Closed amathelier closed 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 ?
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...
@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
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.
Yes I tried first before answering, conda 4.7.12 here. After conda update everything is ok?
I cannot update conda for now because it is on our HPC that is used by many users.
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.
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
I tried to install pygtftk following the readme comments but got the following error:
$ conda create -n pygtftk -c bioconda pygtftk