Digest::Crc32 missing ?

Question

Digest::Crc32 missing ?

sletort opened this issue 8 years ago · comments

When using Jbrowse with docker, I needed to install Digest::Crc32 with cpan to use prepare-refseqs.pl.

$ docker run -v myData:/data/refData -it -p 80:80 --entrypoint=/bin/bash jbrowse/jbrowse-1.12.0
$ prepare-refseqs.pl --fasta /data/refData/Brassica_napus_v4.1.chromosomes.fasta
Can't locate Digest/Crc32.pm in @INC [...]
$ cpan install Digest::Crc32
$ prepare-refseqs.pl --fasta /data/refData/Brassica_napus_v4.1.chromosomes.fasta

Anthony Bretaudeau · Answer 1 · Fri Jan 27 2017 21:32:54 GMT+0800 (China Standard Time)

Thanks Sébastien, it should be fixed with 7bf5da8
Can you test when the new image is built on https://hub.docker.com/r/erasche/jbrowse/builds/ ?

Sébastien Letort · Answer 2 · Fri Jan 27 2017 21:36:41 GMT+0800 (China Standard Time)

Another package is missing : Bio::GFF3::LowLevel::Parser
when using flatfile-to-json.pl

Anthony Bretaudeau · Answer 3 · Fri Jan 27 2017 22:06:23 GMT+0800 (China Standard Time)

Ok, done too

Sébastien Letort · Answer 4 · Fri Jan 27 2017 22:51:04 GMT+0800 (China Standard Time)

Merci.
Another package is missing for a better lisibility of help : perl-doc (with apt-get).

Anthony Bretaudeau · Answer 5 · Fri Jan 27 2017 22:56:30 GMT+0800 (China Standard Time)

Done too !

Helena · Answer 6 · Mon Jan 30 2017 15:23:57 GMT+0800 (China Standard Time)

Thanks @abretaud, appreciate all the help!