bedtools: add manpage

[arjanvandervelde (Arjan van der Velde)]

Hello. I'd like to add a detail to this port that was accidentally left out in the original submission.

Thanks.

-- Arjan

[ryandesign (Ryan Carsten Schmidt)]

Is the manpage really not included in the distfile? And cannot be downloaded from any web site? Where did you get the manpage?

[arjanvandervelde (Arjan van der Velde)]

Hi,

The man page was generated using the source (there is a separate documentation build directory that uses Sphinx to build documentation) but given the heavy dependencies (sphinx which depends on python) for generating just a man page, I figured a pre-generated version would be easier. Also, I have not found a way to control what pyXX-sphinxs gets installed when listed as a dependency which in my case means that macports starts installing a different python version than the one I have installed. In short, I found it less of a hassle to have a pre-generated manpage for people who'd like to build from source.

-- Arjan

[ryandesign (Ryan Carsten Schmidt)]

Replying to vandervelde.ag@…:

The man page was generated using the source (there is a separate documentation build directory that uses Sphinx to build documentation) but given the heavy dependencies (sphinx which depends on python) for generating just a man page, I figured a pre-generated version would be easier.

I understand. I have two problems with this:

1. It's an additional thing for the maintainer of the port to need to remember to do every time the port is updated. I could easily see this being forgotten and the manpage becoming out of sync with the program.
2. It's an additional 162K file that all MacPorts users would need to download and keep on their disk, regardless of whether they're interested in bedtools or not. This is a disproportionately large file for the files directory; it's 100 times greater than the average size of a Portfile.

Therefore I'd like to have the bedtools port build the manpage from its sources, even if you have to add build dependencies. Most users won't have to build from source anyway; they'll get a ​prebuilt binary and won't be made to install the build dependencies. And even if they do build from source, there's a good chance they already have python27 installed because it's depended on my many other ports.

Also, I have not found a way to control what pyXX-sphinxs gets installed when listed as a dependency which in my case means that macports starts installing a different python version than the one I have installed. In short, I found it less of a hassle to have a pre-generated manpage for people who'd like to build from source.

py-sphinx has subports for each supported version of Python, as do all Python module ports. You don't declare a dependency on the py-sphinx stub port; you declare a dependency on the specific subport you want to use. I suggest using py27-sphinx because of python27's popularity.

[arjanvandervelde (Arjan van der Velde)]

Ok. Please find the updated Portfile patch attached. The bedtools.1 is no longer applicable. Thanks.

-- Arjan

[ryandesign (Ryan Carsten Schmidt)]

Thanks. I committed it in r113565 with these changes:

• made py27-sphinx a build dependency instead of a library dependency
• specified the full path to sphinx-build-2.7, just in case
• used the -W argument to system instead of manually using cd

[arjanvandervelde (Arjan van der Velde)]

Thanks you!