Issue running the Docker example

[moldach]

I'm running into issues trying to run the Docker for mity:

$ sudo docker pull drmjc/mity:latest
[sudo] password for mtg: 
latest: Pulling from drmjc/mity
Digest: sha256:7ff790482f5a78c0994cea3341c541c8efac9cdee419fd42dd26a61484b9463d
Status: Image is up to date for drmjc/mity:latest
docker.io/drmjc/mity:latest


$ sudo docker run \
-w "$PWD" \
-v "$PWD":"$PWD" \
mity call \
--prefix ashkenazim \
--out-folder-path test_out \
--region MT:1-500 \
--normalise test_in/HG002.hs37d5.2x250.small.MT.RG.bam \
test_in/HG003.hs37d5.2x250.small.MT.RG.bam \
test_in/HG004.hs37d5.2x250.small.MT.RG.bam 

Unable to find image 'mity:latest' locally
docker: Error response from daemon: pull access denied for mity, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.
See 'docker run --help'.

If I use drjmc/mity instead I get the following error:

$ sudo docker run -w "$PWD" -v "$PWD":"$PWD" drmjc/mity call --prefix ashkenazim --out-folder-path test_out --region MT:1-500 --normalise test_in/HG002.hs37d5.2x250.small.MT.RG.bam test_in/HG003.hs37d5.2x250.small.MT.RG.bam test_in/HG004.hs37d5.2x250.small.MT.RG.bam 
mity version 0.2.1
Calling mitochondrial variants
Traceback (most recent call last):
  File "/usr/local/bin/mity", line 29, in <module>
    args.func(args)
  File "/usr/local/lib/python3.7/site-packages/mitylib/commands.py", line 45, in _cmd_call
    genome = select_reference_genome(args.reference, None)
  File "/usr/local/lib/python3.7/site-packages/mitylib/util.py", line 305, in select_reference_genome
    assert len(res) == 1
AssertionError

Do you have any idea what the issue is here?

[moldach]

Any update on this issue?

$ sudo docker run -it --entrypoint /bin/bash drmjc/mity:latest

root@9731de7956ed:/home# mity call --prefix ashkenazim --region MT:1-500 --normalise --reference hg19 HG002.hs37d5.2x250.small.MT.RG.bam HG003.hs37d5.2x250.small.MT.RG.bam HG004.hs37d5.2x250.small.MT.RG.bam 
mity version 0.2.1
Calling mitochondrial variants
Traceback (most recent call last):
  File "/usr/local/bin/mity", line 29, in <module>
    args.func(args)
  File "/usr/local/lib/python3.7/site-packages/mitylib/commands.py", line 45, in _cmd_call
    genome = select_reference_genome(args.reference, None)
  File "/usr/local/lib/python3.7/site-packages/mitylib/util.py", line 305, in select_reference_genome
    assert len(res) == 1
AssertionError
root@9731de7956

(base) mtg@mtg-ThinkPad-P53:~/DOCKER-CONTAINERS/mity$ ll
total 596884
drwxrwxr-x  4 mtg mtg      4096 Mar 22 14:27 ./
drwxrwxr-x 15 mtg mtg      4096 Mar 15 10:02 ../
-rw-rw-r--  1 mtg mtg  16721227 Mar 22 14:26 HG002.hs37d5.2x250.small.MT.RG.bam
-rw-rw-r--  1 mtg mtg       776 Mar 22 14:26 HG002.hs37d5.2x250.small.MT.RG.bam.bai
-rw-rw-r--  1 mtg mtg  16147308 Mar 22 14:26 HG003.hs37d5.2x250.small.MT.RG.bam
-rw-rw-r--  1 mtg mtg       776 Mar 22 14:26 HG003.hs37d5.2x250.small.MT.RG.bam.bai
-rw-rw-r--  1 mtg mtg  13561458 Mar 22 14:26 HG004.hs37d5.2x250.small.MT.RG.bam
-rw-rw-r--  1 mtg mtg       776 Mar 22 14:26 HG004.hs37d5.2x250.small.MT.RG.bam.bai
-rwxr-xr-x  1 mtg mtg 564682752 Mar 22 13:16 mity.sif*

[drmjc]

Hi,
Acknowledging that I see the same issue & am looking into it.
thanks, Mark

[drmjc]

Hi, this should now be fixed in 0.3.0. Thanks for reporting the issue.