search

amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
https://www.microsoft.com/en-us/research/project/snap/
Apache License 2.0
288 stars 66 forks source link

SNAP name conflicts #41

Closed sjackman closed 9 years ago

sjackman commented 9 years ago

The SNAP name is already taken by the SNAP (Semi-HMM-based Nucleic Acid Parser) gene prediction tool, doi:10.1186/1471-2105-5-59. Conflicting names cause all sorts of trouble and confusion when referring to software and also when installing software. Would you consider renaming the tool? For example

❯❯❯ brew install snap-aligner
==> Installing snap-aligner from homebrew/homebrew-science
Error: Cannot install snap-aligner because conflicting formulae are installed.

  snap: because both install bin/snap
ttriche commented 9 years ago

Also gmap/Gsnap. And snappy too.

Maybe "RTFM" (Really Thorough FASTA Mapper)? :-)

--t

On Dec 31, 2014, at 1:18 PM, Shaun Jackman notifications@github.com wrote:

The SNAP name is already taken by the SNAP (Semi-HMM-based Nucleic Acid Parser) gene prediction tool, doi:10.1186/1471-2105-5-59. Conflicting names cause all sorts of trouble and confusion when referring to software and also when installing software. Would you consider renaming the tool? For example

❯❯❯ brew install snap-aligner ==> Installing snap-aligner from homebrew/homebrew-science Error: Cannot install snap-aligner because conflicting formulae are installed.

snap: because both install bin/snap — Reply to this email directly or view it on GitHub.

sjackman commented 9 years ago

Snapper?

bolosky commented 9 years ago

So then the RNA version would be snapperr? ☺

From: Shaun Jackman [mailto:notifications@github.com] Sent: Wednesday, December 31, 2014 1:55 PM To: amplab/snap Subject: Re: [snap] SNAP name conflicts (#41)

Snapper?

— Reply to this email directly or view it on GitHubhttps://github.com/amplab/snap/issues/41#issuecomment-68471351.

sjackman commented 9 years ago

No, it would be called Snappier, clearly.

sjackman commented 9 years ago

Any resolution to this issue? It's a tad annoying that the SNAP gene prediction software and SNAP aligner can't be installed at the same time. Would you consider adding a suffix to the bin/snap executable to make the name unique? snap-map, snappier, snap-aligner, ampsnap, anything really.

bolosky commented 9 years ago

I'm going to change it to SNAP (all caps) for the Linux build (Windows file names are case insensitive, but I doubt that the other snap works on Windows anyway). Hopefully that will both preserve the name of the tool and avoid file name conflicts. SNAP is an awful backronym anyway (Scalable Nucleotide Alignment Program), so all caps kind of makes sense.

bolosky commented 9 years ago

I changed the Linux/MAX output binary name to SNAP instead of snap. Make clean will delete snap, but if you've installed it somewhere, it's up to you to get rid of it.

sjackman commented 9 years ago

Mac OS uses a case-insensitive file system.

mr-c commented 9 years ago

This is also a problem for Debian where package names are all lowercase and Ian Korf's snap is already packaged.

As for humans, I find 'snap' and 'SNAP' easy to confuse conversationally.

mr-c commented 9 years ago

Oh, I just saw that the project was renamed on the dev branch. Very glad to hear it.

https://groups.google.com/d/msg/snap-user/VSJf1wygiog/O8BCmGBPkL0J

sjackman commented 9 years ago

The new name is snap-aligner.