Question: 2020+ installation problems:
0
gravatar for IrZ
2.2 years ago by
IrZ0
Sweden, Uppsala
IrZ0 wrote:

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

R software error • 784 views
ADD COMMENTlink modified 2.2 years ago by Collin700 • written 2.2 years ago by IrZ0
1

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

ADD REPLYlink written 2.2 years ago by WouterDeCoster43k

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

ADD REPLYlink written 2.2 years ago by Sej Modha4.6k
1
gravatar for Collin
2.2 years ago by
Collin700
United States
Collin700 wrote:

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

ADD COMMENTlink written 2.2 years ago by Collin700

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!

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Christine0

What python version and operating system are you using?

ADD REPLYlink written 2.2 years ago by Collin700

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.

ADD REPLYlink written 2.2 years ago by Christine0
1

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.

ADD REPLYlink written 2.2 years ago by Collin700

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 ..."

ADD REPLYlink written 2.2 years ago by Christine0

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/ )?

ADD REPLYlink written 2.2 years ago by Collin700

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

ADD REPLYlink written 2.2 years ago by Christine0
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