Issue #33 new

help with documentation

Anonymous created an issue

I will begin this question with an apology: I am newish to python, and to bioinformatics, and I am transitioning from wet-bench to dry work. So my question could be viewed as dumb or inappropriate for this forum, but I will ask it anyway.

Could I have some more help with installation and using bx-python? I use galaxy a lot, and I would like to be able to integrate some of galaxy's functions with my own scripts as I become more confident with python.

It seems that there is no documentation really available until you install the package. But I have had problems with the installation, and I would like to make sure that what I'm struggling to install is actually going to do what I want. Even so I have looked through the contents of bx-python to try to find some help or documentation, which I can't find. I read on another wiki issue that there is a help function for at least one of the functions. It seems though that I must first run the function to get there?

Anyway my point is that bx-tools is very inaccessible for me. I don't think an extensive documentation would be necessary, but a little more information on what tools are available, what they each do (or maybe the highlights of the most popular ones) and how to use them (are they modules you import, or do you run them straight from the command prompt). I really think that would also help me and others to decide if the tools are useful for them and whether it's worth going to the trouble of installing them which may require troubleshooting.

Perhaps there's not an interest in expanding the number of users, or people like me should just go back to galaxy, but I have been using a number of other tools similar to bx-python, such as biopython, bedtools, cgatools, without any problem thanks to just a bit more documentation. There are a growing number of us 'inbetweeners' learning bioninformatics and programming on the job, going beyond galaxy but not fluent yet. I would appreciate a little assistance!

Many thanks.

Apologies for the long post and I hope its not too inappropriate.

Comments (3)

  1. Brad Chapman

    Thanks much for checking out bx-python and for the feedback. I absolutely agreed that more documentation would help with the learning curve. Have you see the bx-python wiki, which has basic installation instructions and some examples of using various modules?

    The project would welcome additional documentation for new users and I'd encourage you to become involved. As a practical example, I wrote several items in the Biopython tutorial documentation while learning the library. It was an excellent way to become more familiar with the code and has, hopefully, helped out other users.


  2. Paul_Fawcett

    Like ClearBlueSpring, I am very new to Python. I also have encountered serious issues trying to get the installers to work. Unfortunately, I am constrained by the teaching environment we're using to Windows 7 installations of Python (2.7), and it's not clear from the documentation that this is even possible. I can't seem to make the easy install work (it complains about vcvarsall.bat not being found), and it's not clear to me based on the few comments on the wiki how it might be done manually with the windoze FS. Any advice much appreciated. I need, incidentally, only a small subset of functionality -- the ability to query bigwig files.

    EDIT: I was able to resolve the issue with the vcvarsall.bat by installing Microsoft Visual Studio 2008 express. Unfortunately, easy install still wipes out with an unknown value error relating to a path as shown in the image. And the references are all to a linux install Install JPG

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