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nextflow-io / nextflow

A DSL for data-driven computational pipelines
http://nextflow.io
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Singularity 3.0 Support #897

Closed apeltzer closed 6 years ago

apeltzer commented 6 years ago

Bug report

Out of curiosity, I installed Singularity v3.0.0 which just came out for testing purposes. There are some command that switched behaviour which I'm going to list here for further reference.

Expected behavior and actual behavior

singularity pull should behave similar to before and do this:

singularity pull --name test.sif docker://nfcore/rnaseq

(which should create the image as test.sifor whatever you call it). This is what nextflow uses to my knowledge to fetch an image.

However, this happens:

singularity pull --name test.sif docker://nfcore/rnaseq 
Error: unknown flag: --name
Usage:
  singularity [global options...] pull [pull options...] <URI>

Steps to reproduce the problem

Install Singularity 3.0.0, then pull any image from shub:// or docker:// urls.

Environment

For reference this is the entire help function of the pullcommand:

singularity pull -h
Pull a container from a URI

Usage:
  singularity pull [pull options...] <URI>

Description:
  The 'pull' command allows you to download or build a container from a given
  URI.  Supported URIs include:

  library: Pull an image from the currently configured library
      library://[user[collection/[container[:tag]]]]

  docker: Pull an image from Docker Hub
      docker://user/image:tag

  shub: Pull an image from Singularity Hub to CWD
      shub://user/image:tag

Options:
  -F, --force            overwrite an image file if it exists
  -h, --help             help for pull
      --library string   the library to pull from (default
                         "https://library.sylabs.io")

Examples:
  From Sylabs cloud library
  $ singularity pull library://alpine:latest

  From Docker
  $ singularity pull docker://tensorflow/tensorflow:latest

  From Shub
  $ singularity pull shub://vsoch/singularity-images

For additional help or support, please visit https://www.sylabs.io/docs/
pditommaso commented 6 years ago

You are too slow 😂

apeltzer commented 6 years ago

Okay, just wanted to let you know :-)

pditommaso commented 6 years ago

Let's keep it open, it may require some changes on our side if they don't restore the --name option.

pditommaso commented 6 years ago

See also https://github.com/sylabs/singularity/issues/2214.

pditommaso commented 6 years ago

This is going to be fixed by next Singularity release, see sylabs/singularity#2214.