apptainer image

Archives & Docker Daemon
As well as being hosted in a registry, Docker / OCI containers might be found inside a running Docker daemon, or saved as an archive. Apptainer can build from these locations by using specialized bootstrap agents.

$ docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
sylabsio/lolcow     latest              5a15b484bc65        2 hours ago         188MB

$ apptainer build lolcow_from_docker_cache.sif docker-daemon:sylabsio/lolcow:latest
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:a2022691bf950a72f9d2d84d557183cb9eee07c065a76485f1695784855c5193
 119.83 MiB / 119.83 MiB [==================================================] 6s
Copying blob sha256:ae620432889d2553535199dbdd8ba5a264ce85fcdcd5a430974d81fc27c02b45
 15.50 KiB / 15.50 KiB [====================================================] 0s
Copying blob sha256:c561538251751e3685c7c6e7479d488745455ad7f84e842019dcb452c7b6fecc
 14.50 KiB / 14.50 KiB [====================================================] 0s
Copying blob sha256:f96e6b25195f1b36ad02598b5d4381e41997c93ce6170cab1b81d9c68c514db0
 5.50 KiB / 5.50 KiB [======================================================] 0s
Copying blob sha256:7f7a065d245a6501a782bf674f4d7e9d0a62fa6bd212edbf1f17bad0d5cd0bfc
 3.00 KiB / 3.00 KiB [======================================================] 0s
Copying blob sha256:70ca7d49f8e9c44705431e3dade0636a2156300ae646ff4f09c904c138728839
 116.56 MiB / 116.56 MiB [==================================================] 6s
Copying config sha256:73d5b1025fbfa138f2cacf45bbf3f61f7de891559fa25b28ab365c7d9c3cbd82
 3.33 KiB / 3.33 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: lolcow_from_docker_cache.sif

BootStrap: docker
From: alpine:latest

%labels
  Maintainer Christian Dietrich
  Subread_Version 1.6.3

%apprun exactSNP
  exec exactSNP "${@}"
  
%apprun featureCounts
  exec featureCounts "${@}"
  
%apprun subindel
  exec subindel "${@}"
  
%apprun subjunc
  exec subjunc "${@}"
  
%apprun sublong
  exec sublong "${@}"
  
%apprun subread-align
  exec subread-align "${@}"
  
%apprun subread-buildindex
  exec subread-buildindex "${@}"

%runscript
  exec echo "Available apps: exactSNP, featureCounts, subindel, subjunc, sublong, subread-align, subread-buildindex"

%post
  # Get dependencies
  apk update
  apk add make gcc g++ zlib zlib-dev
  
  # Install Subread
  cd /tmp
  wget https://netcologne.dl.sourceforge.net/project/subread/subread-1.6.3/subread-1.6.3-source.tar.gz
  tar zxf subread-1.6.3-source.tar.gz
  cd subread-*/src
  make -j$(nproc) -f Makefile.Linux
  cp -r ../bin/* /usr/local/bin/

  # Clean up
  apk del make gcc g++ zlib-dev
  rm -rf /var/cache/apk/*
  rm -rf /tmp/*