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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Toil isn't being installed by "bcbio_nextgen.py upgrade -u development --data --tools --cwl" #2710

Closed amizeranschi closed 5 years ago

amizeranschi commented 5 years ago

I've just made a fresh local install of bcbio_nextgen and then upgraded with:

bcbio_nextgen.py upgrade -u development --data --tools --cwl

I noticed that this doesn't install Toil along with Cromwell, Rabix-bunny etc. Is this intended?

Here's a list of packages that the previous command installed (among others):


## Package Plan ##

  environment location: /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/envs/bcbiovm

  added / updated specs:
    - bcbio-nextgen-vm
    - cromwell

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    arvados-cwl-runner-1.3.1.20190301150258|           py27_0         126 KB  bioconda
    arvados-python-client-1.3.1.20190301150258|           py27_0         327 KB  bioconda
    backports.csv-1.0.1        |           py27_0          24 KB  bioconda
    bagit-1.7.0                |             py_0          23 KB  conda-forge
    bcbio-nextgen-vm-0.1.3     |           py27_1         103 KB  bioconda
    boto3-1.9.106              |             py_0          62 KB  conda-forge
    cachecontrol-0.11.7        |             py_0          17 KB  conda-forge
    ciso8601-2.1.1             |py27h14c3975_1000          14 KB  conda-forge
    cromwell-0.37              |                0       333.3 MB  bioconda
    cwltool-1.0.20190228155703 |           py27_0         558 KB  conda-forge
    dx-cwl-0.1.0a20180905      |           py27_0          25 KB  bioconda
    dxpy-0.257.3               |           py27_0         553 KB  bioconda
    findutils-4.6.0            |    h14c3975_1000         611 KB  conda-forge
    fusepy-2.0.4               |           py27_0          22 KB  bioconda
    google-api-python-client-1.6.7|             py_0          41 KB  conda-forge
    google-cloud-sdk-166.0.0   |           py27_0        12.9 MB  bioconda
    graphviz-2.38.0            |    hf68f40c_1011         9.8 MB  conda-forge
    html5lib-1.0.1             |             py_0          89 KB  conda-forge
    isodate-0.6.0              |             py_1          25 KB  conda-forge
    keepalive-0.5              |             py_1          10 KB  conda-forge
    libmagic-5.36              |       h14c3975_0         290 KB  conda-forge
    lockfile-0.12.2            |             py_1          11 KB  conda-forge
    mistune-0.8.4              |py27h14c3975_1000          52 KB  conda-forge
    mypy_extensions-0.4.1      |        py27_1000           9 KB  conda-forge
    oauth2client-1.5.2         |           py27_0          82 KB  bioconda
    pathlib2-2.3.2             |        py27_1000          30 KB  conda-forge
    prov-1.5.1                 |             py_1         152 KB  conda-forge
    pyasn1-modules-0.0.5       |           py27_0          42 KB  bioconda
    pydotplus-2.0.2            |             py_2          23 KB  conda-forge
    python-magic-0.4.15        |        py27_1000          11 KB  conda-forge
    rabix-bunny-1.0.4          |                6        40.9 MB  bioconda
    rdflib-4.2.2               |        py27_1000         547 KB  conda-forge
    rdflib-jsonld-0.4          |           py27_0          31 KB  bioconda
    rsa-3.1.4                  |           py27_0          87 KB  bioconda
    ruamel.ordereddict-0.4.13  |   py27h14c3975_1          37 KB  conda-forge
    ruamel.yaml-0.15.77        |   py27h470a237_0         680 KB  conda-forge
    schema-salad-4.1.20190227145202|           py27_0         332 KB  conda-forge
    sevenbridges-python-0.18.2 |           py27_0         102 KB  bioconda
    shellescape-3.4.1          |             py_1           7 KB  bioconda
    sparqlwrapper-1.8.2        |        py27_1000          37 KB  conda-forge
    synapseclient-1.7.5        |             py_1         107 KB  bioconda
    typing-3.6.6               |        py27_1000          41 KB  conda-forge
    typing_extensions-3.7.2    |        py27_1000          21 KB  conda-forge
    uritemplate-3.0.0          |             py_1           9 KB  conda-forge
    webencodings-0.5.1         |             py_1          12 KB  conda-forge
    ws4py-0.5.1                |             py_0          34 KB  conda-forge
    xattr-0.9.6                |py27h14c3975_1000          24 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       402.1 MB
chapmanb commented 5 years ago

Thanks for the question and sorry about not having Toil right now. Due to Toil not being compatible with the latest cwltool, we're currently not including it as part of the install. It'll conflict with the arvados tools, which require an up to date cwltool. I'm hoping Toil will be compatible soon and we can re-include it, but right now if you want to evaluate toil the best way is in a separate custom environment.

amizeranschi commented 5 years ago

Alright, thanks for explaining the situation. I hope Toil will get updated and reincluded in bcbio soon.