tarball downloads?

[deth...@stanford.edu]

Hi Folks,

Is there a different source for PhyloSift tarballs, since apparently the UC Davis server that used to provide them is dead?
(as mentioned here: https://groups.google.com/forum/#!topic/phylosift/VurF2lB8yBs )

Or is GitHub now the only install option?

And I found the marker database at Figshare, but the file I got is named 'markers_20140913.tgz'.  Is this really the new version, since the name suggests otherwise?

Thanks!
Les

[Guillaume Jospin]

That's the current version we could upload on short notice.

I have a more updated version that I am hoping to push online next week.

There is no automatic download of the markers right now.

I forgot that's how we distributed the package as well. I'll have to post one of those online somewhere.

So yes, right now github is the only place to download the code.

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[Les Dethlefsen]

Thanks!  I’m looking forward to trying PhyloSift on my data.  I’ve made the attempt to use the GitHub installation and the database from FigShare, but I haven’t got it working yet.  I think the ncbi taxonomy data is the current problem.

Les

Les Dethlefsen
Relman Lab
Stanford University
deth...@stanford.edu

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[Guillaume Jospin]

Somehow one of the links out there does not include the ncbi archive.

You should be able to find it here: https://figshare.com/articles/PhyloSift_markers_database/5755404

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[Les Dethlefsen]

Well, I got the ncbi taxonomy, but I still have a bunch of additional dependencies I need to install.  If you could make a tarball available it would save me a lot of work!  It doesn’t solve the issue for other users, but if you’re willing I could provide a shared folder via my Stanford Box account where you could upload it.

Separate question: does the marker DB I got from Figshare include the extended markers?

Les

Les Dethlefsen
Relman Lab
Stanford University
deth...@stanford.edu

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[Guillaume Jospin]

Oh right I need to get that also. Sorry. I’ll upload it as soon as I can. 

No, the extended markers is completely different and the download is so large I am not sure we’ll make it available again or we’ll need to find an alternative solution. So far that dataset is not a priority. 

I just uploaded the tarball to figshare.

https://figshare.com/articles/PhyloSift_markers_database/5755404

Please let me know how it goes.

Sent from my iPhone

[Les Dethlefsen]

Thanks for the rapid response!  Definitely easier to use the tarball than what I was looking at for installing all the dependencies manually.  

I got some errors for a while that I think all had to do with PhyloSift finding the markers. I thought I’d set up the phylosiftrc file to handle my scenario correctly (i.e. not checking for updates or trying to download, marker & ncbi directories correctly specified), but I’m not sure that the phylosiftrc file itself was getting invoked correctly or at all.  Simply making symbolic links within the phyloseq_v1.0.1 directory that pointed to the actual location of ‘markers’ and ‘ncbi’ seemed to work, though.

It’s running on the tutorial data right now…

Les 

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[Guillaume Jospin]

I just uploaded a newer version of the markers.

https://figshare.com/articles/PhyloSift_markers_database/5755404

[Les Dethlefsen]

Thanks, Guillaume!

Just checking though…what I just downloaded decompressed to 2.3Gb on my server, while the old markers file is larger at 2.9Gb.

The newer download contains version.txt that suggests a date from last August:

$ cat markers/version.txt 

20170830

The older file contains version.txt that lists the dead server, then a number I can’t interpret:

$ cat /relman01/shared/databases/PhyloSift/markers/version.txt 

http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift_markers

1413225596

So the smaller marker database is indeed the newest one I should be using?

Les

Les Dethlefsen
Relman Lab
Stanford University
deth...@stanford.edu

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[Guillaume Jospin]

Yes. We removed a bunch of markers that we were not very confident in. That’s why the size is smaller. 

Thanks for checking. 

Sent from my iPhone

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