Installing qiime

Support Requests
#1

Hi,

I am having problems in installing qiime1. I installed miniconda and I created a qiime1 environment with all features of Qiime1. Everything seems to install ok with no errors or warning. However, when I give this command

print_qiime_config.py -t

I get this error:

ValueError: numpy.dtype has the wrong size, try recompiling

So, I tried to update numpy assuming that was the problem so It still didn’t work.

Can you please help me with this?

#2

Using conda should prevent these kind of version problems! Can I just confirm that after installing qiime, you activated the qiime conda environment with:

source activate qiime1

and that you added miniconda to your PATH by adding to ~/.bashrc?

Prepending PATH=/home/<your_username>/miniconda/bin to PATH in /home/<your_username>/.bashrc

#3

Thank you for your suggestion. When miniconda2 was installing, it asked if it should be added in your PATH and i said yes. So I assumed Miniconda was in my PATH, turns out it wasnt and that was the problem.

Thanks!

Anu

1 Like
#4

Hello Matt

I am having another problem with PATH :frowning: Sorry for coming back on this.

I tried running normalize_table.py which uses R packages such as MetagenomeSeq and CSS. I have installed these packages in the R environment of the server. However when I try to run python script, I get this error

Library optparse not found.

To install, open R and run the command:
install.packages(“optparse”)

If you already have the optparse package installed in a local directory,
please store the path to that directory in an environment variable
called “R_LIBRARY_PATH”. This may be necessary if you are running
QIIME on a cluster, and the cluster instances of R don’t know about
your local R libraries. If you don’t know your R library paths, you
can list them by opening R and running with the command, “.libPaths()”.
The current R instance knows about these paths:
[/home/linuxbrew/.linuxbrew/lib/R/3.4/site-library, /home/linuxbrew/.linuxbrew/Cellar/r/3.4.2/lib/R/library]

I see that R was probably installed using brew and the PATH for R is different from the library of R which is:

[1] “/usr/local/lib/R/site-library” “/usr/lib/R/site-library”
[3] “/usr/lib/R/library”

I would like to change the path of R so that it can detect ths site library since it has all the installed packages.

I have tried making an environment variable and it didnt work.

Could you please help me with this.

Thanks!

Anu

#5

R is installed by both linuxbrew and from aptitude, and both installs have separate package libraries.

You should be able to make both installs see each-other’s libraries by adding the following line to your ~/.bashrc:

export R_LIBS=/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library:/home/linuxbrew/.linuxbrew/lib/R/3.4/site-library:/home/linuxbrew/.linuxbrew/Cellar/r/3.4.1/lib/R/library

then making sure that you activate the new environment variable with:

source ~/.bashrc

#6

Thank you so much Matt, it worked!

I really appreciate your help :slight_smile:

Anu