cufflinks: convert to package

[thomas]

Rationale:

• first:
  There is no new release since ~2 years, the current
  one won't build w/o internal files from samtools'
  source tree. (Also it looks like that it needs a rather
  old version of samtools?)

• second:
  This package is the only one in the system that uses
  boost libraries, thus requiring boost to be installed
  with the library bloat.

[donald]

Your whitepace is ugly :-)

cat >$PREFIX/profile <<-EOF
<tab>PATH=$PREFIX/bin:\$PATH
<space><space>LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH
<tab>if [ -d $PREFIX/.compatlibs ]; then LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH ; fi
<space><space>export LD_LIBRARY_PATH

which becomes

PATH=$PREFIX/bin:\$PATH
<space><space>LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH
if [ -d $PREFIX/.compatlibs ]; then LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH ; fi
<space><space>export LD_LIBRARY_PATH

in the profile. Wanna fix cosmetics? If not, just merge yourself. Okay with me.

[pmenzel]

I am still not convinced that pkg-source should be used for distributing stuff built with bee for MarIuX. There is no demand to have different versions of cufflinks around.

https://github.com/cole-trapnell-lab/cufflinks/pull/122 should fix the build issues.

What’s the problem with having boost users?

[thomas]

Your whitepace is ugly :-)

Oops, this is right -- and whitespace-juggling isn't my style either 8)

distributing stuff built with bee

The current package won't build anymore, and we have no clue what pipelines rely on exactly this version with its specific bugs/features. Take a look at the git issues how some output charactristics of this software change w/o beeing marked. I'm not so deep in that topic to judge if this matters. So I'll propose to freeze this piece of software.
(And leave it to people who can handle it -> ie. Sven :)

Additionally this gives new head-room to update boost at will, and here we should clearly switch to a 'header only' install, since the majority of projects that use boost just use the headers.
This will additionally avoid upcomming trouble with python packages that use boost-libs, namely libboost_python, and libboost_numpy -- I don't even know against which python version the current ones are build: python-2.x?, UCS16 or UCS32 flavour? But one thing I clearly know they won't be of any use with python-3.