To add, for Bioperl-related modules add the specific modules you use for your distribution. For instance, if you require Bio::SeqIO::fastq then add that as a dependency.
The reason I bring this up is we are in the process of breaking out a lot of bioperl code into independent modules; if you do something like add 'Bio::Root::Root' as a dependency (a common problem for some reason) then your distribution will likely not work when these land on CPAN. chris On May 3, 2013, at 12:29 PM, Shlomi Fish <shlo...@shlomifish.org> wrote: > Hi Héctor, > > On Fri, 3 May 2013 11:42:16 +0200 > Héctor Valverde Pareja <hvalve...@uma.es> wrote: > >> Hi coleagues! >> >> I have a question about CPAN installation progress. I have recently upload a >> new module to CPAN (Molevol::Complex). It is a part of my work in Molecular >> Evolution of Protein Complexes. This module needs several requirements to >> work properly, such as PAML software >> (http://abacus.gene.ucl.ac.uk/software/paml.html) and DSSP >> (http://swift.cmbi.ru.nl/gv/dssp/). Also it needs Bioperl and Bioperl-run. >> The two formers programs must be installed manually (not through CPAN), so I >> want that during the installation progress of my module, CPAN test if the >> environment variables $ENV{PAMLDIR} and $ENV{DSSPBIN} are correctly declared. >> > > You can put whatever you want in Makefile.PL or Build.PL before writing the > "Makefile" or "Build" files, so you can make sure these things are set there. > >> Also, I want to ask if it is possible to launch Bioperl and Bioperl-run >> installation if they are not installed, apart from the other required >> modules. > > If they are on CPAN, you can list them as dependencies in > PREREQ_PM/'requires'/etc. > >> >> I think this questions are so basic, I am a novice in program distribution >> and I barely understand the correct configuration of Makefile.PL and Makefile >> to reach my mentioned purposes. > > See: > > http://perl-begin.org/topics/cpan/ > > Regards, > > Shlomi Fish > >> >> Thanks >> >> Héctor Valverde >> Universidad de Málaga >> Spain > > > -- > ----------------------------------------------------------------- > Shlomi Fish http://www.shlomifish.org/ > Chuck Norris/etc. Facts - http://www.shlomifish.org/humour/bits/facts/ > > <Su-Shee> Also, .* is the most unspecific regex you can use. It’s like saying: > oh well match something of anything or nothing, and, please, a lot of it ;) > > Please reply to list if it's a mailing list post - http://shlom.in/reply .
