quay.io/cri-iatlas/cibersort:1.0 not public

heimannch commented 1 year ago

I'm trying to run the cibersort workflow and I'm getting an error saying that I'm not authorized to access the resource. I've logged into my docker and quay.io accounts.

cheimann:bin heimann$ docker login
Authenticating with existing credentials...
Login Succeeded
cheimann:bin heimann$ docker login quay.io
Authenticating with existing credentials...
Login Succeeded
cheimann:bin heimann$ cwltool \#workflow/github.com/CRI-iAtlas/iatlas-workflows/Cibersort:develop Dockstore.json
INFO /Library/Frameworks/Python.framework/Versions/3.10/bin/cwltool 3.1.20220224085855
INFO Resolved '#workflow/github.com/CRI-iAtlas/iatlas-workflows/Cibersort:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2FCRI-iAtlas%2Fiatlas-workflows%2FCibersort/versions/develop/plain-CWL/descriptor/cibersort_workflow.cwl'
INFO [workflow ] start
INFO [workflow ] starting step preprocessing
INFO [step preprocessing] start
INFO [job preprocessing] /private/tmp/docker_tmp8v6vwgnx$ docker \
    run \
    -i \
    --mount=type=bind,source=/private/tmp/docker_tmp8v6vwgnx,target=/VwduRl \
    --mount=type=bind,source=/private/tmp/docker_tmpcd8_n06b,target=/tmp \
    --mount=type=bind,source=/Users/heimann/Documents/cri_iatlas/HTAN/ohsu_level3/0000265302_kallisto.tsv,target=/var/lib/cwl/stg6ffa20f2-c94d-4195-9f8e-a0209185ff38/0000265302_kallisto.tsv,readonly \
    --workdir=/VwduRl \
    --read-only=true \
    --user=501:20 \
    --rm \
    --cidfile=/private/tmp/docker_tmpkkgvo8gk/20230322170646-867390.cid \
    --env=TMPDIR=/tmp \
    --env=HOME=/VwduRl \
    quay.io/cri-iatlas/r_tidy_utils:1.0 \
    Rscript \
    /usr/local/bin/format_expression_file.R \
    -i \
    /var/lib/cwl/stg6ffa20f2-c94d-4195-9f8e-a0209185ff38/0000265302_kallisto.tsv \
    -e \
    tpm \
    -g \
    value6 \
    -o \
    output.tsv \
    -m \
    kallisto \
    -s \
    target_id
Parsed with column specification:
cols(
  target_id = col_character(),
  length = col_double(),
  eff_length = col_double(),
  est_counts = col_double(),
  tpm = col_double()
)
INFO [job preprocessing] Max memory used: 2401MiB
INFO [job preprocessing] completed success
INFO [step preprocessing] completed success
INFO [workflow ] starting step cibersort
INFO [step cibersort] start
INFO ['docker', 'pull', 'quay.io/cri-iatlas/cibersort:1.0']
Error response from daemon: unauthorized: access to the requested resource is not authorized
ERROR Workflow error, try again with --debug for more information:
Docker is not available for this tool, try --no-container to disable Docker, or install a user space Docker replacement like uDocker with --user-space-docker-cmd.: Command '['docker', 'pull', 'quay.io/cri-iatlas/cibersort:1.0']' returned non-zero exit status 1.

andrewelamb commented 1 year ago

@heimannch Yeah that's because Cibersort itself is not publicly available, so I'm not allowed to disseminate it.

heimannch commented 1 year ago

Oh I see. How should I proceed to run this workflow? Should I send you the data?

andrewelamb commented 1 year ago

Yeah that's probably the easiest for now.

andrewelamb commented 1 year ago

Hey Carol,

The input files need to have three columns,

["sample", "ran_seq_expr", "hgnc"]

and they need to have hgnc names

On Thu, Mar 23, 2023 at 12:49 PM Carolina Heimann @.***> wrote:

Closed #26 https://github.com/CRI-iAtlas/iatlas-workflows/issues/26 as completed.

— Reply to this email directly, view it on GitHub https://github.com/CRI-iAtlas/iatlas-workflows/issues/26#event-8831739689, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABXC32ISBGK242ZXT6XM6ADW5SSNVANCNFSM6AAAAAAWEQAC3A . You are receiving this because you were assigned.Message ID: @.***>

CRI-iAtlas / iatlas-workflows

quay.io/cri-iatlas/cibersort:1.0 not public #26