Re: [PATCH] Add fraggenescan.

[Ben Woodcroft]

On 28/12/15 10:38, Leo Famulari wrote:
> On Mon, Dec 28, 2015 at 07:53:27AM +1000, Ben Woodcroft wrote:
> > On 20/12/15 23:03, Ricardo Wurmus wrote:
> [...]
>
> > > > +               (substitute* "run_hmm.c"
> > > > +                 (("^  strcat\\(train_dir, \\\"train/\\\"\\);")
> > > > +                  (string-append "  strcpy(train_dir, \"" share 
> > > > "/train/\");")))
> > > Why do you replace “strcat” with “strcpy” here?
> > The line above does a strcpy we don't want, so strcat would keep that. I
> > could remove the line above if you want, but this effectively makes no
> > difference to the running of the program.
> It looks like this substition has two parts:
> 1) Provide the correct path to some resources ("train files") for the
> program.
> 2) Change a function call from strcat() to strcpy().
>
> Can you elaborate more on part 2?
>
> I undertand that the intended effect is to discard a value assigned to
> 'train_dir' [0] in the previous function call. This discarded value is
> 'argv[0]' minus 12 bytes [1]. The reason for this is that the program is
> looking for the "train files" in the same directory as 'argv[0]', but we
> have installed the "train files" somewhere else. Is that right?
Yes that is right. As is often the case for bioinformatics programs, it 
isn't intended to be 'installed', you are just expected to add the 
directory where compilation happens to your $PATH. So they don't mind 
stretching the conventions.
> You mention in a comment in the patch that this program and other
> programs expect the "train files" to be in one place, but we are
> patching this line to account for the fact that we have installed them
> in another location.  Will the other programs have to be patched as
> well?
Yep, and I believe I have done so. Did I miss something?

If you mean other programs that use fraggenescan, they would most likely 
only call "run_FragGeneScan.pl" so I don't see an issue there.
> If so, do you think it would be better to let the files be
> installed in the unusual location chosen by upstream?
Not after the work I did trying to do the 'right' thing.. I would 
imagine this program will not likely be updated with much, and if there 
was major updates I would guess that they would require substantive 
changes to the package definition anyway.

[..]

Thanks for the thoughts. I hope there wasn't too much gut feeling in my 
reply.
ben