing banners.

== Using the Wiki ==
* [http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Wiki Formatting Cheatsheet]
* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]
* [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

== When You Travel ==

[[Media:CBCB_travel_request_form_oct_2014.pdf‎]] form to fill out to obtain information for travel reimbursement

[[Media:Travel_101_cbcb_revised_4-2013.pdf]] for more detailed travel info