[Shipwright] Shipwright help

[Benjamin Hitz]

On May 16, 2011, at 3:13 PM, Benjamin Hitz wrote:

> 
> Let's say (real example)
> I have a git distribution of a perl package which normally depends on a cpan module.  I want to make it depend on the git/repo version of that perl module instead.
> 
> The example is I have a perl package (based on a package called Bio-Graphics-Browser2) which depends on Bio-Perl.  However, Bio-Perl (like Gbrowse itself) is highly unstable and often needs to be updated directly from git (or svn, but you follow).
> 
> So when I import the main package it has a line for
> requires: 
>  cpan-Bio-Perl: 
>    version blah
> 
> I can change this to 
> requires:
>  bioperl-live.git: (which is what Shipwright calls the thing when I import the git repo)
> 
> Should I set a version?  Or does this map to revision number, or should I leave this blank?
> 
> And this is only for perl modules... if I have a perl module that depends on some C program (and a bunch of these do) can I specify in the require.yml or do I have to write a custom build script?
> 
> Thanks,
> Ben
> 
>> 
>> Hi Ben
>> 
>> When importing, it's true that Shipwright will run Build.PL, its aim is to
>> get a more accurate dependency list, no other intensions at all.
>> you can specify --require-yml to tell Shipwright the dependency directly, in
>> this case Shipwright won't run Build.PL at all.
>> I attached an example of require.yml so you know what it looks like.
>> 
>> When building, the build script for each dist lives in scripts/dist-name/build,
>> you can hack it what ever you want, look Shipwright::Manual::CustomizeBuild
>> for more info about this.
>> 
>> 
>> best wishes
>> sunnavy
>> 
>> On 11-05-13 10:48, Benjamin Hitz wrote:
>>> Fernan, Nicholas, Sunnavy -
>>> 
>>> I have some general questions about Shipwright and in particular trying to import a couple of perl mods:  Bio::DB::BigFile (Bio-BigFile-1.06) and Bio::DB:Sam (Bio-SamTools-1.28).  These are (optional, but I need them) dependencies for other the main application (GBrowse, which has a big tangled dep tree).
>>> 
>>> Where I am a little stuck is that Bio-BigFile depends on a C software "package" (actually just 2 files a .h and library for linking) called jkent.   The problem is that the Build.PL for Bio-BigFile is written strangely and interactively.  When shipwright import is run it of course tries to install the cpan package, which in turns looks for the jkent libraries.  I can put the jkent files in the shipyard... but I am not sure how to answer the questions about where to tell BigFile to find the files it needs... It can use an env variable to find them, so I guess there must be some protocol for setting an ENV variable within the shipyard build process.
>>> 
>>> I guess what is tripping me up philosophically is that when the Build script is run - it is looking for the libraries ON THE BUILD MACHINE not the final destination... how do I specific "use the libraries that were installed when shipwright installs the jkent from source).    
>>> 
>>> Hope that make some amount of sense.  This is my first attempt at using Shipwright, but if it works for this project I would like to use it for some Catalyst apps (yet-to-be-written) as well.
>>> 
>>> Also, if there is a mailing list or irc channel, you could point me to it...
>>> 
>>> Thanks for your time,
>>> Ben
>>> 
>>> 
>>> --
>>> Ben Hitz 
>>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
>>> Stanford University ** hitz at genome.stanford.edu
>>> 
>>> 
>>> 
> <require.yml>
>> 
> 
> --
> Ben Hitz 
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
> Stanford University ** hitz at genome.stanford.edu
> 
> 
> 

--
Ben Hitz 
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** hitz at genome.stanford.edu