Hi all,

I have a few general questions about best practices in tool development
and would like to collect a few opinions. 
Maybe the Intergalactic Utilities Commission can discuss some points at
their first meeting.

1. How to handle dependencies that are not guaranteed to exist for a
large time. Sometimes I'm very sceptical about whether upstream will
keep every software version for the next X years, which I will define in
my tools, e.g. some ftp server for binaries or some beta-versions of
actually used software (bowtie2?). Is it possible/wished to create a
repository for such software?

2. How to handle different compiler versions or other system level
changes? For example with the new gcc-4.7 some 'include'-definitions
changed and because of that bowtie2 is not compiling any more. Should we
add a feature to ship patches in our tools for such simple workarounds?
Or should we rather wait for a new upstream version and not support our
tool on such systems?

3. Should we standardize the version numbering of tools to reflect if a
update is important or not? 
For example something like foo.bar.baz. 
foo = major tool-dependency changing: expected result changes 
bar = minor tool-dependency changing due to bug fixing: results can
change but it is not expected
baz = no expected changes in the result due to wrapper changes
(help-text, adding of new parameters, etc.).

I think in the end we need to decide how much effort do we put into
reproducibility over the next X years and how do we guarantee that,
either as Community or as Intergalactic Utilities Commission.

What did you think?

[1] http://gcc.gnu.org/gcc-4.7/porting_to.html

Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/

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