https://github.com/elipapa/emacs-compbio-kit
emacs customizations geared towards computational biology and bioinformatics (R & Python)
https://github.com/elipapa/emacs-compbio-kit
Last synced: 2 months ago
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emacs customizations geared towards computational biology and bioinformatics (R & Python)
- Host: GitHub
- URL: https://github.com/elipapa/emacs-compbio-kit
- Owner: elipapa
- Created: 2011-02-10T23:12:23.000Z (over 14 years ago)
- Default Branch: master
- Last Pushed: 2012-03-05T22:59:43.000Z (over 13 years ago)
- Last Synced: 2025-01-14T14:58:30.874Z (9 months ago)
- Language: Emacs Lisp
- Homepage: https://github.com/elipapa/emacs-compbio-kit
- Size: 184 KB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.asciidoc
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README
emacs-compbio-kit
=================
The focus of this set of emacs customization is to provide a smooth experience while working in computational biology and bioinformatics under Mac OSX.
Python (with ipython) and R (with ESS) are the tools I spend most of my time with.
== package managers
this is what i understand at the moment (feb 10 2011) about package managers:
- package.el is used as the package manager in official emacs
- at the moment package.el does not support git repositories, as far as i can tell
- it seems that the development on package.el is stalled at the moment, but it will be the official emacs package manager (which is probably a shame, considering that...)
- el-get can grab git repos as well as apt-get and package.el(elpa) repos
- epackage/DELPS can do something similar
So:
it was best to move the big LISPs directories (org-mode and ESS) out of my version control and put them in some other version control (el-get or package.el through ELPA)
- two feasible ways to do so:
1. use git submodules (See http://github.com/eschulte/emacs-starter-kit/ for an example) and do a git pull for everything you need
2. use el-get, which automates retrieval of git repos, etc.
I decided to try the second option because it has the least setup time. Since it's probable I won't remember all the git submodules architecture next time I change stuff around in this folder, I figured it would be best to choose a method that was easily parseable.
Some of the reasoning is also given by the author of el-get (http://tapoueh.org/articles/news/_el-get_reaches_1.0.html)
=== el-get
To update: issue 'M-x el-get-update' or go to the directory ~/.emacs.d/el-get/el-get and do a 'git pull'
(At least in emacs < 24.1) one needs to either install 'package.el' as a recipe or set the 'package-user-dir' variable appropriately
el-get-remove still does not work. usually i just eliminate name from .status.el and remove directory