I'm trying to learn how to use BioMart via the Perl api. It has to be obtained via CVS and I can't remember how to use this. The last time I set a CVS client up was years ago and then after that I just had to click 'go'
The docs for biomart say to do this from the CVS command line
I thought I would have a go using the CVS features in eclipse and used the following
Host: cvs.sanger.ac.uk
Repository path: /cvsroot/biomart
user: cvsuser
password: CVSUSER (the password was given in the docs)
This seemed to get me a bucketload of Perl code but I didn't enter any release info in my settings so I don't know if I have the correct code.
Please can you tell me how I modify the information given in the biomart docs for use in my basic CVS client
I suspect that if you don't specify a release version, you'll get the latest version. Provided that the code appears to work as per the examples, I would not be too concerned.
Note that you can also fetch biomart-perl via SVN, according to these notes from GMOD:
You don't say what OS you are using. Linux or OSX provide both CVS and SVN clients for command-line usage, as per the examples. I don't use Windows but I believe that TortoiseCVS and Tortoise SVN are popular clients.
another basic question, sorry, but I don't know the difference between CVS and SVN.I'm using Windows. I used turoiseSVN years ago but I can't remember much at all. My head is in a whirl at the moment as I'm returning to bioinformatics after a long absence and there is so much to take in!!
They are both version control systems. CVS is older, SVN has different features. Many people moved to SVN from CVS but now of course there are many newer version control systems (Git, Mercurial...), so people are moving to them. I would not worry too much about the internals, provided that you know how to install and use a client - your goal is just to fetch someone else's code.
From what I understand, BioMart is moving away from the Perl API to a pure Java-based one in v0.8. I also recall the perl API being particularly noisy (with warnings) using more recent versions of perl (perl 5.10 or newer).
I think you checked the whole repository out of CVS. I used the CVS repository perspective of Eclipse to connect to the CVS server you specified, and checked out the HEAD revision of the biomart-perl. The index.html file in ./htdocs/ indicates that it is the latest 0.7 version of the library.
Sorry for the basic question but I don't know what a HEAD revision is. I need to find out more about this myself but if its possible to answer this question for me in one or two sentences without too much trouble I would appreciate it.
The CVS repository hosts the latest version of the biomart-perl code that works with the current release of BioMart (version 0.7).
Another good place to get immediate help about BioMart is the mart-dev mailing list: mart-dev@ebi.ac.uk. You can subscribe to it by sending a mail to majordomo@ebi.ac.uk with the email body containing "subscribe mart-dev". Even though the list is hosted by EBI, it is the best way to get in touch with the BioMart creators (who are at OICR, really).
I was surprised how hard it was to find simple information on CVS without having to wade through pages of user manual. The head field is simply the latest revision of the code and the -r flag is the tag option so you can set this in any CVS GUI
another basic question, sorry, but I don't know the difference between CVS and SVN.I'm using Windows. I used turoiseSVN years ago but I can't remember much at all. My head is in a whirl at the moment as I'm returning to bioinformatics after a long absence and there is so much to take in!!
They are both version control systems. CVS is older, SVN has different features. Many people moved to SVN from CVS but now of course there are many newer version control systems (Git, Mercurial...), so people are moving to them. I would not worry too much about the internals, provided that you know how to install and use a client - your goal is just to fetch someone else's code.