Translating and Compiling Delila Programs with P2C

The Delila programs can be automatically translated to C using David Gillespie's p2c translater. They then can be compiled by the gcc compiler.

Date/Time
Any program that uses the getdatetime routine to stamp output with the date and time must have the correct version of that routine. You must replace the time package with the correct one.

Archive of Delila programs.

To translate

Obtain the current version of p2c (p2c 1.21 "alpha 2") from the p2c archive. Contact: Dave Gillespie daveg@synaptics.com. (Note: version 1.20 of p2c, in the archive at CalTech, will not compile makelogo correctly.)
I have mirrored the p2c package so that it is available if the original source is not.
You will need three files:
- include file: p2c.h
- pascal library: p2clib.c
- In your home directory (assuming Unix operating system) you will need to have a control file for p2c (it's called .p2crc) with following lines:
```
  LiteralFiles 2
  NestedComments 2
  StructFiles 1
  
```
You may get a warning about "SYSTEM" which you can ignore.

To compile

A directory containing C versions of programs is available. I used the p2c program to automatically convert them to C. Translated programs have generally compiled and run fine.

Unfortunately if you do not have a Sun workstation you will need to get the libraries from the p2c package and compile them on your machine.
You will need the p2c.h file. This can be stored in /usr/local/include in a directory called 'p2c', which is the location given in the -I flag for gcc, below.
You will need several /usr/local/lib files. Put the files into /usr/local/lib/p2c. These are in the files picked up by -L/usr/local/lib flag for gcc, below.
The first program to try is test.

You can compile test.c with the gcc compiler:

gcc test.c -o test -I/usr/local/include -L/usr/local/lib -lm -lp2c

Script for Translation and Compilation

Translation from Pascal and compilation can be conveniently done by the tc conversion script, which uses the gcc C compiler. For translation you will need a p2crc file. The test program to use for this is test.p.

Run Time Problems

NOTES ON PROBLEMS:

I tried the test program and NOTHING HAPPENS
Under a Unix operating system, if you try the test program and NOTHING HAPPENS (i.e. you get a prompt back with no output) it is likely that you have a Unix 'test' program in your path. Say this:
which test
if it says '/bin/test' or something like that, then try this:
./test
to force the local one to be used.
What the heck is Pascal system error 0?
If you get this message from the p2c compiled alpro program:
protseq: Pascal system error 0
it means that there is no file named protseq! It is unfortunate that the compiler statement is not clear. All you have to do in each case is either supply the appropriate file or make an empty one. For the protseq, you need data in the file. To set an example up type these lines:
wget ftp://ftp.ncifcrf.gov/pub/delila/globin.fasta
mv golbin.fasta protseq
(You can either use wget to grab the file or you can use the link provided.)
For makelogo, if you get this message:
wave: Pascal system error 0
you missed the wave file; use:
touch wave
to make the empty file. You can have an empty file until you are ready to try putting waves on the logos (this is described on the makelogo manual page).
If weird things happen, you can email me. An article by Simon Tatham, How to Report Bugs Effectively, is quite good at explaining what a programmer needs to be able to fix a bug. (Here is my copy in case that one disappears like Jeff Covey's did!)

If you try p2c and it works or if you have trouble compiling, please email me. So far it works for:

Computer Operating System Programs

Sun Solaris 2.6 all?

Silicon Graphics IRIX 6.5 alpro, makelogo

Schneider Lab
origin: 1999 April 30
updated: 2006 Jan 30

Computer	Operating System	Programs
Sun	Solaris 2.6	all?
Silicon Graphics	IRIX 6.5	alpro, makelogo