Name conflict

[Carlos Morais]

Hi,

    I am interested in using SNAP, it seems to be really fast. I wonder how would you suggest to name it since there is already a (much older) software called SNAP (Semi-HMM-based Nucleic Acid Parser): http://korflab.ucdavis.edu/software.html

Regards,
    Carlos

[Carlos Morais]

Any suggestions?

[Bill Bolosky]

I changed the binary to be SNAP instead of snap so that it won’t conflict with the other tool on systems that are case-sensitive, meaning Unix/Linux machines.  I don’t believe that the other snap runs on Windows, so that doesn’t matter.  However, someone else pointed out that MacOS has a case insensitive file system (though it’s less clear that the other snap runs on MacOS).  I’m not quite sure what to do, but I’m reluctant to just completely change the name of the tool, it would be confusing at this point and doubtless would just conflict with something else.  (I’d probably come up with bwa for Bolosky’s Wicked Aligner J.)

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[Carlos Morais]

Thanks for the reply, but I think difference by case would be confusing anyway.
I'm gonna use snap-ucb

[Carlos Morais]

Just complaining again.

I am installing a software which depends on this snap and having trouble for it not to execute Korflab's snap.

The other snap is still very in use and I only see this problem incresing in the future.

In my humble opinion, you should take very seriously the possibility of renaming it, for the sake of your users.

Some suggestions:
snap-ucb
ucb-snap
bsnap (B from "Bolosky" and "Berkeley")
snap-align
snap-aligner

[Ying W]

You can do a `which snap` to figure out where your snap executable is and then rename it using `sudo mv /location/to/snap /location/to/snap-newname

[Carlos Morais]

Sorry Ying, you completely failed to understand the issue.

SNAP (Scalable Nucleotide Alignment Program) is an excellent name, but it has already been taken.
SNAP (Semi-HMM-based Nucleic Acid Parser) is the homonymous (older) software from Korf Lab (http://korflab.ucdavis.edu/software.html)

This may not seem a big issue, but it is. The binaries having the same may cause (imagine environments with dozens of users and hundreds of interdependent software):
1) Careless installation of one software may override binaries from another
2) Install binaries in different places and loose track of what snap are you calling from your PATH
Just rename the binaries? Then...
3) There will be no uniform distribution, different admins will rename differently
4) Users run one software with the other in mind inside their pipelines
5) Software that depends on SNAP to work need to have their code changed and/or recompiled to work with the alternative name.

In short, the way SNAP binaries are named makes this software a TROUBLEMAKER.
It is workable having the same name of others (my own name is very popular here).
What I am asking THE AUTHORS is to CHANGE the BINARIES distributed while the software is young.
In the future, this problem tends to GROW BIGGER AND HARDER to deal with.

Thanks for the attention.

Carlos

[Bill Bolosky]

I changed the name (again) to be snap-aligner (only for systems that use Makefile, so not Windows).  This is in 1.0dev.75.

 

--Bill

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[Carlos Morais]

Thanks A LOT, Bill.

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