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. With: 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? Björn [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/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
