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BioContainers

Cluster nodes automount a CernVM-File System at /cvmfs/singularity.galaxyproject.org/. This provides a universal file system namespace to Singularity images for the BioContainers project, which comprises container images automatically generated from Bioconda software packages. The Singularity images are organized into a directory hierarchy following the convention:

/cvmfs/singularity.galaxyproject.org/FIRST_LETTER/SECOND_LETTER/PACKAGE_NAME:VERSION--CONDA_BUILD

For example:

singularity exec /cvmfs/singularity.galaxyproject.org/s/a/samtools:1.13--h8c37831_0 samtools --help

The Bioconda package index lists all software available in /cvmfs/singularity.galaxyproject.org/, while the BioContainers registry provides a searchable interface.

NOTE: There will be a 10-30 second delay when first accessing /cvmfs/singularity.galaxyproject.org/ on a compute node on which it is not currently mounted; in addition, there will be a delay when accessing a Singularity image on a compute node where it has not already been accessed and cached to node-local storage.

BioContainers images in Docker Hub

A small number of Biocontainers images are available only in DockerHub under the biocontainers organization, and are not available on Cannon under /cvmfs/singularity.galaxyproject.org/.

See BioContainers GitHub for a complete list of BioContainers images available in DockerHub (note that many of the applications listed in that GitHub repository have since been ported to Bioconda, and are thus available in /cvmfs/singularity.galaxyproject.org, but a subset are still only available in DockerHub).

These images can be fetched and built on Cannon using the singularity pull command:

singularity docker://biocontainers/<image>:<tag>

For example, for the container cellpose with tag 2.1.1_vc1 (cellpose Docker Hub page):

singularity pull --disable-cache docker://biocontainers/cellpose:2.1.1_cv1
[jharvard@holy2c02302 bio]$ singularity pull --disable-cache docker://biocontainers/cellpose:2.1.1_cv1
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
2023/03/13 15:58:16  info unpack layer: sha256:a603fa5e3b4127f210503aaa6189abf6286ee5a73deeaab460f8f33ebc6b64e2
2023/03/13 15:58:17  info unpack layer: sha256:b00aaacf759c581712fa578a6b4e8e0b9fc780919a5d835a168457b754755644
2023/03/13 15:58:17  info unpack layer: sha256:372d780866a7e569457582348fbf850edc018b6b015335a4a56403fe299ff04b
2023/03/13 15:58:17  info unpack layer: sha256:feb836cf9ff261a0d9feb57f8808540cbb140d6d9e957af5daad2767d65fec36
2023/03/13 15:58:17  info unpack layer: sha256:6a0e4abca74a97205cba7ecb141fd4210bfab67dddb55e3a1fdaa6bcefbc44de
2023/03/13 15:58:17  info unpack layer: sha256:74be8ddfa7b55475808017bc4d978a439c2eeaeb252027c39bd6f29259355993
2023/03/13 15:58:20  info unpack layer: sha256:0a112f1bbdd8edefa7d2a40ad647c75067bb501ab4a3bfdacb5166727382db74
2023/03/13 15:58:20  info unpack layer: sha256:4012abce08aacd374ad001e1f9fd6d9fe864b01eadcf978306c70b4407b5c17b
2023/03/13 15:58:20  info unpack layer: sha256:2e0aab8a3f9f8d9f50931dfb7e8f751e0909249e82f56632a9bb6d2509387f74
2023/03/13 15:58:22  info unpack layer: sha256:d0819e2d86c5e671097843a5448232b3eff97d2685ab1ef97feac45be4ae54cc
2023/03/13 15:58:23  info unpack layer: sha256:376d1cd1a59141b316dc49fae4153aeaf5aa47f7e174651ca8bca98e734bd5f2
2023/03/13 15:58:59  info unpack layer: sha256:7bef5b9ba6503c93f4ad31d5664e7cffa42dd2b5368158a022d543e07979115b
2023/03/13 15:59:00  info unpack layer: sha256:75dc70b21417624a19747e6f6706571348f7c388a6efbb8a646da3e13b95a6de
2023/03/13 15:59:01  info unpack layer: sha256:bad0c0ea6165e4bb565161ee2d7779fd0555657ecf494f50c9a9710acfefcbe3
INFO:    Creating SIF file...

The sif image file cellpose_2.1.1_cv1.sif will be created:

[jharvard@holy2c02302 bio]$ ls -lh
total 2.5G
-rwxr-xr-x 1 jharvard jharvard_lab 2.4G Mar 13 15:59 cellpose_2.1.1_cv1.sif
-rwxr-xr-x 1 jharvard jharvard_lab  72M Mar 13 12:06 lolcow_latest.sif

BioContainer and package tips

  • The registry https://biocontainers.pro may be slow
  • We recommend to first check the Bioconda package index, as it quickly provides a complete list of Bioconda packages, all of which have a corresponding biocontainers image in /cvmfs/singularity.galaxyproject.org/
  • If an image doesn't exist there, then there is a small chance there might be one generated from a Dockerfile in BioContainer GitHub
  • If your package is listed in the BioContainer GitHub, search for the package in Docker Hub, under the biocontainers organization(e.g. search for biocontainers/<package>)