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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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New installation instructions using Conda #2162

Closed cuttlefishh closed 8 years ago

cuttlefishh commented 8 years ago

@tanaes and @gregcaporaso please comment. Then let's merge and get these instructions online.

ghost commented 8 years ago

Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1725/

cuttlefishh commented 8 years ago

@gregcaporaso I see the build finished, but I can't see the the output. Does this allow us to see the new webpages? What needs to happen before the new webpages can go live?

gregcaporaso commented 8 years ago

@cuttlefishh, the build will not generate the html for you - generally you would do that locally to confirm that everything looks right. Have you done that yet? The scikit-bio instructions are relevant for this. Aside from confirming that the HTML looks right, I'll want to review/test the content. I will be able to do that by tomorrow, and post back here.

gregcaporaso commented 8 years ago

I have a few comments after reviewing the text. I haven't tested building myself though - could you do that and confirm that it looks good?

tanaes commented 8 years ago

I've been preferentially installing executables in my conda environments to minimize version conflicts between installations, and because conda is prepending $PATH with its own bin. On Thu, Jul 21, 2016 at 2:23 PM Greg Caporaso notifications@github.com wrote:

I have a few comments after reviewing the text. I haven't tested building myself though - could you do that and confirm that it looks good?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/biocore/qiime/pull/2162#issuecomment-234388475, or mute the thread https://github.com/notifications/unsubscribe-auth/AH6JALfsYIPgcWKXyijXY5E3SPXn1Zdgks5qX-NggaJpZM4JRRrq .

gregcaporaso commented 8 years ago

How do the conda docs recommend handling this?

mortonjt commented 8 years ago

@tanaes is right. The conda docs have some tutorials on how to do this.

Also put together a tutorial here on how to use it.

gregcaporaso commented 8 years ago

@mortonjt, that is covering setting environment variables (not what I'm asking about).

gregcaporaso commented 8 years ago

Note: I just want to make sure we're not telling users to do something that conda discourages, for example, since we're going to have to support users in working with whatever we tell them to do here. Really the ideal thing would be to link to something in the conda docs for this, since it's not QIIME-specific. That lets us have to maintain as little as possible. For example, if something changes with conda and these instructions were no longer relevant, we're going to have to figure that out and update our instructions. That's possible if we're telling users to do something that isn't officially supported. However, if this is how users are supposed to do this, it's fine to include this part of the instructions.

wasade commented 8 years ago

Fwiw, I believe that's effectively what bioconda does with, say, blast. From what I can tell, conda is near analogous to setting --prefiex=foo where foo is the base path of your environment

On Jul 21, 2016 14:56, "Jon Sanders" notifications@github.com wrote:

I've been preferentially installing executables in my conda environments to minimize version conflicts between installations, and because conda is prepending $PATH with its own bin. On Thu, Jul 21, 2016 at 2:23 PM Greg Caporaso notifications@github.com wrote:

I have a few comments after reviewing the text. I haven't tested building myself though - could you do that and confirm that it looks good?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/biocore/qiime/pull/2162#issuecomment-234388475, or mute the thread < https://github.com/notifications/unsubscribe-auth/AH6JALfsYIPgcWKXyijXY5E3SPXn1Zdgks5qX-NggaJpZM4JRRrq

.

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gregcaporaso commented 8 years ago

I know that it works, but that still doesn't answer my question about whether we're suggesting something that isn't officially supported (and therefore might break without warning). I did some searching and haven't found an answer. Let's see what they say in reply to this.

gregcaporaso commented 8 years ago

I made some changes and tested the HTML - closing this in favor of #2164.

I ended up dropping the part about modifying files in the environment's bin directory. I'm really not comfortable with that pending a reply to my question about whether that's ok on the Anaconda forum. But aside from that, I think it's probably just going to add confusion. The users who are following these instructions are either going to be novice users who won't need to do that, or power users, who would be able to figure it out on their own.

@cuttlefishh, thanks so much for pushing this forward. I'm going to post the HTML to the website now so this will be live.

ghost commented 8 years ago

Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1726/