Upgrading qiime in bio-linux from 1.7 to 1.8

[bob-loblaw]

I was wondering if anyone had any experience with this? I know there is the qiime deploy script, which I'm going to try but I was hoping someone had some experience trying this.

[Palecomic]

The best place to ask about this is the bio-linux mailing list http://nebc.nerc.ac.uk/about-us/mailing-lists Tim Booth is pretty responsive.

Doesn't Qiime come installed as standard on Bio-linux though - so updates would be via apt and the standard package updater rather than the deploy script?

[bob-loblaw]

The best place to ask about this is the bio-linux mailing list http://nebc.nerc.ac.uk/about-us/mailing-lists Tim Booth is pretty responsive.

Doesn't Qiime come installed as standard on Bio-linux though - so updates would be via apt and the standard package updater rather than the deploy script?

Ah thanks. Yeah it does come with bio-linux as standard. Ah I see now, the built in packages with bio-linux can actually be updated through the normal ubuntu update manager, I think I already knew that, I must be a bit slow today. Thanks for the reply!

Edit: After updating qiime is still version 1.7, I'm guessing the bio linux people just haven't rolled out the new version yet.

[bstamps]

Have you tried QIIME-Deploy? https://github.com/qiime/qiime-deploy

Relatively simple way to upgrade/install QIIME on any Linux box.

[bob-loblaw]

Have you tried QIIME-Deploy? https://github.com/qiime/qiime-deploy

Relatively simple way to upgrade/install QIIME on any Linux box.

I haven't tried it, I'm not really sure how it'll affect the installation of qiime already on the machine.

[bstamps]

Do you need QIIME 1.7 still functional? Basically if QIIME was installed by its defaults (~/qiime_software/) it should update any packages inside of this directory, install a qiime-1.8.0-release/ directory, and then activate 1.8. You can check out https://github.com/qiime/qiime-deplo...sions-of-qiime if you want to keep multiple versions of QIIME going for what I'm assuming would be consistency-for-publication reasons, or comparisons.

[bob-loblaw]

Well I'm not too worried about 1.7 being overwritten, as long as 1.8 is fully functional. I'm just worried that it'll run into a problem and I'll be left with 2 half installed versions of QIIME, neither completely functional. I may just try it, see how it goes.

[bstamps]

Give it a shot- I've never had issues with App-Deploy before. The last script executed is the activation of the qiime-1.8.0-release/ directory, so if there are any other failures prior, you'll still have 1.7.0 active and working.

[Andrea Campisano]

any updates on this

I'm in exactly the same situation and i was wondering how the experiment went... did you try deploying the Qiime 1.8 version?

How did it work? Did it erase the 1.7 or did they both coexist?

I am very worried about doing this as i would probably need to reinstall if the 1.8 installation failed.
thanks
Andrea