`/usr/bin/env: ‘python2.7’: No such file or directory`

I also tried building from source, which produces some error messages but ultimately does seem able to install.

Reprex

wget https://dnanexus-sdk.s3.amazonaws.com/dx-toolkit-v0.320.0-source.tar.gz
tar -xvf dx-toolkit-v0.320.0-source.tar.gz 
cd dx-toolkit
make
source environment

Output

make

``` make -C src all make[1]: Entering directory '/home/bms20/dx-toolkit/src' (if [ ! -e "/home/bms20/dx-toolkit/src/../src/python/dxpy/toolkit_version.py" ]; then \ echo "version = 'UNKNOWN_VERSION'" > "/home/bms20/dx-toolkit/src/../src/python/dxpy/toolkit_version.py"; \ echo -e "package com.dnanexus;\nclass DXToolkitVersion {\n public static final String TOOLKIT_VERSION = \"0.0.0\";\n}" > "/home/bms20/dx-toolkit/src/../src/java/src/main/java/com/dnanexus/DXToolkitVersion.java"; \ echo UNKNOWN_VERSION > "/home/bms20/dx-toolkit/src/../build/info/version"; \ fi) (if [ -d "/home/bms20/dx-toolkit/src/../.git" ]; then \ export GIT_TOOLKIT_VERSION=$((git describe --match 'v*.*.*' || git rev-parse --short HEAD) | sed -e 's/-[0-9]-/+/'); \ echo "version = '${GIT_TOOLKIT_VERSION/#v/}'" > "/home/bms20/dx-toolkit/src/../src/python/dxpy/toolkit_version.py"; \ echo -e "package com.dnanexus;\nclass DXToolkitVersion {\n public static final String TOOLKIT_VERSION = \"$GIT_TOOLKIT_VERSION\";\n}" > "/home/bms20/dx-toolkit/src/../src/java/src/main/java/com/dnanexus/DXToolkitVersion.java"; \ echo $GIT_TOOLKIT_VERSION > "/home/bms20/dx-toolkit/src/../build/info/version"; \ fi) make -j -l 2.0 -C ../contrib api_wrappers make[2]: Entering directory '/home/bms20/dx-toolkit/contrib' make -C ./perl lib/DNAnexus/API.pm make[3]: Entering directory '/home/bms20/dx-toolkit/contrib/perl' make[3]: 'lib/DNAnexus/API.pm' is up to date. make[3]: Leaving directory '/home/bms20/dx-toolkit/contrib/perl' make -C ./ruby lib/dxruby/api.rb make[3]: Entering directory '/home/bms20/dx-toolkit/contrib/ruby' make[3]: 'lib/dxruby/api.rb' is up to date. make[3]: Leaving directory '/home/bms20/dx-toolkit/contrib/ruby' make[2]: Leaving directory '/home/bms20/dx-toolkit/contrib' mkdir -p "/home/bms20/dx-toolkit/src/../share/dnanexus/src" cp -a cpp "/home/bms20/dx-toolkit/src/../share/dnanexus/src" mkdir -p "/home/bms20/dx-toolkit/src/../share/dnanexus/lib" cp -R -v bash "/home/bms20/dx-toolkit/src/../share/dnanexus/lib" 'bash' -> '/home/bms20/dx-toolkit/src/../share/dnanexus/lib/bash' 'bash/dx_helpers.sh' -> '/home/bms20/dx-toolkit/src/../share/dnanexus/lib/bash/dx_helpers.sh' python -c 'import sys; exit("dx-toolkit is not compatible with Python < 2.7" if sys.version_info < (2, 7) else 0)' rm -rf "/home/bms20/dx-toolkit/src/../share/dnanexus/lib/python3.9/site-packages" "/home/bms20/dx-toolkit/src/../build/py_env3.9" python/dist mkdir -p "$(dirname '/home/bms20/dx-toolkit/src/../share/dnanexus/lib/python3.9/site-packages')" python3 -m venv "/home/bms20/dx-toolkit/src/../build/py_env3.9" unset PYTHONPATH; source "/home/bms20/dx-toolkit/src/../build/py_env3.9/bin/activate"; pip3 install --upgrade -r python/requirements_setuptools.txt Collecting pip==19.2 Downloading pip-19.2-py2.py3-none-any.whl (1.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 7.9 MB/s eta 0:00:00 Collecting setuptools==41.4.0 Downloading setuptools-41.4.0-py2.py3-none-any.whl (580 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 580.3/580.3 KB 5.2 MB/s eta 0:00:00 Collecting wheel==0.33.4 Downloading wheel-0.33.4-py2.py3-none-any.whl (21 kB) Installing collected packages: wheel, setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 58.1.0 Uninstalling setuptools-58.1.0: Successfully uninstalled setuptools-58.1.0 Attempting uninstall: pip Found existing installation: pip 22.0.4 Uninstalling pip-22.0.4: Successfully uninstalled pip-22.0.4 Successfully installed pip-19.2 setuptools-41.4.0 wheel-0.33.4 unset PYTHONPATH; source "/home/bms20/dx-toolkit/src/../build/py_env3.9/bin/activate"; cd python; python setup.py bdist_wheel running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/dxpy copying dxpy/__init__.py -> build/lib/dxpy copying dxpy/api.py -> build/lib/dxpy copying dxpy/app_builder.py -> build/lib/dxpy copying dxpy/app_categories.py -> build/lib/dxpy copying dxpy/asset_builder.py -> build/lib/dxpy copying dxpy/compat.py -> build/lib/dxpy copying dxpy/dxlog.py -> build/lib/dxpy copying dxpy/exceptions.py -> build/lib/dxpy copying dxpy/executable_builder.py -> build/lib/dxpy copying dxpy/ssh_tunnel_app_support.py -> build/lib/dxpy copying dxpy/system_requirements.py -> build/lib/dxpy copying dxpy/toolkit_version.py -> build/lib/dxpy copying dxpy/workflow_builder.py -> build/lib/dxpy creating build/lib/dxpy/bindings copying dxpy/bindings/__init__.py -> build/lib/dxpy/bindings copying dxpy/bindings/auth.py -> build/lib/dxpy/bindings copying dxpy/bindings/download_all_inputs.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxanalysis.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxapp.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxapp_container_functions.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxapplet.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxdatabase.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxdatabase_functions.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxdataobject_functions.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxfile.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxfile_functions.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxglobalworkflow.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxjob.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxproject.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxrecord.py -> build/lib/dxpy/bindings copying dxpy/bindings/dxworkflow.py -> build/lib/dxpy/bindings copying dxpy/bindings/mount_all_inputs.py -> build/lib/dxpy/bindings copying dxpy/bindings/search.py -> build/lib/dxpy/bindings creating build/lib/dxpy/cli copying dxpy/cli/__init__.py -> build/lib/dxpy/cli copying dxpy/cli/cp.py -> build/lib/dxpy/cli copying dxpy/cli/download.py -> build/lib/dxpy/cli copying dxpy/cli/exec_io.py -> build/lib/dxpy/cli copying dxpy/cli/org.py -> build/lib/dxpy/cli copying dxpy/cli/parsers.py -> build/lib/dxpy/cli copying dxpy/cli/workflow.py -> build/lib/dxpy/cli creating build/lib/dxpy/packages copying dxpy/packages/__init__.py -> build/lib/dxpy/packages creating build/lib/dxpy/scripts copying dxpy/scripts/__init__.py -> build/lib/dxpy/scripts copying dxpy/scripts/dx.py -> build/lib/dxpy/scripts copying dxpy/scripts/dx_app_wizard.py -> build/lib/dxpy/scripts copying dxpy/scripts/dx_build_app.py -> build/lib/dxpy/scripts copying dxpy/scripts/dx_build_applet.py -> build/lib/dxpy/scripts creating build/lib/dxpy/templating copying dxpy/templating/__init__.py -> build/lib/dxpy/templating copying dxpy/templating/bash.py -> build/lib/dxpy/templating copying dxpy/templating/python.py -> build/lib/dxpy/templating copying dxpy/templating/utils.py -> build/lib/dxpy/templating creating build/lib/dxpy/utils copying dxpy/utils/__init__.py -> build/lib/dxpy/utils copying dxpy/utils/batch_utils.py -> build/lib/dxpy/utils copying dxpy/utils/completer.py -> build/lib/dxpy/utils copying dxpy/utils/config.py -> build/lib/dxpy/utils copying dxpy/utils/describe.py -> build/lib/dxpy/utils copying dxpy/utils/exec_utils.py -> build/lib/dxpy/utils copying dxpy/utils/executable_unbuilder.py -> build/lib/dxpy/utils copying dxpy/utils/file_load_utils.py -> build/lib/dxpy/utils copying dxpy/utils/genomic_utils.py -> build/lib/dxpy/utils copying dxpy/utils/job_log_client.py -> build/lib/dxpy/utils copying dxpy/utils/local_exec_utils.py -> build/lib/dxpy/utils copying dxpy/utils/pathmatch.py -> build/lib/dxpy/utils copying dxpy/utils/pretty_print.py -> build/lib/dxpy/utils copying dxpy/utils/printing.py -> build/lib/dxpy/utils copying dxpy/utils/resolver.py -> build/lib/dxpy/utils copying dxpy/utils/spelling_corrector.py -> build/lib/dxpy/utils creating build/lib/dxpy/templating/templates copying dxpy/templating/templates/Readme.md -> build/lib/dxpy/templating/templates creating build/lib/dxpy/templating/templates/bash creating build/lib/dxpy/templating/templates/bash/basic copying dxpy/templating/templates/bash/basic/dxapp.json -> build/lib/dxpy/templating/templates/bash/basic creating build/lib/dxpy/templating/templates/bash/basic/src copying dxpy/templating/templates/bash/basic/src/code.sh -> build/lib/dxpy/templating/templates/bash/basic/src creating build/lib/dxpy/templating/templates/bash/parallelized copying dxpy/templating/templates/bash/parallelized/dxapp.json -> build/lib/dxpy/templating/templates/bash/parallelized creating build/lib/dxpy/templating/templates/bash/parallelized/src copying dxpy/templating/templates/bash/parallelized/src/code.sh -> build/lib/dxpy/templating/templates/bash/parallelized/src creating build/lib/dxpy/templating/templates/bash/scatter-process-gather copying dxpy/templating/templates/bash/scatter-process-gather/dxapp.json -> build/lib/dxpy/templating/templates/bash/scatter-process-gather creating build/lib/dxpy/templating/templates/bash/scatter-process-gather/src copying dxpy/templating/templates/bash/scatter-process-gather/src/code.sh -> build/lib/dxpy/templating/templates/bash/scatter-process-gather/src creating build/lib/dxpy/templating/templates/python creating build/lib/dxpy/templating/templates/python/basic copying dxpy/templating/templates/python/basic/dxapp.json -> build/lib/dxpy/templating/templates/python/basic creating build/lib/dxpy/templating/templates/python/basic/src copying dxpy/templating/templates/python/basic/src/code.py -> build/lib/dxpy/templating/templates/python/basic/src creating build/lib/dxpy/templating/templates/python/basic/test copying dxpy/templating/templates/python/basic/test/test.py -> build/lib/dxpy/templating/templates/python/basic/test creating build/lib/dxpy/templating/templates/python/parallelized copying dxpy/templating/templates/python/parallelized/dxapp.json -> build/lib/dxpy/templating/templates/python/parallelized creating build/lib/dxpy/templating/templates/python/parallelized/src copying dxpy/templating/templates/python/parallelized/src/code.py -> build/lib/dxpy/templating/templates/python/parallelized/src creating build/lib/dxpy/templating/templates/python/parallelized/test copying dxpy/templating/templates/python/parallelized/test/test.py -> build/lib/dxpy/templating/templates/python/parallelized/test creating build/lib/dxpy/templating/templates/python/scatter-process-gather copying dxpy/templating/templates/python/scatter-process-gather/dxapp.json -> build/lib/dxpy/templating/templates/python/scatter-process-gather creating build/lib/dxpy/templating/templates/python/scatter-process-gather/src copying dxpy/templating/templates/python/scatter-process-gather/src/code.py -> build/lib/dxpy/templating/templates/python/scatter-process-gather/src creating build/lib/dxpy/templating/templates/python/scatter-process-gather/test copying dxpy/templating/templates/python/scatter-process-gather/test/test.py -> build/lib/dxpy/templating/templates/python/scatter-process-gather/test running build_scripts creating build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-clone-asset -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-docker -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-download-all-inputs -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-fetch-bundled-depends -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-generate-dxapp -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-jobutil-add-output -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-jobutil-dxlink -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-jobutil-new-job -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-jobutil-parse-link -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-jobutil-report-error -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-log-stream -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-mount-all-inputs -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-notebook-reconnect -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-print-bash-vars -> build/scripts-3.9 copying and adjusting /home/bms20/dx-toolkit/src/python/scripts/dx-upload-all-outputs -> build/scripts-3.9 changing mode of build/scripts-3.9/dx-clone-asset from 644 to 755 changing mode of build/scripts-3.9/dx-docker from 644 to 755 changing mode of build/scripts-3.9/dx-download-all-inputs from 644 to 755 changing mode of build/scripts-3.9/dx-fetch-bundled-depends from 644 to 755 changing mode of build/scripts-3.9/dx-generate-dxapp from 644 to 755 changing mode of build/scripts-3.9/dx-jobutil-add-output from 644 to 755 changing mode of build/scripts-3.9/dx-jobutil-dxlink from 644 to 755 changing mode of build/scripts-3.9/dx-jobutil-new-job from 644 to 755 changing mode of build/scripts-3.9/dx-jobutil-parse-link from 644 to 755 changing mode of build/scripts-3.9/dx-jobutil-report-error from 644 to 755 changing mode of build/scripts-3.9/dx-log-stream from 644 to 755 changing mode of build/scripts-3.9/dx-mount-all-inputs from 644 to 755 changing mode of build/scripts-3.9/dx-notebook-reconnect from 644 to 755 changing mode of build/scripts-3.9/dx-print-bash-vars from 644 to 755 changing mode of build/scripts-3.9/dx-upload-all-outputs from 644 to 755 installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/__init__.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/api.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/app_builder.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/app_categories.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/asset_builder.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/compat.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/dxlog.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/exceptions.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/executable_builder.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/ssh_tunnel_app_support.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/system_requirements.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/toolkit_version.py -> build/bdist.linux-x86_64/wheel/dxpy copying build/lib/dxpy/workflow_builder.py -> build/bdist.linux-x86_64/wheel/dxpy creating build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/__init__.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/auth.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/download_all_inputs.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxanalysis.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxapp.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxapp_container_functions.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxapplet.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxdatabase.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxdatabase_functions.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxdataobject_functions.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxfile.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxfile_functions.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxglobalworkflow.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxjob.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxproject.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxrecord.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/dxworkflow.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/mount_all_inputs.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings copying build/lib/dxpy/bindings/search.py -> build/bdist.linux-x86_64/wheel/dxpy/bindings creating build/bdist.linux-x86_64/wheel/dxpy/cli copying build/lib/dxpy/cli/__init__.py -> build/bdist.linux-x86_64/wheel/dxpy/cli copying build/lib/dxpy/cli/cp.py -> build/bdist.linux-x86_64/wheel/dxpy/cli copying build/lib/dxpy/cli/download.py -> build/bdist.linux-x86_64/wheel/dxpy/cli copying build/lib/dxpy/cli/exec_io.py -> build/bdist.linux-x86_64/wheel/dxpy/cli copying build/lib/dxpy/cli/org.py -> build/bdist.linux-x86_64/wheel/dxpy/cli copying build/lib/dxpy/cli/parsers.py -> build/bdist.linux-x86_64/wheel/dxpy/cli copying build/lib/dxpy/cli/workflow.py -> build/bdist.linux-x86_64/wheel/dxpy/cli creating build/bdist.linux-x86_64/wheel/dxpy/packages copying build/lib/dxpy/packages/__init__.py -> build/bdist.linux-x86_64/wheel/dxpy/packages creating build/bdist.linux-x86_64/wheel/dxpy/scripts copying build/lib/dxpy/scripts/__init__.py -> build/bdist.linux-x86_64/wheel/dxpy/scripts copying build/lib/dxpy/scripts/dx.py -> build/bdist.linux-x86_64/wheel/dxpy/scripts copying build/lib/dxpy/scripts/dx_app_wizard.py -> build/bdist.linux-x86_64/wheel/dxpy/scripts copying build/lib/dxpy/scripts/dx_build_app.py -> build/bdist.linux-x86_64/wheel/dxpy/scripts copying build/lib/dxpy/scripts/dx_build_applet.py -> build/bdist.linux-x86_64/wheel/dxpy/scripts creating build/bdist.linux-x86_64/wheel/dxpy/templating copying build/lib/dxpy/templating/__init__.py -> build/bdist.linux-x86_64/wheel/dxpy/templating copying build/lib/dxpy/templating/bash.py -> build/bdist.linux-x86_64/wheel/dxpy/templating copying build/lib/dxpy/templating/python.py -> build/bdist.linux-x86_64/wheel/dxpy/templating copying build/lib/dxpy/templating/utils.py -> build/bdist.linux-x86_64/wheel/dxpy/templating creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates copying build/lib/dxpy/templating/templates/Readme.md -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/basic copying build/lib/dxpy/templating/templates/bash/basic/dxapp.json -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/basic creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/basic/src copying build/lib/dxpy/templating/templates/bash/basic/src/code.sh -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/basic/src creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/parallelized copying build/lib/dxpy/templating/templates/bash/parallelized/dxapp.json -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/parallelized creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/parallelized/src copying build/lib/dxpy/templating/templates/bash/parallelized/src/code.sh -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/parallelized/src creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/scatter-process-gather copying build/lib/dxpy/templating/templates/bash/scatter-process-gather/dxapp.json -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/scatter-process-gather creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/scatter-process-gather/src copying build/lib/dxpy/templating/templates/bash/scatter-process-gather/src/code.sh -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/bash/scatter-process-gather/src creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/basic copying build/lib/dxpy/templating/templates/python/basic/dxapp.json -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/basic creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/basic/src copying build/lib/dxpy/templating/templates/python/basic/src/code.py -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/basic/src creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/basic/test copying build/lib/dxpy/templating/templates/python/basic/test/test.py -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/basic/test creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/parallelized copying build/lib/dxpy/templating/templates/python/parallelized/dxapp.json -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/parallelized creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/parallelized/src copying build/lib/dxpy/templating/templates/python/parallelized/src/code.py -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/parallelized/src creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/parallelized/test copying build/lib/dxpy/templating/templates/python/parallelized/test/test.py -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/parallelized/test creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/scatter-process-gather copying build/lib/dxpy/templating/templates/python/scatter-process-gather/dxapp.json -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/scatter-process-gather creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/scatter-process-gather/src copying build/lib/dxpy/templating/templates/python/scatter-process-gather/src/code.py -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/scatter-process-gather/src creating build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/scatter-process-gather/test copying build/lib/dxpy/templating/templates/python/scatter-process-gather/test/test.py -> build/bdist.linux-x86_64/wheel/dxpy/templating/templates/python/scatter-process-gather/test creating build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/__init__.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/batch_utils.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/completer.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/config.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/describe.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/exec_utils.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/executable_unbuilder.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/file_load_utils.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/genomic_utils.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/job_log_client.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/local_exec_utils.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/pathmatch.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/pretty_print.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/printing.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/resolver.py -> build/bdist.linux-x86_64/wheel/dxpy/utils copying build/lib/dxpy/utils/spelling_corrector.py -> build/bdist.linux-x86_64/wheel/dxpy/utils running install_egg_info running egg_info creating dxpy.egg-info writing dxpy.egg-info/PKG-INFO writing dependency_links to dxpy.egg-info/dependency_links.txt writing entry points to dxpy.egg-info/entry_points.txt writing requirements to dxpy.egg-info/requires.txt writing top-level names to dxpy.egg-info/top_level.txt writing manifest file 'dxpy.egg-info/SOURCES.txt' reading manifest file 'dxpy.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'dxpy.egg-info/SOURCES.txt' Copying dxpy.egg-info to build/bdist.linux-x86_64/wheel/dxpy-0.320.0-py3.9.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data creating build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-clone-asset -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-docker -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-download-all-inputs -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-fetch-bundled-depends -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-generate-dxapp -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-jobutil-add-output -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-jobutil-dxlink -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-jobutil-new-job -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-jobutil-parse-link -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-jobutil-report-error -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-log-stream -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-mount-all-inputs -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-notebook-reconnect -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-print-bash-vars -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts copying build/scripts-3.9/dx-upload-all-outputs -> build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-clone-asset to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-docker to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-download-all-inputs to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-fetch-bundled-depends to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-generate-dxapp to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-jobutil-add-output to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-jobutil-dxlink to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-jobutil-new-job to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-jobutil-parse-link to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-jobutil-report-error to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-log-stream to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-mount-all-inputs to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-notebook-reconnect to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-print-bash-vars to 755 changing mode of build/bdist.linux-x86_64/wheel/dxpy-0.320.0.data/scripts/dx-upload-all-outputs to 755 creating build/bdist.linux-x86_64/wheel/dxpy-0.320.0.dist-info/WHEEL creating 'dist/dxpy-0.320.0-py2.py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'dxpy/__init__.py' adding 'dxpy/api.py' adding 'dxpy/app_builder.py' adding 'dxpy/app_categories.py' adding 'dxpy/asset_builder.py' adding 'dxpy/compat.py' adding 'dxpy/dxlog.py' adding 'dxpy/exceptions.py' adding 'dxpy/executable_builder.py' adding 'dxpy/ssh_tunnel_app_support.py' adding 'dxpy/system_requirements.py' adding 'dxpy/toolkit_version.py' adding 'dxpy/workflow_builder.py' adding 'dxpy/bindings/__init__.py' adding 'dxpy/bindings/auth.py' adding 'dxpy/bindings/download_all_inputs.py' adding 'dxpy/bindings/dxanalysis.py' adding 'dxpy/bindings/dxapp.py' adding 'dxpy/bindings/dxapp_container_functions.py' adding 'dxpy/bindings/dxapplet.py' adding 'dxpy/bindings/dxdatabase.py' adding 'dxpy/bindings/dxdatabase_functions.py' adding 'dxpy/bindings/dxdataobject_functions.py' adding 'dxpy/bindings/dxfile.py' adding 'dxpy/bindings/dxfile_functions.py' adding 'dxpy/bindings/dxglobalworkflow.py' adding 'dxpy/bindings/dxjob.py' adding 'dxpy/bindings/dxproject.py' adding 'dxpy/bindings/dxrecord.py' adding 'dxpy/bindings/dxworkflow.py' adding 'dxpy/bindings/mount_all_inputs.py' adding 'dxpy/bindings/search.py' adding 'dxpy/cli/__init__.py' adding 'dxpy/cli/cp.py' adding 'dxpy/cli/download.py' adding 'dxpy/cli/exec_io.py' adding 'dxpy/cli/org.py' adding 'dxpy/cli/parsers.py' adding 'dxpy/cli/workflow.py' adding 'dxpy/packages/__init__.py' adding 'dxpy/scripts/__init__.py' adding 'dxpy/scripts/dx.py' adding 'dxpy/scripts/dx_app_wizard.py' adding 'dxpy/scripts/dx_build_app.py' adding 'dxpy/scripts/dx_build_applet.py' adding 'dxpy/templating/__init__.py' adding 'dxpy/templating/bash.py' adding 'dxpy/templating/python.py' adding 'dxpy/templating/utils.py' adding 'dxpy/templating/templates/Readme.md' adding 'dxpy/templating/templates/bash/basic/dxapp.json' adding 'dxpy/templating/templates/bash/basic/src/code.sh' adding 'dxpy/templating/templates/bash/parallelized/dxapp.json' adding 'dxpy/templating/templates/bash/parallelized/src/code.sh' adding 'dxpy/templating/templates/bash/scatter-process-gather/dxapp.json' adding 'dxpy/templating/templates/bash/scatter-process-gather/src/code.sh' adding 'dxpy/templating/templates/python/basic/dxapp.json' adding 'dxpy/templating/templates/python/basic/src/code.py' adding 'dxpy/templating/templates/python/basic/test/test.py' adding 'dxpy/templating/templates/python/parallelized/dxapp.json' adding 'dxpy/templating/templates/python/parallelized/src/code.py' adding 'dxpy/templating/templates/python/parallelized/test/test.py' adding 'dxpy/templating/templates/python/scatter-process-gather/dxapp.json' adding 'dxpy/templating/templates/python/scatter-process-gather/src/code.py' adding 'dxpy/templating/templates/python/scatter-process-gather/test/test.py' adding 'dxpy/utils/__init__.py' adding 'dxpy/utils/batch_utils.py' adding 'dxpy/utils/completer.py' adding 'dxpy/utils/config.py' adding 'dxpy/utils/describe.py' adding 'dxpy/utils/exec_utils.py' adding 'dxpy/utils/executable_unbuilder.py' adding 'dxpy/utils/file_load_utils.py' adding 'dxpy/utils/genomic_utils.py' adding 'dxpy/utils/job_log_client.py' adding 'dxpy/utils/local_exec_utils.py' adding 'dxpy/utils/pathmatch.py' adding 'dxpy/utils/pretty_print.py' adding 'dxpy/utils/printing.py' adding 'dxpy/utils/resolver.py' adding 'dxpy/utils/spelling_corrector.py' adding 'dxpy-0.320.0.data/scripts/dx-clone-asset' adding 'dxpy-0.320.0.data/scripts/dx-docker' adding 'dxpy-0.320.0.data/scripts/dx-download-all-inputs' adding 'dxpy-0.320.0.data/scripts/dx-fetch-bundled-depends' adding 'dxpy-0.320.0.data/scripts/dx-generate-dxapp' adding 'dxpy-0.320.0.data/scripts/dx-jobutil-add-output' adding 'dxpy-0.320.0.data/scripts/dx-jobutil-dxlink' adding 'dxpy-0.320.0.data/scripts/dx-jobutil-new-job' adding 'dxpy-0.320.0.data/scripts/dx-jobutil-parse-link' adding 'dxpy-0.320.0.data/scripts/dx-jobutil-report-error' adding 'dxpy-0.320.0.data/scripts/dx-log-stream' adding 'dxpy-0.320.0.data/scripts/dx-mount-all-inputs' adding 'dxpy-0.320.0.data/scripts/dx-notebook-reconnect' adding 'dxpy-0.320.0.data/scripts/dx-print-bash-vars' adding 'dxpy-0.320.0.data/scripts/dx-upload-all-outputs' adding 'dxpy-0.320.0.dist-info/METADATA' adding 'dxpy-0.320.0.dist-info/WHEEL' adding 'dxpy-0.320.0.dist-info/entry_points.txt' adding 'dxpy-0.320.0.dist-info/top_level.txt' adding 'dxpy-0.320.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel export DXPY_WHEEL_FILENAME=$(basename python/dist/dxpy-*.whl) ; \ unset PYTHONPATH; source "/home/bms20/dx-toolkit/src/../build/py_env3.9/bin/activate"; pip3 install --ignore-installed --prefix="/home/bms20/dx-toolkit/src/.." python/dist/${DXPY_WHEEL_FILENAME}[xattr] Processing ./python/dist/dxpy-0.320.0-py2.py3-none-any.whl Collecting argcomplete>=1.9.4 (from dxpy==0.320.0) Using cached https://files.pythonhosted.org/packages/d3/e5/c5509683462e51b070df9e83e7f72c1ccfe3f733f328b4a0f06804c27278/argcomplete-2.0.0-py2.py3-none-any.whl Collecting websocket-client==0.57.0 (from dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/4c/5f/f61b420143ed1c8dc69f9eaec5ff1ac36109d52c80de49d66e0c36c3dfdf/websocket_client-0.57.0-py2.py3-none-any.whl (200kB) |████████████████████████████████| 204kB 28.6MB/s Collecting requests<=2.26.0,>=2.8.0 (from dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/92/96/144f70b972a9c0eabbd4391ef93ccd49d0f2747f4f6a2a2738e99e5adc65/requests-2.26.0-py2.py3-none-any.whl (62kB) |████████████████████████████████| 71kB 1.9MB/s Collecting cryptography<37,>=3.4.2; python_version > "3.5" (from dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/13/70/e35fc8a742bfc030df62e017e9eafb103ac5c2e3cea1ff340fd9af9d365e/cryptography-36.0.2-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (3.6MB) |████████████████████████████████| 3.6MB 101.0MB/s Collecting python-dateutil>=2.5 (from dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/36/7a/87837f39d0296e723bb9b62bbb257d0355c7f6128853c78955f57342a56d/python_dateutil-2.8.2-py2.py3-none-any.whl (247kB) |████████████████████████████████| 256kB 61.3MB/s Collecting psutil>=3.3.0 (from dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/62/1f/f14225bda76417ab9bd808ff21d5cd59d5435a9796ca09b34d4cb0edcd88/psutil-5.9.1-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (281kB) |████████████████████████████████| 286kB 43.7MB/s Collecting xattr==0.9.6; (sys_platform == "linux2" or sys_platform == "linux") and extra == "xattr" (from dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/60/80/a1f35bfd3c7ffb78791b2a6a15c233584a102a20547fd96d48933ec453e7/xattr-0.9.6.tar.gz Collecting six (from websocket-client==0.57.0->dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/d9/5a/e7c31adbe875f2abbb91bd84cf2dc52d792b5a01506781dbcf25c91daf11/six-1.16.0-py2.py3-none-any.whl Collecting certifi>=2017.4.17 (from requests<=2.26.0,>=2.8.0->dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/e9/06/d3d367b7af6305b16f0d28ae2aaeb86154fa91f144f036c2d5002a5a202b/certifi-2022.6.15-py3-none-any.whl (160kB) |████████████████████████████████| 163kB 48.8MB/s Collecting charset-normalizer~=2.0.0; python_version >= "3" (from requests<=2.26.0,>=2.8.0->dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/06/b3/24afc8868eba069a7f03650ac750a778862dc34941a4bebeb58706715726/charset_normalizer-2.0.12-py3-none-any.whl Collecting idna<4,>=2.5; python_version >= "3" (from requests<=2.26.0,>=2.8.0->dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/04/a2/d918dcd22354d8958fe113e1a3630137e0fc8b44859ade3063982eacd2a4/idna-3.3-py3-none-any.whl (61kB) |████████████████████████████████| 61kB 647kB/s Collecting urllib3<1.27,>=1.21.1 (from requests<=2.26.0,>=2.8.0->dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/ec/03/062e6444ce4baf1eac17a6a0ebfe36bb1ad05e1df0e20b110de59c278498/urllib3-1.26.9-py2.py3-none-any.whl (138kB) |████████████████████████████████| 143kB 111.6MB/s Collecting cffi>=1.12 (from cryptography<37,>=3.4.2; python_version > "3.5"->dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/e2/25/00fd291e0872d43dabe070e7b761ba37453a1a94bd6e28c31b73112d8f0c/cffi-1.15.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (444kB) |████████████████████████████████| 450kB 98.4MB/s Collecting pycparser (from cffi>=1.12->cryptography<37,>=3.4.2; python_version > "3.5"->dxpy==0.320.0) Downloading https://files.pythonhosted.org/packages/62/d5/5f610ebe421e85889f2e55e33b7f9a6795bd982198517d912eb1c76e1a53/pycparser-2.21-py2.py3-none-any.whl (118kB) |████████████████████████████████| 122kB 115.8MB/s Building wheels for collected packages: xattr Building wheel for xattr (setup.py) ... done Created wheel for xattr: filename=xattr-0.9.6-cp39-cp39-linux_x86_64.whl size=16785 sha256=ac1574543f87ce0e1ac8b5b00ce6f6401340d2f9828a702ee5eb8520a9689770 Stored in directory: /home/bms20/.cache/pip/wheels/8f/2d/20/eaf8403b661a46b93a1da3031f56eacb18eaae912d8a1683da Successfully built xattr Installing collected packages: argcomplete, six, websocket-client, certifi, charset-normalizer, idna, urllib3, requests, pycparser, cffi, cryptography, python-dateutil, psutil, xattr, dxpy WARNING: The script normalizer is installed in '/home/bms20/dx-toolkit/src/../bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. WARNING: The script xattr is installed in '/home/bms20/dx-toolkit/src/../bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. WARNING: The scripts dx, dx-app-wizard, dx-build-app and dx-build-applet are installed in '/home/bms20/dx-toolkit/src/../bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed argcomplete-2.0.0 certifi-2022.6.15 cffi-1.15.0 charset-normalizer-2.0.12 cryptography-36.0.2 dxpy-0.320.0 idna-3.3 psutil-5.9.1 pycparser-2.21 python-dateutil-2.8.2 requests-2.26.0 six-1.16.0 urllib3-1.26.9 websocket-client-0.57.0 xattr-0.9.6 mv "/home/bms20/dx-toolkit/src/.."/lib/python?.?/site-packages "/home/bms20/dx-toolkit/src/../share/dnanexus/lib/python3.9/site-packages" make -j -l 2.0 -C dx-verify-file install DESTDIR=/home/bms20/dx-toolkit/src/.. PREFIX=/ make[2]: Entering directory '/home/bms20/dx-toolkit/src/dx-verify-file' mkdir -pv build mkdir: created directory 'build' cd build && cmake .. -DCMAKE_BUILD_TYPE:STRING=RELEASE -DSTATIC_BOOST=1 -DCMAKE_EXE_LINKER_FLAGS="-lpthread" /bin/sh: 1: cmake: not found make[2]: *** [Makefile:27: all] Error 127 make[2]: Leaving directory '/home/bms20/dx-toolkit/src/dx-verify-file' make[1]: *** [Makefile:85: dx-verify-file] Error 2 make[1]: Leaving directory '/home/bms20/dx-toolkit/src' make: *** [Makefile:18: all] Error 2 ```

Test

dx -h

usage: dx [-h] [--version] command ...

DNAnexus Command-Line Client, API v1.0.0, client v0.320.0

dx is a command-line client for interacting with the DNAnexus platform.  You can log in, navigate,
upload, organize and share your data, launch analyses, and more.  For a quick tour of what the tool
can do, see

  https://documentation.dnanexus.com/getting-started/tutorials/cli-quickstart#quickstart-for-cli

For a breakdown of dx commands by category, run "dx help".

dx exits with exit code 3 if invalid input is provided or an invalid operation is requested, and
exit code 1 if an internal error is encountered.  The latter usually indicate bugs in dx; please
report them at

  https://github.com/dnanexus/dx-toolkit/issues

optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
  --version   show program's version number and exit

Still, not sure why the latest binary distribution requires Python2.7. Has it simply not been updated in a long time?

dnanexus / dx-toolkit