Communal Software - Revision history

Lmendelo at 18:55, 3 March 2015

2015-03-03T18:55:01Z

← Older revision		Revision as of 18:55, 3 March 2015
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	= WARNING! =		= WARNING! =
	~~This information is outdated~~. ~~See~~ [[CBCB Software Modules]] ~~for using CBCB Communal Software~~.
			<p style="color: #e70000; font-weight: bold; font-size: medium;">WARNING: <code>/fs/sz-user-supported/</code> and <code>/cbcb/software</code> has been deprecated as of March 2015. Please move towards using Red Hat 7 machines and [[CBCB Software Modules]]. </p>

	== Introduction ==		== Introduction ==

Lmendelo at 18:09, 3 March 2015

2015-03-03T18:09:47Z

← Older revision		Revision as of 18:09, 3 March 2015
Line 1:		Line 1:

			= WARNING! =
			This information is outdated. See [[CBCB Software Modules]] for using CBCB Communal Software.

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

Dsommer: /* Planned Maintenance (Summer 2010) */

2012-08-03T13:04:08Z

Planned Maintenance (Summer 2010)

← Older revision		Revision as of 13:04, 3 August 2012
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	== Planned Maintenance (Summer ~~2010~~) ==		== 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 ~~2010~~. So far this list includes:		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:
	* [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS] -- Already installed		* [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS] -- Already installed
	* [http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/index.html blastall 2.2.23] -- May not be worth upgrading from 2.2.18. Will look at release notes.		* [http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/index.html blastall 2.2.23] -- May not be worth upgrading from 2.2.18. Will look at release notes.

Dsommer: /* Carl's World */

2012-08-03T13:03:45Z

Carl's World

← Older revision		Revision as of 13:03, 3 August 2012
Line 36:		Line 36:
	Velvet 1.0.13		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) ==		== Planned Maintenance (Summer 2010) ==

Gpertea: /* Core Software */

2010-12-01T21:23:00Z

Core Software

← Older revision		Revision as of 21:23, 1 December 2010
Line 24:		Line 24:
	Bio::Perl		Bio::Perl
	Biopython		Biopython
	Bowtie 0.12.2		Bowtie 0.12.7
	Celera Assembler 6.1		Celera Assembler 6.1
	gcc 4.5.1		gcc 4.5.1
			GMap,GSnap 2010-07-27
			Java (JRE only) 1.6.0_22
	NCBI blast		NCBI blast
	Newbler 2.5		Newbler 2.5
	R		R
			Samtools 0.1.9
	SOAPdeNovo 1.04		SOAPdeNovo 1.04
	Velvet 1.0.13		Velvet 1.0.13

Dpuiu: /* Core Software */

2010-11-17T13:32:45Z

Core Software

← Older revision		Revision as of 13:32, 17 November 2010
Line 21:		Line 21:

	Software list:		Software list:
	Name version		'''Name version'''
	Bio::Perl		Bio::Perl
	Biopython		Biopython
	Bowtie		Bowtie 0.12.2
	Celera Assembler 6.1		Celera Assembler 6.1
	gcc 4.5.1		gcc 4.5.1
	NCBI blast		NCBI blast
	Newbler 2.3		Newbler 2.5
	R		R
	SOAPdeNovo 1.04		SOAPdeNovo 1.04

Dpuiu: /* Introduction */

2010-11-15T15:56:14Z

Introduction

@@ Line 8: / Line 8: @@
 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 file.
+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.
 == Carl's World ==

Tgibbons: /* Introduction */

2010-06-04T18:58:12Z

Introduction

← Older revision		Revision as of 18:58, 4 June 2010
Line 1:		Line 1:
	== Introduction ==		== Introduction ==
	Communal CBCB software is installed in		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/		/fs/sz-user-supported/
	There are two primary subdirectories which differ by architecture. For the most part, 32bit software is installed in		There are two primary subdirectories which differ by architecture. For the most part, 32bit software is installed in

Tgibbons: Created page

2010-06-04T18:56:43Z

Created page

New page

== Introduction ==
Communal CBCB software is 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 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.

== 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:
* [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS] -- Already installed
* [http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/index.html blastall 2.2.23] -- May not be worth upgrading from 2.2.18. Will look at release notes.
* [http://hmmer.janelia.org/ HMMer3] -- Installed.
** [http://pfam.sanger.ac.uk/ Pfam 24.0]
* PERL -- May attempt to standardize default version across servers.
** [http://www.bioperl.org/wiki/Main_Page BioPERL]
* Python -- May attempt to standardize default version across servers.
** [http://biopython.org/wiki/Main_Page BioPython]
*** [http://numpy.scipy.org/ NumPy]
*** [http://www.reportlab.com/software/opensource/ 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.