trouble installing RESCRIPt

Community Plugin Support
1

Hi, I am having the same issue as described in this thread when installing RESCRIPt:

RESCRIPt plugin not found even though installed

I sucessfully installed it inside my qiime2-2021.4 environment using the commands described on the github page (but with --user flag because I am using a remote computing cluster):

pip install git+https://github.com/bokulich-lab/RESCRIPt.git --user

The message I got after reads:

Collecting git+https://github.com/bokulich-lab/RESCRIPt.git
Cloning GitHub - bokulich-lab/RESCRIPt: REference Sequence annotation and CuRatIon Pipeline to /tmp/pip-req-build-06q0ww91
Building wheels for collected packages: rescript
Running setup.py bdist_wheel for rescript ... done
Stored in directory: /tmp/pip-ephem-wheel-cache-72hlz2kf/wheels/c8/65/fa/4a3cf80279607ababb41e29474cdbe4728564941f215c8bdb0
Successfully built rescript
distributed 1.21.8 requires msgpack, which is not installed.
Installing collected packages: rescript
Successfully installed rescript-2021.8.0.dev0+3.g1ce2142
You are using pip version 10.0.1, however version 21.1.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

However when I try run qiime rescript I get ther error:

Error: QIIME 2 has no plugin/command named 'rescript'.

From the post linked about I know I need to "add the package files to the $PATH variable for the active environment" I'm using. I am unsure how to do this and would appreciate any guidance! Thank you

2

Hi @anna-schrecengost,

I assume you followed the directions for Option 2: Install within QIIME 2 environment?

Did you remember to run the following command after the pip install?
qiime dev refresh-cache

If you did, then perhaps the version of pip on your system is too old? As your output shows:

-Cheers!
-Mike

2 Likes
3

Hi @SoilRotifer,

Thank you so much for your reply! You were right, that totally worked. I did need to do a bit more troubleshooting to figure out how to call the updated pip version rather than the older version that was installed on the computing cluser I'm using. I did that by installing an updated version of pip inside my qiime2-2021.4 environment and then calling pip3 instead of pip. Then I was able to install using pip3 without the --user flag. So I think part of the issue was that using the pip --user flag installed the plugin into my local python directory instead of anaconda's directory (which I needed to do because of permissions errors). This might be something that pops up for people installing the plugin inside a conda environment on a computing cluster.

2 Likes
4

That's great news @anna-schrecengost. :partying_face:

Thank you for sharing your trouble-shooting tips! :raised_hands:

1 Like