brew install ufits zlib issue about amptk

[nextgenusfs]

What OS? Do you have another terminal window open running home-brew?

[cour10eygrace]

Linux ubuntu 14.04 running in virtualbox..no other terminal running

[nextgenusfs]

I've not seen this one before, try the following:

brew doctor
brew update
brew install zlib
brew install ufits

[nextgenusfs]

You may need to tap the dupes repository before installing zlib, i.e.

brew tap homebrew/dupes
brew install zlib

[cour10eygrace]

still receiving the same zlib error. I have also received this warning..not
sure if it is related.
Warning: Homebrew's share was not found in your XDG_DATA_DIRS but you have
this variable set to include other locations.
Some programs like vapigen may not work correctly.

On Wed, Nov 2, 2016 at 2:03 PM, Jon Palmer [email protected] wrote:

You may need to tap the dupes repository before installing zlib, i.e.

brew tap homebrew/dupes
brew install zlib

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Courtney G. Collins
PhD candidate - Botany and Plant Sciences, Diez lab
University of California, Riverside
http://courtneygcollins.weebly.com

[nextgenusfs]

Ok, how about this:

brew install ufits --ignore-dependencies

This should tell you if it is a ufits problem or a dependencies problem. You actually don't need any of the dependencies per say, but they will speed up processing, allow for Ion Torrent data usage, and dada2 clustering.

You can then try the dependencies separately, i.e.

brew install vsearch
brew install R
brew install bedtools

If you still have a problem with the first command, then something is wrong with your LinuxBrew installation.

[nextgenusfs]

You can also install UFITS without using home-brew, just need to install some of the tools manually.

To install via github, do:

#clone repository
git clone https://github.com/nextgenusfs/ufits.git
#put into path
export PATH="/path/to/ufits/directory:$PATH"
#install python modules
pip install -U biopython natsort numpy pandas matplotlib psutil h5py biom-format

You will then need to install manually the following to get full functionality: vsearch, usearch, and R .

[cour10eygrace]

The --ignore dependencies worked thank you!!!

On Wed, Nov 2, 2016 at 5:29 PM, Jon Palmer [email protected] wrote:

Ok, how about this:

brew install ufits --ignore-dependencies

This should tell you if it is a ufits problem or a dependencies problem.
You actually don't need any of the dependencies per say, but they will
speed up processing, allow for Ion Torrent data usage, and dada2 clustering.

You can then try the dependencies separately, i.e.

brew install vsearch
brew install R
brew install bedtools

If you still have a problem with the first command, then something is
wrong with your LinuxBrew installation.

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You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
#9 (comment),
or mute the thread
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.

Courtney G. Collins
PhD candidate - Botany and Plant Sciences, Diez lab
University of California, Riverside
http://courtneygcollins.weebly.com