I am having some issues installing vcf2gwas via Singularity - the cluster that I have access to as a graduate student does not allow the use of Docker. Now, it seems like Singularity is able to build images from docker images. When I pull vcf2gwas with:
Hey Frank,
I am having some issues installing vcf2gwas via Singularity - the cluster that I have access to as a graduate student does not allow the use of Docker. Now, it seems like Singularity is able to build images from docker images. When I pull vcf2gwas with:
apptainer build vcf2gwas.sif docker://fvogt257/vcf2gwasINFO: Starting build... Getting image source signatures Copying blob b00aaacf759c skipped: already exists
Copying blob 07b969182718 skipped: already exists
Copying blob cf69ec4fb1d1 skipped: already exists
Copying blob e39a3f73ab73 skipped: already exists
Copying blob e54453959df3 skipped: already exists
Copying blob fddd2767c7ef skipped: already exists
Copying blob a603fa5e3b41 skipped: already exists
Copying blob 3f7bf64971b8 skipped: already exists
Copying blob 7e351095b52f skipped: already exists
Copying blob 03d961a6e310 skipped: already exists
Copying config f9baaba86b done
Writing manifest to image destination Storing signatures 2023/03/31 12:33:08 info unpack layer: sha256:a603fa5e3b4127f210503aaa6189abf6286ee5a73deeaab460f8f33ebc6b64e2 2023/03/31 12:33:08 warn xattr{etc/gshadow} ignoring ENOTSUP on setxattr "user.rootlesscontainers" 2023/03/31 12:33:08 warn xattr{/tmp/build-temp-2045752423/rootfs/etc/gshadow} destination filesystem does not support xattrs, further warnings will be suppressed 2023/03/31 12:33:09 info unpack layer: sha256:b00aaacf759c581712fa578a6b4e8e0b9fc780919a5d835a168457b754755644 2023/03/31 12:33:09 warn xattr{var/cache/apt/archives/partial} ignoring ENOTSUP on setxattr "user.rootlesscontainers" 2023/03/31 12:33:09 warn xattr{/tmp/build-temp-2045752423/rootfs/var/cache/apt/archives/partial} destination filesystem does not support xattrs, further warnings will be suppressed 2023/03/31 12:33:09 info unpack layer: sha256:07b9691827181afb85e2027be1b34b948a9de4110f0253de4e0c9dfcf1559f7b 2023/03/31 12:33:10 warn xattr{var/cache/apt/archives/partial} ignoring ENOTSUP on setxattr "user.rootlesscontainers" 2023/03/31 12:33:10 warn xattr{/tmp/build-temp-2045752423/rootfs/var/cache/apt/archives/partial} destination filesystem does not support xattrs, further warnings will be suppressed 2023/03/31 12:33:10 info unpack layer: sha256:cf69ec4fb1d1d974ad18c827b094bb4a4242791b94344e6f059ed9d0b8eb62be 2023/03/31 12:33:10 info unpack layer: sha256:3f7bf64971b8ca870b8bc8476ffc783c777f6bb3bb53e50d8e719f1ea1bad697 2023/03/31 12:33:10 warn xattr{var/cache/apt/archives/partial} ignoring ENOTSUP on setxattr "user.rootlesscontainers" 2023/03/31 12:33:10 warn xattr{/tmp/build-temp-2045752423/rootfs/var/cache/apt/archives/partial} destination filesystem does not support xattrs, further warnings will be suppressed 2023/03/31 12:33:10 info unpack layer: sha256:e39a3f73ab73f3ee1fe90b2ddc32e0a076ac3fd0a3e883829dc1d098297070df 2023/03/31 12:33:10 info unpack layer: sha256:03d961a6e310495bd57d612b9b881bd9e806e81e45dbce23fa446b97a982b8c4 2023/03/31 12:33:12 warn xattr{var/cache/apt/archives/partial} ignoring ENOTSUP on setxattr "user.rootlesscontainers" 2023/03/31 12:33:12 warn xattr{/tmp/build-temp-2045752423/rootfs/var/cache/apt/archives/partial} destination filesystem does not support xattrs, further warnings will be suppressed 2023/03/31 12:33:12 info unpack layer: sha256:7e351095b52f1941dec871083562523edbe6e62a4a48013571bbb7f8f29f0ee4 2023/03/31 12:33:51 info unpack layer: sha256:e54453959df31032add4368e40e25cd34c06250bacaf04d9a5002e6edf36fd4f 2023/03/31 12:33:51 info unpack layer: sha256:fddd2767c7ef1769ebd33f6ef4389271e57b23583326a7e027ab8ad67cee0193 INFO: Creating SIF file... INFO: Build complete: vcf2gwas.sif
Everthing seems to build alright and I am left with a .sif file that supposedly should allow me to run vcf2gwas.
However, when I ask Singularity to run
testwith vcf2gwas, it returns:If I go inside of an instance using:
apptainer shell vcf2gwas.sifand then runtestNothing is returned and no test files are generated (no error is thrown either).
Do you have any idea if your docker image is suitable for conversion to Singularity? Do you have any reason to believe otherwise?
I am super keen to use this package, please let me know if you have any insight here.
Cheers, Tommy