Comments (6)
The intention is for them to be used together (see .travis.yml). Basically, some of the reqs are not available in conda. The preference for conda over pip is that it is much more reliable than pip especially for scipy and matplotlib.
from american-gut.
However, if one doesn't use conda he will have problems with installing ag. You should maybe write an INSTALL.md to explain the bootstraping in more details.
from american-gut.
It's not feasible to support everyones specific environment and our
intention is to support the general case on Linux and OSX. conda is not a
requirement itself, but it greatly simplifies setup of the environment, and
is a standard in the scientific python community. In fact, I think
everything in the pip list has at this point migrated to conda. That being
said, I do agree that having an INSTALL.md would be useful to include in
the repository. We would also be excited for a pull request that would
expand pip support if you're interested in contributing.
On Wed, Mar 9, 2016 at 11:28 AM, Ivo Ugrina [email protected]
wrote:
However, if one doesn't use conda he will have problems with installing
ag. You should maybe write an INSTALL.md to explain the bootstraping in
more details.—
Reply to this email directly or view it on GitHub
#203 (comment)
.
from american-gut.
Just to be clear, I completely understand that it is not possible to satisfy everyones wishes and I really value the time and effort you've included in making this free and open 👍
As for the pip, I'm working on INSTALL.md for Debian 8 (bare), pip, virtenv ;) You'll get the pull request soon I hope :)
from american-gut.
Ah, that's fantastic! Looking forward to it, and thank you for prodding the code :)
from american-gut.
Resolved with commit #211
from american-gut.
Related Issues (20)
- Add round 8 acc to processing notebook
- Processing Notebooks HOT 1
- Zeros truncated in AG data mapping file HOT 5
- The shared_otus ipynb tries to download a file that no longer exists HOT 1
- Add Travis CI
- HMP table does not have taxonomy HOT 1
- Cannot import biom file in R HOT 7
- Mislabeled metadata HOT 2
- We need a contributing.md document
- Primary processing revitalized HOT 1
- Conflicting Python resources and virtualenvs HOT 8
- Analysis Summary Pipeline
- Generate PNG instead of PDF for per-sample-results HOT 4
- install trouble - conflicting ipython requirements HOT 11
- The way American-Gut repo was intended to be used? HOT 5
- Creation of 18S processing notebooks
- Latest ipymd does not play well with ipython notebooks HOT 1
- Help running module2_v1.0 notebook HOT 1
- nbviewer error
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from american-gut.