keeping track of versions

[mgogol]

What are some good strategies for keeping track of which versions you're using of bowtie/tophat/cufflinks/samtools, etc.? I know you can just write down what you used, but...

We have an internal wiki where we track what's currently installed and the date, so that offers one way of tracking it.

One colleague suggested dotkit.

https://computing.llnl.gov/?set=jobs&page=dotkit

Does anyone have any other good suggestions on managing these multiple packages with different versions? What do you do if you get additional samples for a project that you did 6 months ago?

[drio]

If you want to do it by hand, explore the --prefix option in most configures. That will help you if the package you are working on follows some open sources basic standards.

Also, for alignments, your bams should keep (header / @PG) the info of the aligner and version used.

Take a look to this also. You should be able to hack it to get version control.