[Debian-med-packaging] Wrapper for spades (Was: spades_3.6.2+dfsg-1_amd64.changes ...)

[Sascha Steinbiss]

Hi Andreas,

>>>>> Something that caught my eye is that SPades includes a copy of the RSA
>>>>> MD5 implementation, which contains an advertising clause which is
>>>>> probably not DFSG compliant. It might be possible to patch the code
>>>>> similar to [1] (replace with Colin Plumb's free implementation).
>>>>> Interesting that other packages retain that code (e.g. [2]).
[...]
> True. Will give it a thourough look later. Yesterday I wanted to make
> sure that Samtools can migrate to testing because it would also have
> been holding up REAPR.

Sometimes problems solve themselves. Looks like the problematic md5.h
can just be excluded from the package with no ill effects.

>>>> Any opinion about the wrapper issue?
>>>
>>> I don't feel so strongly but tend to agree with Joey Hess's stance [1]
>>> and would consider SPAdes to be an interface here. So I'd propose to
>>> move all upstream executables to /usr/lib/spades/bin and symlink both
>>> /usr/bin/{dip,tru}?spades and /usr/bin/{dip,tru}?spades.py to their
>>> counterparts in /usr/lib/spades/bin. From what I gather from upstream
>>> the original 'spades' binary is not meant to be run directly anyway.
>>> This could mean having to patch the python wrapper to force the use of
>>> the /usr/lib version of the original 'spades' binary.
>>
>> Installing files to /usr/lib/spades/bin is one part of my suggestion.
>> If users are not supposed to call the programms directly we should even
>> stay away from linking those binaries that do not provide a direct user
>> interface to /usr/bin.  That why I was considering the wrapper instead
>> who sets the PATH and calls the according *.py files which then can
>> find the proper binaries.

I tried switching to the wrapper but when trying to run it, it seems to
be trying to access other files (e.g. VERSION) in a wrong directory.
Looks like I might need some more time...

Cheers
Sascha


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