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mlell / tapas

Evaluate the effectiveness of any short read mapper and its parameters using artificially generated reads. See the "releases" page for download: https://github.com/mlell/tapas/releases. The manual can be found at https://mlell.github.io/tapas.
MIT License
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Rcpp version pinned in r_deps list #3

Open sdx23 opened 3 years ago

sdx23 commented 3 years ago

In the r_deps list the version of Rcpp is pinned to 0.12.15. This prevents installation with "newer" versions of R (such as 3.5.3 :). I'm not too much into R but if I understood correctly one cannot arbitrarily mix Rcpp and R versions.

The following installation procedure worked for me (providing Rcpp via r-essentials):

git clone https://github.com/mlell/tapas tapas
cd tapas
module load Anaconda/3.7
conda create -n tapas -c bioconda -c r python=3.6 r=3.6 r-essentials
source activate tapas
nano scripts/gen/r_deps.txt  # remove the line containing Rcpp
scripts/gen/install_dependencies
pip install -r scripts/gen/py_requirements.txt --target scripts/lib/python-ext/
bash scripts/gen/gen-launchers.sh
mlell commented 3 years ago

Yes, this is true. Currently I try to manage the repository to work for the software described in the Singularity recipe which is added to the tree by now. The frozen versions are meant to document the status when the paper on TAPAS was published but this causes problems increasingly. I will update the dependencies, however, not in the coming two weeks for time reasons. Thanks for reporting all the problems!

jlapaijmans commented 3 years ago

This solution is working brilliantly for me. If we find a moment, we could add a link to this issue or some such in the readme, in case other people have the same problem and require the same solution!