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RECETOX / RIAssigner

RIAssigner is a python tool for retention index (RI) computation for GC-MS data.
MIT License
4 stars 6 forks source link

Creating a Dockerfile for RIAssigner #100

Closed kozo2 closed 9 months ago

kozo2 commented 10 months ago

It seems that RIAssigner has strict dependent package versions. (Therefore, I haven't been able to try running RIAssigner yet.) Could you tell me what kind of environment you have where RIAssigner runs without any issues? I would like to Dockerize that.

hechth commented 9 months ago

Hi @kozo2, sorry for the long delay - you can install the package using conda or use the existing biocontainer at: https://biocontainers.pro/tools/riassigner

docker pull quay.io/biocontainers/riassigner:0.3.3--pyhdfd78af_0

kozo2 commented 9 months ago

Hi @hechth, no need to apologize at all. I completely understand that you must be busy.

you can install the package using conda or use the existing biocontainer at: https://biocontainers.pro/tools/riassigner

docker pull quay.io/biocontainers/riassigner:0.3.3--pyhdfd78af_0

Thank you! It worked well! I close this issue.

(base) $ docker pull quay.io/biocontainers/riassigner:0.3.3--pyhdfd78af_0
0.3.3--pyhdfd78af_0: Pulling from biocontainers/riassigner
73349e34840e: Pull complete
acab339ca1e8: Pull complete
1ee03f166404: Pull complete
Digest: sha256:a4b56c866a9df417109b67788662226b2d1a58343891f542175f8592ed207cdc
Status: Downloaded newer image for quay.io/biocontainers/riassigner:0.3.3--pyhdfd78af_0
quay.io/biocontainers/riassigner:0.3.3--pyhdfd78af_0
(base) $ docker run -it quay.io/biocontainers/riassigner:0.3.3--pyhdfd78af_0 bash
root@4470769010c5:/# cd
root@4470769010c5:~# pwd
/root
root@4470769010c5:~# python
Python 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:10)
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from RIAssigner.compute import Kovats
>>> from RIAssigner.data import MatchMSData, PandasData
>>>