{bio} [goolf-1.7.20] QIIME-1.9.1 and dependencies (WIP)

[pescobar]

This works for me but it won't work out of the box for others. The BLAST easyconfig has a hardcode path to my blastdb files. Many source tarballs need to be manually downloaded.

I have tested all the easyconfigs so it supports offline installation (no internet access required to download python libs)

This is heavily based on a previous PR from @boegel #1057 and adapted to the requirements of latest QIIME 1.9.1

[boegel]

@pescobar If you intend to get this merged, it'll have to be split up into smaller PRs, this is going to be impossible to merge.

[pescobar]

@boegel not urgent for me to get it merged "soon". I added the PR mainly to have it as reference and in case it's useful for anyone else but in any case I will try to get it merged in coming weeks/months unless you have a better one for QIIME

[verdurin]

We've had a request for this, so I'd be happy to help.

[fgeorgatos]

Splitting the PR has the downside of very fragmented merge attempts with
all the extra work that it implies... It has happened before a few times !

On Wednesday, 24 August 2016, Adam Huffman notifications@github.com wrote:

We've had a request for this, so I'd be happy to help.

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[pescobar]

This PR requires an easyconfig for matplotlib/1.4.3. QIIME doesn't work with higher matplotlib versions

[boegel]

@pescobar do you remember why you had to include this exactly?

[pescobar]

@boegel one of the perl extensions in my Perl easyconfig required it.

I think this one: https://github.com/hpcugent/easybuild-easyconfigs/blob/5e8d4bdce1bc259e51a1794a21d4a81257c9f6aa/easybuild/easyconfigs/p/Perl/Perl-5.22.2-goolf-1.7.20.eb#L534

[verdurin]

@pescobar - would you accept PRs to provide this for foss and intel 2016b?

[pescobar]

@verdurin I cannot commit to spend too much time with this PR this week. I am overloaded of work.

I can try to work a little bit on this but I cannot commit sorry

[pescobar]

@verdurin btw, if your need to get QIIME installed quick check this one #3868

[boegel]

@verdurin I'm working on QIIME with intel/2016b in bits & pieces, PRs working towards it coming up

Once that is in place, doing the same with foss/2016b should be trivial.

@verdurin Are you up for reviewing my incoming PRs?

[RvDijk]

@boegel ping on the intel and foss versions?

[boegel]

@RvDijk little progress I'm afraid... This is certainly still on my to do list, but it's buried below other stuff that needs to be taken care of first.

I doubt I'll have a lot of time for this, until mid-February.

Are you willing to help out? Maybe we can join efforts on this together with @verdurin?

[verdurin]

@boegel - just received a reminder from a user about this, so happy to collaborate, yes.

[RvDijk]

@boegel I'm also happy to help.

[boegel]

@verdurin, @RvDijk I opened a WIP PR with the QIIME easyconfig (see #3993), but most of the dependencies are still missing... I have some of them as WIP (e.g. biom-format, emperor, scikit-bio), I'll look into those ASAP.

Any help here is appreciated, each of the dependencies should be checked whether they're still a dep, which version requirements they have, etc.
See https://github.com/biocore/qiime/blob/master/setup.py

[migueldiascosta]

@pescobar, this PR is being closed for the following reason(s): no activity for > 6 months, obsoleted by more recent PRs.
Please don't hesitate to reopen this PR or add a comment if you feel this contribution is still relevant.
For more information on our policy w.r.t. closing PRs, see https://easybuild.readthedocs.io/en/latest/Contributing.html#why-a-pull-request-may-be-closed-by-a-maintainer