biocore_recipes

Conda recipes for biocore projects.

Setting up the build environment

We follow the instructions in the conda docs, but here's an overview of the process.

Since we have conda already installed, we update it and use it to install conda-build. In linux, we also install patchelf

$ conda update conda
$ conda install conda-build
$ conda install patchelf

Creating recipes

Most recipes were created using the skeleton command

conda skeleton pypi pckg

but they usually require some manual edits (setting requirements versions, some tests commands...).

To keep them up to date it should be enough to update their dependencies and version string, but it'd be nice if that was automatic... They can also be built from git tags or track branches, but here we're currently building them from PyPI releases (or a master branch).

Building packages

First, let's make sure everything is updated when building packages:

$ conda update conda conda-build patchelf

$ conda build --numpy 1.9 cogent
$ conda build --numpy 1.9 pynast
$ conda build --numpy 1.9 qcli
$ conda build --numpy 1.9 pyqi
$ conda build --numpy 1.9 emperor
$ conda build --numpy 1.9 biom-format
$ conda build --numpy 1.9 burrito-fillings
$ conda build --numpy 1.9 burrito
$ conda build --numpy 1.9 qiime-default-reference
$ conda build --numpy 1.9 qiime

Sharing packages

If registered in binstar (like PyPI, for conda builds) and logged in the build command will give, if successful, a command to update the binary package. It can be done automatically by configuring conda config --set binstar_upload yes. For example,

$ conda install binstar
$ binstar login
$ binstar upload ...pck-x.y.z-py27_0.tar.bz2

Testing

Let's test if installing works by creating a new, clean environment and installing it from binstar

$ conda create -n test_env python
$ source activate test_env
(test_env)$ conda install -c https://conda.binstar.org/jorge mypkg

Common issues

An error like ImportError: /lib64/libc.so.6: version GLIBC_2.14' not found ...` means that you're trying to install a package built in a newer machine in another one with an older GLIBC. If you intend to distribute it, try building it in an oldish machine.