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dputhier / pygtftk

A python package and a set of shell commands to handle GTF files
GNU General Public License v3.0
44 stars 6 forks source link

Conda installation not working #140

Closed amathelier closed 3 years ago

amathelier commented 3 years ago

I tried to install pygtftk following the readme comments but got the following error: $ conda create -n pygtftk -c bioconda pygtftk

Fetching package metadata ............. Solving package specifications:

InvalidSpecError: Invalid spec: =20190808

dputhier commented 3 years ago

Thank you Anthony for your feedback and your interest in pygtftk. IGot the same on Linux... In fact, we are experiencing problems with the last bioconda release of pygtftk. It is working under OSX (but provides an older version). We will try to fix that asap. @guillaumecharbonnier any idea ?

guillaumecharbonnier commented 3 years ago

On Linux, you need to have conda-forge, bioconda et defaults channels in this strict order in your ~/.condarc.

Alternatively, you can create your environnment using yaml file like this one: conda env create -f pygtftk.yaml

where pygtftk.yaml contains:

name:
  pygtftk
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - pygtftk

To get a recent version on macOS, you should append the channel guillaumecharbonnier below the defaults in the yaml. Until https://github.com/dputhier/pygtftk/issues/139 is solved...

dputhier commented 3 years ago

@guillaumecharbonnier I got the same issue... Did you tried on your side ?

$ conda env create -f pygtftk.yaml
Fetching package metadata ...................
Solving package specifications:

InvalidSpecError: Invalid spec: =20190808

$ cat pygtftk.yaml
name:
  pygtftk
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - pygtftk
amathelier commented 3 years ago

It might be a conda version issue (not sure). I was able to install on one of my machine (Ubuntu 18.04) but not on the other (el7). Two different versions of conda were used: conda 4.3.21 (not working) and conda 4.8.5 (working). Not sure if it helps.

guillaumecharbonnier commented 3 years ago

Yes I tried first before answering, conda 4.7.12 here. After conda update everything is ok?

amathelier commented 3 years ago

I cannot update conda for now because it is on our HPC that is used by many users.

guillaumecharbonnier commented 3 years ago

In the meantime or if they have reason not to update, you can install miniconda in your own folder and use the latest conda version.

dputhier commented 3 years ago

Updating conda using "conda update conda" did also the trick for me. Thank you @amathelier for the workaround. I will close this issue that seems more to be related to conda. Feel free to re-open it if needed. Best Denis