Tips and tricks

nf-core/rnaseq

R container and notebook

This workshop is designed to be portable and reproducible. We have provided the Rmd file and RStudio/4.0.1 container for you to use:

Additional training

Troubleshooting

Error when trying to run rserver on Nimbus

When you run the command

mkdir -p /tmp/rstudio-server  

PASSWORD='abc' singularity exec \  
    -B /tmp/rstudio-server:/var/lib/rstudio-server \  
    -B /tmp/rstudio-server:/var/run/rstudio-server \  
    -B /home/ubuntu/working_directory/Day-2:/home \   
    rstudio_4.1.0.sif \  
    rserver --auth-none=0 --auth-pam-helper-path=pam-helper --server-user ubuntu

If an error similar to the one below pops up -

11 Oct 2023 23:14:42 [rserver] ERROR system error 98 (Address already in use); OCCURRED AT rstudio::core::Error rstudio::core::http::initTcpIpAcceptor (rstudio::core::http::SocketAcceptorService&, const string&, const string&) src/cpp/server/ServerInit.cpp:103; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:704

Do the following

rm -r  /tmp/rstudio-server
sudo lsof -i :8787

If you see:

COMMAND PID           USER   FD   TYPE DEVICE SIZE/OFF NODE NAME
rserver 747 rstudio-server    7u  IPv4  19251      0t0  TCP *:8787 (LISTEN)

Run the command:

sudo kill <PID>

Here substitute with the corresponding PID value e.g. 747 above

RStudio not loading in browser

If you need to end your session, exit your browser and on Nimbus, run the following command:

kill -9 $(lsof -t -c rsession)

Loop device error on Nimbus

When running Singularity containers on Nimbus you may come across an error:

FATAL:   container creation failed: mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs 
error: while mounting image /proc/self/fd/3: failed to find loop device: could not attach image file to loop device: no loop devices available

Run the following commands to resolve this issue:

lsmod | grep loop

sudo modprobe loop

sudo losetup -f

/dev/loop9