Welcome to BASE-hacks

This trac is set up for having a way to communicate changes made to third party packages in order to get them to work with ​BASE. We try to convince the third party package maintainers to accept our changes but when that is not possible we add the packages to this site.

One way to find out which changes was made is to compare different revisions of source using the subversion repository browsing capabilities of trac, or read the the package specific wiki pages.

The package wiki pages contain more information about the changes made to the packages, licensing information, and where to get the original program code.

Question should be directed to the BASE mailing lists, ​https://base.thep.lu.se/wiki/MailingLists

Hosted packages

Package	Description	Version	Home site	Comment
AffxFusion	Package for reading Affymetrix data files	1.09	​http://www.affymetrix.com/support/developer/fusion/index.affx
JSON.simple	A package for working with JSON objects.	1.1.1	​https://code.google.com/archive/p/json-simple/
MeV plug-in for BASE	MultiExperiment Viewer (MeV) is a versatile microarray analysis tool	4.0.01	​http://www.tm4.org/mev.html	Deprecated see ​BASE MeV for later versions
Picard	Picard comprises Java-based command-line utilities that manipulate SAM files (and create Fastq files)	1.128	​http://picard.sourceforge.net/	Deprecated Use the standard Picard software instead
Trimmomatic	A flexible read trimming tool for Illumina NGS data	0.32	​http://www.usadellab.org/cms/?page=trimmomatic

Subversion structure

For each package we modify we try to follow the vendor branches procedure outlined at ​http://svnbook.red-bean.com/en/1.7/svn.advanced.vendorbr.html

You can check out the BASE-hacks subversion repository with

svn checkout https://dev.thep.lu.se/basehacks/svn/ basehacks