2020+ installation problems:

Question

[IrZ]

Hi there! I read this paper http://www.pnas.org/content/113/50/14330.full.pdf Evaluating the evaluation of cancer driver genes and I was so keen to use 20/20+ so I downloaded and followed the instructions. However at the point where I am typing $ which 2020plus.py and expect to get the location of the 2020plus.py script back, I get ... nothing. I am not sure what might have went wrong in the whole process, so I appreciate if anyone has any input on that. I searched here for other isssues on 2020+ but I found nothing also.

Thanks in advance

[WouterDeCoster]

This also looks like a "general" installation problem - not necessarily 20/20+ (which is a horrible name for googling).

In the installation instructions the following line is crucial:

Make sure that you have add the 20/20+ directory to your PATH variable

[Sej Modha]

I am not familiar with this tool but trying to figure out if it's properly installed. Did you install all dependencies specified here: https://github.com/KarchinLab/2020plus and have you tried to run tests available in the latest release: https://github.com/KarchinLab/2020plus/releases

Answer 1

[Collin]

I assume you are at this part of the installation: http://2020plus.readthedocs.io/en/latest/installation.html#check-your-path-variable

Make sure you add the directory where you placed 20/20+ to your .bashrc file in your home directory.

export PATH=$PATH:/path/to/2020plus

Where "/path/to/2020plus" is the path where 20/20+ is located. I'm going to update the website to make this a little more obvious.

Collin

[Christine]

Hi, Collin. Thanks a lot for your suggestion. I'm also using 20/20+ these days, but I met the error message like this "TypeError: cannot serialize '_io.TextIOWrapper' object" when I typed the commend "mut_annotate --summary -n 1 -i genes.fa -b genes.bed -m mutations.txt -p 10 -c 1.5 -o summary_output.txt". Could you please tell me what is the problems and what should I do to solve it? Thank you very much. looking forward to your reply!

[Collin]

What python version and operating system are you using?

[Christine]

Thanks for your reply. My python version is "Python 3.6.3 ", and the operating system is "CentOS release 6.9". I have installed the necessary packages, so I don't konw where the errors came from.

[Collin]

Are you missing any of the following files: genes.fa, genes.bed, or mutations.txt (FASTA, BED, or mutation file)? The instructions on the probabilistic2020 web site (http://probabilistic2020.readthedocs.io/en/latest/tutorial.html ) are meant for three hypothetical files, and actually need to be provided.

[Christine]

Thanks a lot. genes.fa, genes.bed, or mutations.txt are provided. And I have successfully got oncogene_output.txt and tsg_output.txt when I used the three hypothetical files to run oncogene and tsg sub-command. What's more, when I type "mut_annotate -h", it does show the usage of this command. Once I type the command of Simulated Features (or Simulated MAF), it reports the errors. And it still produces a "summary_output.txt"(or maf_output.txt) which only contains the first line, such as "Gene strand Chromosome Start_Position End_Position ..."

[Collin]

The simulations are mostly useful for 20/20+. What are you intending to do that isn't already done in the pipeline for 20/20+ 2020plus.readthedocs.io/en/latest/ )?

[Christine]

Okay. I checked the pipeline and used the "snakemake" command. I have got the results through 20/20+ pipeline now. Thank you very much.