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Frequently Asked Questions

Installation Guide

How can I install Singularity?

Follow this link to install Singularity (Version 3) for your pipelines. For your convenience, attached below are the commands needed to download the newest version in a Linux environment:

## Remove old version of Singularity
# sudo rm -rf /usr/local/libexec/singularity /usr/local/var/singularity /usr/local/etc/singularity /usr/local/bin/singularity /usr/local/bin/run-singularity /usr/local/etc/bash_completion.d/singularity

## Install Singularity Version 3
apt-get install -y build-essential libssl-dev uuid-dev libgpgme11-dev libseccomp-dev pkg-config squashfs-tools
wget https://dl.google.com/go/go1.12.7.linux-amd64.tar.gz
tar -C /usr/local -xzf go1.12.7.linux-amd64.tar.gz
export PATH=$PATH:/usr/local/go/bin
export VERSION=3.2.1 
wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz
tar -xzf singularity-${VERSION}.tar.gz
cd singularity
./mconfig && make -C ./builddir 
sudo make -C ./builddir install

How can I install Docker?

Follow this link to install Docker for pipelines, or follow the commands below:

## Uninstall Old Versions of Docker
# sudo apt-get remove docker docker-engine docker.io

## Install Docker
sudo apt install docker.io

How can I install JAVA?

Installing Java v8+ for Nextflow:

apt-get install -y openjdk-8-jdk && 
apt-get install -y ant && 
apt-get clean;

# Fix certificate issues
apt-get update && 
apt-get install ca-certificates-java && 
apt-get clean && 
update-ca-certificates -f;
export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/

How can I install Nextflow?

JAVA (v8+) should be installed before installing Nextflow. Once Java has been successfully installed, click this link to install Nextflow or use the commands below:

## To install to your ~/bin directory:
mkdir ~/bin
cd ~/bin
curl -fsSL get.nextflow.io | bash

# Add Nextflow binary to your bin PATH or any accessible path in your environment:
chmod 755 nextflow
mv nextflow ~/bin/
# OR system-wide installation:
# sudo mv nextflow /usr/local/bin

Connection Issues

Why can't I validate my SSH Keys?

If you're having trouble validating your SSH keys, here are a few things to check:

  1. Make sure you copy the entire key, including the initial part (e.g. "ssh-rsa"). The key should span the entire file, like in the following example:

      ssh-rsa
  AA1AB3N4nX3a....................
  ................................
  ................................
  ...............b9Rj @viafoundry

  2. The SSH protocol requires specific permissions for files and directories to establish secure connections. Please execute the following commands to make sure your SSH-related files are properly secured:

      chmod 700 ~/.ssh
  chmod 600 ~/.ssh/authorized_keys

  3. Ensure that your home directory is not writable by other users. Setting the permissions of your home directory to 777 can create security issues and block SSH connections. Instead, set the permissions to more secure options such as 750, 755 or 754.

How can I create SSH keys in my computer?

You can find your SSH key pairs on your local machine at their default location: ~/.ssh/id_rsa for private and ~/.ssh/id_rsa.pub for public key. If no keys exist there or you want to create new ones, then on the command line, enter:

ssh-keygen -t rsa

You will be prompted to supply a filename and a password. If you want to accept the default filename (and location) for your key pair, just press Enter without entering a filename. Your SSH keys will be generated using the default filename (id_rsa and id_rsa.pub), and they will be saved in the "~/.ssh/" directory in your machine.

Run Questions

I can't reach my files in the file window

There might be a connection issue. Please check to make sure you've followed these steps:

  1. The SSH protocol requires specific permissions for files and directories to establish secure connections. Please execute the following commands to make sure your SSH-related files are properly secured:

      chmod 700 ~/.ssh
  chmod 600 ~/.ssh/authorized_keys

  2. Ensure that your home directory is not writable by other users. Setting the permissions of your home directory to 777 can create security issues and block SSH connections. Instead, set the permissions to more secure options such as 750, 755 or 754.

Error: Run directory cannot be created

It's possible that there's an issue with your connection. Please check the Why can't I validate my SSH Keys section to ensure you've followed all the necessary steps.

Profile Questions

How should I configure my executor settings?

In Via Foundry, there are four different sections to control executor settings: the first two are defined in Profile - Run Environment, and the remaining two are adjusted in the Advanced tab of the run page. If you select an executor other than "Local" or "Ignite", Via Foundry prompts you to enter additional settings, such as the queue/partition, memory, CPU, and time.

1. Executor of Nextflow (navigate to Profile - Run Environments):

This setting controls how Via Foundry initiates Nextflow. Currently, Via Foundry supports the Local, SGE, SLURM, and LSF executors to initiate Nextflow. For the SGE, SLURM, and LSF executors, Via Foundry only uses them to run Nextflow itself, so the time limit should be long enough to execute all processes in the pipeline. For local execution, Via Foundry limits the total amount of memory and CPU that can be used, so these values should be close to the maximum capacity of your computer.

  • Suggested parameters for SGE/SLURM/LSF: long (queue) 8 (GB Memory) 1 (CPU) 5000-8000 (min, Time)
  • Suggested parameters for Local: 100 (GB Memory) 8 (CPU)

2. Executor of Nextflow Jobs (navigate to Profile - Run Environments):

This setting will be used as the default setting for submitted jobs by Nextflow if you don't set any parameters in the Advanced section of your run page.

  • Suggested parameters for SGE/SLURM/LSF: short (queue) 20 (GB Memory) 1 (CPU) 240 (min, Time)
  • Suggested parameters for Local: 20 (GB Memory) 1 (CPU)

3. Executor Settings for All Processes (in the advanced tab of run page):

These settings will overwrite those in Executor of Nextflow Jobs and set default parameters for all Nextflow Jobs.

  • Suggested parameters for SGE/SLURM/LSF: short (queue) 20 (GB Memory) 1 (CPU) 240 (min, Time)
  • Suggested parameters for Local: 20 (GB Memory) 1 (CPU)

4. Executor Settings for Each Process (in the advanced tab of run page):

If a particular process requires different parameters than the defaults (which are defined in the Executor Settings for All Processes or Executor of Nextflow Jobs sections), you can overwrite the general settings by clicking the checkbox of the process that you want to change. This will only affect the settings of the selected process and keep the original settings for the rest of the processes.

  • Suggested parameters for SGE/SLURM/LSF: long (queue) 20 (GB Memory) 4 (CPU) 1000-5000 (min, Time)
  • Suggested parameters for Local: 20 (GB Memory) 4 (CPU)

Note: If non-standard resources or settings are required for the executor, then you can specify these parameters by using Other Options box. For instance, to submit an SGE job with 3 CPU using parallel environments, you can enter -pe orte 3 (to use MPI for distributed-memory machines) or -pe smp 3 (to use OpenMP for shared-memory machines) in the Other Options box, leaving the CPU box empty.