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medvir / SmaltAlign

Quick iterative alignment of reads against a given reference using smalt.
MIT License
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wts.R and cov_plot.R hashbang, location of Rscript #5

Closed mihuber closed 5 years ago

mihuber commented 5 years ago

The scripts wts.R and cov_plot.R are not working for me (and users other than @sschmutz) with #!/home/schmutz.stefan/miniconda3/envs/SmaltAlign/bin/Rscript hashbang.

sschmutz commented 5 years ago

It's working in conda's base environment conda activate base and then Rscript wts.R or cov_plot.R <file directory>.

There was a version conflict of the R package seqinr and another tool. I can try again and include all necessary packages in the SmaltAlign environment.yml document.

Having the right version of the tools is critical with SmaltAlign. If you install the newest versions of all dependencies, it doesn't work.

mihuber commented 5 years ago

No, I think the problem is that it looks for Rscript in your home, which I don't have access.

(base) mihuber@timavo:/analyses/Diagnostics/virome/190204_1000428184$ ../../Repositories/SmaltAlign/cov_plot.R ../190204_1000428184/ -bash: ../../Repositories/SmaltAlign/cov_plot.R: /home/schmutz.stefan/miniconda3/envs/SmaltAlign/bin/Rscript: bad interpreter: No such file or directory

sschmutz commented 5 years ago

I removed the Rscript Shebang. Now you have to specify that you want to run that script with Rscript by yourself:

conda activate base
Rscript <path/to/SmaltAlign>/wts.R <path/to/files>