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update guidelines
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daler committed Aug 30, 2016
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Expand Up @@ -140,6 +140,22 @@ currently pin in
If you need to pin another library, please notify @bioconda/core, and we will
set up a corresponding environment variable.

It's not uncommon to have difficulty compiling package into a portable conda
package. Since there is no single solution, here are some examples of how
bioconda contributors have solved compiling issues to give you some ideas on
what to try:

- [ococo](recipes/ococo) edits the source in `build.sh` to accommodate the C++ compiler on OSX
- [muscle](recipes/muscle) patches the makefile on OSX so it doesn't use static libs
- [metavelvet](recipes/metavelvet), [eautils](recipes/eautils),
[preseq](recipes/preseq) have several patches to their makefiles to fix
`LIBS` and `INCLUDES`, `INCLUDEARGS`, and `CFLAGS`
- [mapsplice](recipes/mapsplice) includes an older version of samtools; the
included samtools' makefile is patched to work in conda envs.
- [mosaik](recipes/mosaik) has platform-specific patches -- one removes
`-static` on linux, and the other sets `BLD_PLATFORM` correctly on OSX
- [mothur](recipes/mothur) and [soapdenovo](recipes/soapdenovo) have many fixes to makefiles

## General command-line tools
If a command-line tool is installed, it should be tested. If it has a shebang
line, it should be patched to use `/usr/bin/env` for more general use.
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