[Biopython-dev] List of Biopython dependencies

Eric Talevich eric.talevich at gmail.com
Wed Jan 8 22:51:45 UTC 2014

On Wed, Jan 8, 2014 at 1:55 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Wednesday, January 8, 2014, Eric Talevich wrote:
>> Folks,
>> It appears that there are two lists of Biopython dependencies on the wiki:
>> http://biopython.org/wiki/List_of_applications_executed_via_Biopython
>> http://biopython.org/wiki/Download#Required_Software
>> There is potential for confusion here. Shall we merge these lists on the
>> Download page?
> Tiago started the list of applications page while updating the
> buildbots - it is as noted a work in progress. Maybe it should
> be just command line applications, which can then be linked
> to from the downloads page?

So the list of command line applications on the Download page would be
moved to the separate Wiki page? Seems reasonable if the list is long.

We could follow Debian's approach of splitting the list into Depends
>> (strict requirements, e.g. Python), Recommended (non-essential but
>> important, e.g. numpy and reportlab), and Suggested (everything else).
> That split makes sense for libraries, but is it also sensible
> for command line applications Biopython can call?

The sub-headings could be:
- Required software
- Recommended Python libraries [needed to enable significant functionality]
- Additional Python libraries [used by individual Biopython modules for
additional features]
"In addition Biopython includes wrapper code for calling a number of third
party command line tools [link]"

I imagine this format would be useful to sysadmins (and maybe distro
package maintainers, too). But it may be just as well to merge the
"required" and "recommended" lists and just note caveats inline as is
currently done.

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