brokit-wrapped applications that are not currently installed in the QIIME VM

[gregcaporaso]

related to #19 (see comment from @josenavas)

• usearch (but we can't install that)
• clustalw (1.83, which is what cogent wraps, is available from here)
• mafft (see qiime-deploy-conf's #36) - I can't find the wrapped version (6.602), and a slightly later version (6.815b, installed from .deb) fails the brokit unit tests; it turns out that I do have the PyCogent-wrapped version installed on compy though.
• FastTree v1 (do we need this?) available here

[antgonza]

We can add the last 3 to the qiime deploy, do you have the links?

BTW Which version of FastTree are we installing right now? How do we intend
to call v1 and current version (FastTree and FastTreev1)?

[josenavas]

I think the current app controller expects for FastTree, so we probably will need to modify it so it is waiting for FastTreev1.

[gregcaporaso]

I can't get FastTree v1 tests to pass with any of several versions of FastTree v1.x.x. I tried v1.0.0, v1.0.5 (the last of the v1.0.x series) and v 1.9.0 (the last of the v1.x.x series)...

[wasade]

Can we just drop v1?
On Apr 21, 2014 12:07 PM, "Greg Caporaso" [email protected] wrote:

I can't get FastTree v1 tests to pass with any of several versions of
FastTree v1.x.x. I tried v1.0.0, v1.0.5 (the last of the v1.0.x series) and
v 1.9.0 (the last of the v1.x.x series)...

Reply to this email directly or view it on GitHubhttps://github.com//issues/20#issuecomment-40959139
.

[antgonza]

Should we remove?

[rob-knight]

yes

On Apr 21, 2014, at 12:12 PM, Antonio Gonzalez <[email protected]mailto:[email protected]> wrote:

Should we remove?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/20#issuecomment-40959595.

[gregcaporaso]

+1

This is now QIIME's #1516, and also discussed in #19.