I’m administering a multi-user linux environment. I have virtual environments for qiime1.9.1 and qiime2-2019.4 that are accessible to all users. Someone requested a new 2019.7 installation. Using the administrative account, I followed the instructions on the installing qiime natively page, but it installed the environment to that user’s local directory instead of the shared environment directory. Miniconda was installed to a shared location as per another post on this topic. I tried to set the env directory in the .condarc file as described here but it doesn’t seem to work. I’m a little confused about how I even set this up back in May, which I’m sure I did following an online guide. There is a user called conda who owns all of the shared directories. Seems like there is probably an obvious solution to someone more familiar with conda than I am. I eventually tried installing qiime to the wrong place and simply moving the install directory to where it should be (see below output). Upon moving the directory, conda immediately found the environment in the right place, but when I activated it, the qiime script complained about a bad python interpreter. I changed the path in the shebang line to correct this and the environment opens, but now it can’t find the default config file. Will this install work? Are there additional steps I will need to take? Is there a better way to do this with my existing system configuration? I would prefer to have a simple way to install updated environments without going through a lot of mess in the process. I can’t believe I didn’t copy down what I was doing when I made the installation, because otherwise it works perfectly.
Conda install location:
ecoss@QIIME-MACHINE:~$ ls -l /usr/bin/conda/conda/
total 8
drwxr-xr-x 1 conda conda 1268 Sep 20 11:01 bin
drwxr-xr-x 1 conda conda 16 May 17 14:30 compiler_compat
drwxr-xr-x 1 conda conda 10 Sep 20 10:59 condabin
drwxr-xr-x 1 conda conda 2456 Sep 20 11:01 conda-meta
drwxr-xr-x 1 conda conda 86 May 17 15:38 envs
drwxr-xr-x 1 conda conda 38 May 17 15:16 etc
drwxr-xr-x 1 conda conda 1950 Sep 20 11:01 include
drwxr-xr-x 1 conda conda 4038 Sep 20 11:01 lib
drwxr-xr-x 1 conda ecoss 6 Sep 20 10:59 libexec
-rw-r-xr-x 1 conda conda 4134 Apr 17 14:29 LICENSE.txt
drwxr-xr-x 1 conda ecoss 8 Sep 20 10:59 man
drwxr-xr-x 1 conda conda 82804 Sep 20 11:11 pkgs
drwxr-xr-x 1 conda conda 120 Sep 20 10:59 share
drwxr-xr-x 1 conda conda 16 May 17 14:30 shell
drwxr-xr-x 1 conda conda 168 Sep 20 10:59 ssl
drwxr-xr-x 1 conda conda 14 May 17 14:30 x86_64-conda_cos6-linux-gnu
Existing environments:
ecoss@QIIME-MACHINE:~$ conda env list
# conda environments:
#
base * /usr/bin/conda/conda
qiime1.9.1 /usr/bin/conda/conda/envs/qiime1.9.1
qiime2-2019.4 /usr/bin/conda/conda/envs/qiime2-2019.4
Contents of .condarc
ecoss@QIIME-MACHINE:~$ cat .condarc
auto_activate_base: false
#CONDA_ENVS_PATH=~/my-envs:/usr/bin/conda/conda/envs
Activation of new environment after moving the directory (q2 is an alias for activation):
ecoss@QIIME-MACHINE:~$ q2
-bash: /usr/bin/conda/conda/envs/qiime2-2019.7/bin/qiime: /home/ecoss/.conda/envs/qiime2-2019.7/bin/python: bad interpreter: No such file or directory
Non-admin user activating qiime2-2019.7 environment after updating shebang line in qiime script:
lva123@QIIME-MACHINE:~ q2
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Fontconfig error: Cannot load default config file
(qiime2-2019.7) lva123@QIIME-MACHINE:~ grep q2 .bashrc
alias q2=“conda activate qiime2-2019.7”