All the definitions can be found as working singularity containers at the Singularity Hub Repository

PacBio SmrtLink Images

This is a singularity definition file which permits to package the current PacBio smrtlink tools

• V2.3 for legacy reasons
• smrtlink_5.1.0.26412 + the isoseq3
• smrtlink_5.1.0.26412 + FALCON UNZIP
• smrtlink v6.0.0.47841 (currently not working as PacBio does not distribute the software directly, download locally to make it work)

The images are rather large and not fully tested.

Falcon Unzip

I included now as well a FALCON binary installation in a singularity definition file. This installs via bioconda samtools, mummer and minimap2. It then pulls the release (latest stable: falcon-2018.03.12-04.00) and installs it in the same directory.

How to

• install singularity on your machine (I tested only on Fedora myself)

• make sure you have sudo rights

• proceed with the build (an example)

   sudo singularity build --sandbox Directory Image.def
  

• convert into an image

   sudo singularity build MyImage.img Directory
  

• execute an app

   singularity exec --bind $PWD MyImage.img blasr input.bam reference.fasta
  

In theory, the --bind should not be necessary to mount the current folder and data passed to the Image directly. This is working on my Fedora machine but not on some other CentOS7 machines.