Noobie question

[jrcodina]

Hi, sorry if this seems waaay to simple, but I need to use this tool and I don't know how to start. I am going step by step but, how can I run this kind of command?

$ cd sigflow
$ ln -s $PWD/sigflow.R /usr/local/bin/sigflow # You can choose another place instead of /usr/bin/sigflow

R studio tells me: Error: unexpected '$' in "$".

I have seen that all the code presented has this type of things. Should I run it on another machine rather than R?

Thank you in advance.

[ShixiangWang]

The $ means you have to run these commands in terminal instead of RStudio console.

[jrcodina]

Thank you! I have followed these steps in the terminal and got an error when trying to call sigflow:

sigflow -h

But it says bash: sigflow: command not found.

Any idea of what could be happening?

[ShixiangWang]

Could you show commands snapshot after you clone the sigflow repo? If you execute the commands under the sigflow directory, it should work. The not found error shows that the sigflow command is not properly linked to /usr/local/bin/sigflow.

[ShixiangWang]

More specifically. The following commands should run in R console:

install.packages("docopt")
install.packages("BiocManager")
BiocManager::install("sigminer", dependencies = TRUE)
# Update Sigminer version
install.packages("remotes")
remotes::install_github("ShixiangWang/sigminer")
# Install specific version by
# remotes::install_github("ShixiangWang/[email protected]")

The following commands should run in terminal:

git clone https://github.com/ShixiangWang/sigflow

cd sigflow
ln -s $PWD/sigflow.R /usr/local/bin/sigflow  # You can choose another place instead of /usr/bin/sigflow

sigflow -h

[jrcodina]

It worked thank you very much! And sorry for the late response.

[ShixiangWang]

@jrcodina96 You're welcome.