A script that sets up the environment is needed.

[likit]

Installing conda-rdkit and create a conda environment for the pipeline is quite difficult for users. To facilitate the process, we should have a Python script that does all the work. I'll be working on that.

[chaninn]

Thanks for the heads up, that would be nice to have.

On Fri, Mar 27, 2015 at 6:11 PM, Likit Preeyanon notifications@github.com
wrote:

Installing conda-rdkit and create a conda environment for the pipeline is
quite difficult for users. To facilitate the process, we should have a
Python script that does all the work. I'll be working on that.

—
Reply to this email directly or view it on GitHub
#2.

Associate Professor Chanin Nantasenamat, Ph.D.
Head, Center of Data Mining and Biomedical Informatics
Faculty of Medical Technology, Mahidol University
999 Phutthamonthon 4 Road, Salaya, Nakhon Pathom 73170
Tel. 02 441 4371 ext 2715
Fax 02 441 4380

[likit]

I uploaded install.py, which can download and build rdkit. However, upon further consideration, I'm now thinking of using conda to build a conda package and upload it to binstar instead. Likewise, I will use setuptools to make a Python package and upload it to pypi. This way users can use either conda or pip to install our package. Conda and setuptools can install specific version of all dependencies, so we won't have a problem when running our program on different machines/environments.

Here is a tutorial for conda build, if you're interested.
http://conda.pydata.org/docs/build_tutorials.html

[likit]

Turns out we can build a recipe for a package we need and then build a conda package from it. Next, we upload the build to binstar, so we can create an environment directly from the build. I started with a recipe for protpy, which is required for PCM workflow and pushed it to a new repo called conda-recipes. I'll create an organization account on binstar to keep all the build used in our projects. More on this later.

[chaninn]

Can you name the organization cdmbi

Thanks

On Sunday, March 29, 2015, Likit Preeyanon notifications@github.com wrote:

Turns out we can build a recipe for a package we need and then build a
conda package from it. Next, we upload the build to binstar, so we create
an environment directly from it. I started with a recipe for protpy, which
is required for PCM workflow and pushed it to a new repo called
conda-recipes. I'll create an organization account on binstar to keep all
the build used in our projects. More on this later.

—
Reply to this email directly or view it on GitHub
#2 (comment).

Associate Professor Chanin Nantasenamat, Ph.D.
Head, Center of Data Mining and Biomedical Informatics
Faculty of Medical Technology, Mahidol University
999 Phutthamonthon 4 Road, Salaya, Nakhon Pathom 73170
Tel. 02 441 4371 ext 2715
Fax 02 441 4380

[likit]

Definitely.

[chaninn]

Great.

On Sunday, March 29, 2015, Likit Preeyanon notifications@github.com wrote:

Definitely.

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Reply to this email directly or view it on GitHub
#2 (comment).

Associate Professor Chanin Nantasenamat, Ph.D.
Head, Center of Data Mining and Biomedical Informatics
Faculty of Medical Technology, Mahidol University
999 Phutthamonthon 4 Road, Salaya, Nakhon Pathom 73170
Tel. 02 441 4371 ext 2715
Fax 02 441 4380