Which Version Control System Is Most Common For Bioinformatics?

Question

[Farhat]

Which version control system do you prefer to use in your projects and which one is more commonly used. I tried using SVN and CVS but never got the hang of them. I currently use git for most of my projects. Which one is more common among bioinformaticians?

[Michael Kuhn]

earlier question on the same topic

[Steve Moss]

I love using bitbucket and mercurial personally! I should think git and github or svn and sourceforge are most common though?

Answer 1

[User 59]

Having made the progression from CVS to SVN to git, I have to say I prefer the latter, although it's taken me a while to wrap my head around it where I always felt quite comfortable with CVS/SVN. Using github has helped a lot, but as I found out yesterday the web based merging tools leave a little to be desired.

I follow dozens of coders and bioinformatics projects on github, you can't deny that the social element makes the system far more valuable than just having an SVN repository tucked away somewhere. I spend a good hour yesterday poring over other peoples code there, it's a great resource, and certainly for NGS tools seems to be a popular repository, backed by a popular SCM.

[Sean Davis]

I can't say enough about how social coding, enabled by tools like git and platforms like github, has changed the way I approach my daily work. No longer does one need commit privileges to make a difference. The same is possible with non-distributed systems like SVN, but git and github (and other DVCS) go to another level.

Answer 2

[Michael Kuhn]

Mercurial is also quite nice, and it's easier to understand as you don't have this "two step" check-in (with index and repository) like git. There's also public and private hosting on bitbucket.

Answer 3

[Pascal]

CVS is very old-fashioned now and it's slow when you start to have many tags and branches. I would not consider CVS anymore for a brand new project but rather if you inherit repositories (although there many tools to export to SVN). AFAIK there is no further developments on CVS software, only maintenance, for years.

SVN is more performant than CVS and as Gjain said, it is very common nowadays.

Git, as you may have seen, is gaining a great momentum now in software development for distributed development teams and for many other things.

IMHO, you are on the safe zone using either Git or Svn.

When choosing, take into account if your Development environment and Testing environment (e.g Unit Test) are well compatible with the source repository software.

Answer 4

[Niek De Klein]

There are a few mentioned here. By the looks of that thread it is very diverse which one is used, depending on the group background.

Answer 5

[Gjain]

• SVN is very common and easy to use. we use it internally.
• Sourceforge is the other one we use.

Some other uncommon and application specific version system that I know of:

• MEMOSys
• HGsubversion: for python users

[Michael Schubert]

There's a difference between a VCS and a platform that provides one. From what I worked with, SVN (hosted on either an own server, Sourceforge, or Google Code) is the most widely used but Git (esp. on Github) catches up.

[Gjain]

yeah that is true. Many people are moving to Github. Thanks