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gt1 / biobambam2

Tools for early stage alignment file processing
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Conflicting executable names #44

Closed sjackman closed 7 years ago

sjackman commented 7 years ago

Biobambam2's bamtofastq conflicts with Bedtool's bamToFastq and Biobambam2's fastaexplode conflicts with Exonerate's fastaexplode. You may want to consider renaming these two tools. Adding a prefix to the tool names, such as biobambam-fastaexplode is a good way to avoid collisions.

gt1 commented 7 years ago

I think this is more of a packaging issue. This project exists for long enough that just renaming any of the programs at this stage is likely to be confusing people who are already using it.

sjackman commented 7 years ago

Hi, German. I'm packaging biobambam2 for Homebrew-Science. I plan to rename the two executables to biobambam-bamtofastq and biobambam-fastaexplode, unless you have an alternative suggestion.

mmokrejs commented 7 years ago

Hi German, I also propose renaming the binaries in a same way (a Gentoo package creator). Currently we have: https://cgit.gentoo.org/proj/sci.git/commit/?id=51fe11a3b2a3519a325f9cb86f1b27ea0cf9ec62

gt1 commented 7 years ago

Hi,

I would suggest to use configure's option --program-prefix to set a different prefix for the binaries.

Best, German

sjackman commented 7 years ago

For compatibility between distributions, it's best if we agree on the same solution. @mmokrejs Shall we set --program-prefix=biobambam to set the prefix of all executables, or rename only those two executables with known conflicts, bamtofastq and fastaexplode?

mmokrejs commented 7 years ago

I would rename just the two but I would add suffix, so bamtofastq_biobambam2 and fastaexplode_biobambam2. It is easier to locate the renamed binary in shel via bamtofastq and pressing TAB twice. ;-)

sjackman commented 7 years ago

I prefer hyphens to underscores. Easier to see and no shift required when typing. How about bamtofastq-biobambam2 and fastaexplode-biobambam2 Include or omit the 2 suffix?