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dnanexus / dx-toolkit

DNAnexus platform client libraries
http://autodoc.dnanexus.com/
Apache License 2.0
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No dx-verify-file from dx command line tool installed with pip3 #630

Closed violetbrina closed 4 years ago

violetbrina commented 4 years ago

Migrating to python3 including my dx cli, but the dx-verify-file command is not there.

This is all I have in my venv bin:

./                   dx-build-applet*       dx-jobutil-report-error*  python@
../                  dx-build-report-html*  dx-log-stream*        python-argcomplete-check-easy-install-script*
__pycache__/                 dx-clone-asset*        dx-mount-all-inputs*      python-argcomplete-tcsh*
activate                 dx-docker*         dx-notebook-reconnect*    python3@
activate-global-python-argcomplete*  dx-download-all-inputs*    dx-print-bash-vars*   register-python-argcomplete*
activate.csh                 dx-fetch-bundled-depends*  dx-upload-all-outputs*    tqdm*
activate.fish                dx-generate-dxapp*     easy_install*         wsdump.py*
chardetect*              dx-jobutil-add-output* easy_install-3.7*     xattr*
dx*                  dx-jobutil-dxlink*     pip*
dx-app-wizard*               dx-jobutil-new-job*    pip3*
dx-build-app*                dx-jobutil-parse-link* pip3.7*

Please add dx-verify-file to pip, it is very helpful for our workflow.

kpjensen commented 4 years ago

dx-verify-file is a standalone c++ executable that is not included with the pypi / pip installation, only the tarball download https://documentation.dnanexus.com/downloads#installation-of-java-r-and-c-sdk-from-tarball. It rarely changes, so you could move the dx-verify-file binary to somewhere in your PATH globally so that it is available in each venv.