On Monday 19 March 2007 8:28 pm, Hamptonio wrote: > Hi, > > I became interested in SAGE after I found it to be the easiest way to > install cddlib and gmp, and now I am getting hooked. My research is > very schizophrenic: besides some computational algebra/geometry coming > from dynamical systems, I am also interested in mathematical biology > and bioinformatics. There is an open-source project called biopython > (http://biopython.org/wiki/Biopython) that I am using in a > bioinformatics course right now. It would be very nice if there was a > biopython optional package for SAGE. I am willing to try and create > one, but I thought I would post here first to see if anyone had any > preliminary advice before I waste my time. > > Biopython currently requires Numeric, but all the parts I need seem to > work OK using numpy. The developers are currently working on > switching over entirely to numpy. It also requires something called > mxTextTools, but I think that should be OK since its open source and > has a very permissive license.
Adding biopython is a good idea. Prompted by your email, I created a package for it, which I've posted here: http://www.sagemath.org/packages/optional/ If you do $ export SAGE_SERVER="www.sagemath.org" from bash, you can get it with sage -i biopython-1.43 My biophython-1.43 package includes mxTextTools, so it's very easy to install. Also, it seems that biophython-1.43 works fine with numpy. If it doesn't, Numeric is a well-supported optional sage package: "sage -i numeric-24.2". One very annoying thing that somebody needs to get to the bottom of, is that it seems necessary to hit enter several times half-way through the install, or it just pauses forever. This probably has something to do with maybe mxTextTools's installing doing something obnoxious. Feedback is appreciated. By the way, this document gives a basic idea of how spkg's are created: http://www.sagemath.com/doc/html/prog/node23.html In short, an spkg is just a bzip2'd tarball, with a file spkg-install that gets run in the environment of SAGE, e.g., "python" is SAGE's Python, etc., and it is supposed to install code to $SAGE_LOCAL. William William --~--~---------~--~----~------------~-------~--~----~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/ -~----------~----~----~----~------~----~------~--~---
