A Plasmid Editor

This repository contains the TCL script for the plasmid editor written by M. Wayne Davis.

http://jorgensen.biology.utah.edu/wayned/ape/

I made a couple of changes to this repository in an attempt to make it easier to install/use on a linux host. The hosts I work with all use environment modules[1] and so I am providing an example module file and instructions assuming an environment similar to mine.

Environment modules installation

Our environment modules installation is based in /sw where all the modules are in /sw/modules and the project root is /sw/local. Thus the top of the module file defines those directories and attempts to automagically detect everything else. With that in mind, installation using environment modules is the following:

1. Pull the repository into the directory: /sw/local/ape/some_version_number
2. Copy the modulefile (currently modules/202007) to /sw/modules/ape/some_version_number
3. module add ape
4. Invoke ape and the first time it should ask for the location of the data files.

Manual installation

The installation without environment modules is also quite simple:

1. pull the repository.
2. edit bin/ape so that the variable APE_DIR points to the location of the repository.
3. Put bin/ape in an alias or in the PATH.
4. The first time ape is run on a new host, it will bring up a little box asking where the various files are located. Tell it to go to the downloaded location.

What did I do?

This repository is an essentially unchanged copy of M. Wayne Davis' code. If one wishes to perform a similar extraction on a different version of the editor, here is what I did. In an attempt to make that easier, I included a copy of the tclkit[2] and sdx.kit[3] I used.

1. Go into the bin/ directory of the repository.
2. Download the ApE windows zip file and unzip it into the $(pwd).
3. Extract the data with: tclkit sdx.kit unwrap ApE_win_current.exe, this creates the ApE_win_current.vfs/ directory containing the tcl script, the accessory files, and the miscellaneous stuff used by tclkit/sdx.
4. Copy out the main script with: cp ApE_win_current.vfs/lib/app-AppMain/AppMain.tcl ..
5. Copy the accessory files, I usually delete the existing files first, but I doubt that is necessary: rsync -av ApE_win_current.vfs/Accessory\ Files/ ..
6. Delete the windows specific material: rm -r ../lib
7. Clean up the $(pwd).

References

1. https://modules.readthedocs.io/en/latest/
2. https://wiki.tcl-lang.org/page/basekit (I used the original)
3. https://wiki.tcl-lang.org/page/sdx