Question: What Is The Best Way To Share Scripts Between Members Of A Lab?
gravatar for Giovanni M Dall'Olio
10.7 years ago by
Barcelona, Spain
Giovanni M Dall'Olio420 wrote:

One of the most awful problems in my group is avoiding to rewrite scripts that have been already written by others. Since we have different projects and we work with different data, everybody ends up writing its own scripts in his favorite programming language, and it is very frequent to waste an afternoon on writing a new program and then discover that your workmate already had a script to do that.

Apart from the most logical answer ("talk with your workmates"), we are thinking about having a common place to store our best scripts, and if possible work together on them. It would be similar to an image library like this: , where to put the script and an example of its output (most of our scripts produce graphs), and if possible integrated with Git.

Do you have any idea? How to you cope with the problem in your lab?

general subjective • 1.5k views
ADD COMMENTlink written 10.7 years ago by Giovanni M Dall'Olio420
gravatar for István Albert
10.7 years ago by
István Albert ♦♦ 310
University Park
István Albert ♦♦ 310 wrote:

Integrating with the source code management tool is essential, that way when code gets changed everyone can easily get the updated version. Wikis are also a good idea.

ADD COMMENTlink written 10.7 years ago by István Albert ♦♦ 310
gravatar for Simon Cockell
10.7 years ago by
Simon Cockell50 wrote:

If you want to see the code, but also store associated information, such as expected outputs etc, then a wiki probably is the best choice (we prefer DokuWiki here), although this would involve a lot of manual effort to document each script.

Use of a site such as GitHub would give you version control + a handy place to read code, although it is not free to host private repositories there, which I guess is what the majority of labs would require.

If privacy is not a concern, then I would consider GitHub gists for code, which can then be embedded in a Posterous blog for comments. Posterous automatically unfolds Gist URLs into code samples in blog posts, so then you can annotate them easily. This would be a lot less manual effort than a wiki.

ADD COMMENTlink written 10.7 years ago by Simon Cockell50
gravatar for Biorelated
10.7 years ago by
Biorelated20 wrote:

You might also want to setup a simple snippets database. Navysnip application by Jason Strutz is easy to install and run if you have ruby and rubyonrails installed.

git clone git:// cd navysnip sudo rake gems:install rake db:migrate ruby script/server Then visit your app at http://localhost:3000

check out for complete details

ADD COMMENTlink written 10.7 years ago by Biorelated20
gravatar for Etal
10.7 years ago by
Athens, GA
Etal70 wrote:

My lab uses a network-attached storage unit which every Linux workstation mounts by NFS at startup. It was reasonably cheap -- a couple hundred dollars per TB. We also keep copies of public databases on there. We put data sets on there as we're working on them, and also put the more important scripts in a Mercurial repositiory.

As Marcos and Istvan mentioned, a wiki integrated with your VCS would be wise, and Trac is the obvious choice for that.

ADD COMMENTlink written 10.7 years ago by Etal70
gravatar for Suk211
10.7 years ago by
state college
Suk21160 wrote:

This might be useful .

A Quick Guide to Organizing Computational Biology Projects

ADD COMMENTlink written 10.7 years ago by Suk21160
gravatar for Marcos De Carvalho
10.7 years ago by
Porto Alegre, RS, Brasil
Marcos De Carvalho20 wrote:

I would recommend you to setup a wiki for your group. If you do not have a server readily you can always use one of the many wiki services available for free like Wikispaces

ADD COMMENTlink written 10.7 years ago by Marcos De Carvalho20
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