Closed mdozmorov closed 4 years ago
Dear Mikhail,
Thank you for pointing this out.
Unfortunately, there are several command-line tool dependencies that don't work with the the latest versions in each case.
In the next issue you suggested to build a Docker container. I think this is an excellent idea and I will start working on this.
Do you think a conda environment would also be useful?
Many thanks, Hajk
Dear Mikhail,
I now updated the installation instructions for the Linux tools using the most recent tool versions: https://hajkd.github.io/LTRpred/articles/Introduction.html#install-tool-dependencies-on-linux
I decided to make these instructions only available for Linux
since I am referring macOS
and Windows
users to the ltrpred Docker container.
Once more thank you very much for making me aware of this issue of the tool versions and I will make sure to keep the tools up to date in the future.
Many thanks, Hajk
Great work, and the software works now. Please, fix minor instruction issues, so we can close this issue:
Dear Mikhail,
I am very happy to hear that both containers are running on your machine.
Thank you for spotting the typos and for your suggestions to improve the documentation.
As suggested, I now added README files to https://hub.docker.com/r/drostlab/ltrpred and https://hub.docker.com/r/drostlab/ltrpred_rstudio .
In addition, I addressed all your points in the Vignette and pushed the updates to the repository:
Thank you very much for your help with this!
Best wishes, Hajk
The LTRpred package requires six command-line tools, https://hajkd.github.io/LTRpred/articles/Introduction.html#installation. The installation instructions need to be updated as they refer to tools that are 2-3 versions older than the current ones. Consequently, installation instructions differ. For example:
doesn't work. Only the latest version can be downloaded:
Same for GenomeTools and others - installation instructions should be updated.