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    d-salgado
    @d-salgado
    so if you have to make some reading of BAM file you need to have packaged or made available the sambamba program
    Wolfgang Maier
    @wm75
    You can inspect the recipe to find out
    d-salgado
    @d-salgado
    ok thank I will do
    Wolfgang Maier
    @wm75
    but really, rather test the Galaxy tool in action and complain if you find sth not working
    d-salgado
    @d-salgado
    @wm75 I have managed to install planemo on a fresh VM. I have git cloned the tools-iuc repo. when I cd into freec directory I manage to run planemo lint however it is failling for planemo serve.
    Here is in output of my planemo serve command :
    parallels@parallels-Parallels-Virtual-Platform:~/GalaxyTools/tools-iuc/tools/freec$ planemo serve
    git --git-dir /home/parallels/.planemo/gx_repo config remote.origin.fetch '+refs/:refs/'
    git --git-dir /home/parallels/.planemo/gx_repo config remote.origin.mirror true
    git --git-dir /home/parallels/.planemo/gx_repo remote update >/dev/null 2>&1
    galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
    git clone --branch master /home/parallels/.planemo/gx_repo /tmp/tmpgswkcvu4/galaxy-dev
    Cloning into '/tmp/tmpgswkcvu4/galaxy-dev'...
    done.
    if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/parallels/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /usr/bin/virtualenv -p /usr/bin/python3 $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}
    galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
    Activated a virtualenv for Galaxy
    /home/parallels/.planemo/gx_venv_3
    Set COMMON_STARTUP_ARGS to --dev-wheels
    Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample
    Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample
    Initializing static/welcome.html from welcome.html.sample
    Activating virtualenv at /home/parallels/.planemo/gx_venv_3
    Traceback (most recent call last):
    File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
    File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
    File "/home/parallels/.planemo/gx_venv_3/lib/python3.8/site-packages/pip/main.py", line 19, in <module>
    sys.exit(_main())
    File "/home/parallels/.planemo/gx_venv_3/lib/python3.8/site-packages/pip/_internal/cli/main.py", line 73, in main
    command = create_command(cmd_name, isolated=("--isolated" in cmd_args))
    File "/home/parallels/.planemo/gx_venv_3/lib/python3.8/site-packages/pip/_internal/commands/init.py", line 96, in create_command
    module = importlib.import_module(module_path)
    File "/usr/lib/python3.8/importlib/init.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
    File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
    File "<frozen importlib._bootstrap>", line 991, in _find_and_load
    File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
    File "<frozen importlib._bootstrap_external>", line 783, in exec_module
    File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
    File "/home/parallels/.planemo/gx_venv_3/lib/python3.8/site-packages/pip/_internal/commands/install.py", line 24, in <module>
    from pip._internal.cli.req_command import RequirementCommand
    File "/home/parallels/.planemo/gx_venv_3/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 20, in <module>
    from pip._internal.operations.prepare import RequirementPreparer
    File "/home/parallels/.planemo/gx_venv_3/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 16, in <module>
    from pip._internal.distributions import (
    File "/home/parallels/.planemo/gx_venv_3/lib/python3.8/site-packages/pip/_internal/distributions/init.py", line 2, in <module>
    from pip._internal.distributions.wheel import WheelDistribution
    File "/home/parallels/.planemo/gx_venv_3/lib/python3.8/site-packages/pip/_internal/distributions/wheel.py", line 5, in <module>
    from pip._internal.utils.wheel
    @wm75 do you have an idea of what could cause the problem ? Sory if this is a python beginer problem but I am not used to play with python
    Björn Grüning
    @bgruening
    @d-salgado there is something missing from your stacktrace
    Wolfgang Maier
    @wm75
    @d-salgado gitter has a mac char limit on single posts. In python it's usually the end of the traceback that's interesting.
    d-salgado
    @d-salgado
    from pip._internal.utils.wheel import pkg_resources_distribution_for_wheel
    File "/home/parallels/.planemo/gx_venv_3/lib/python3.8/site-packages/pip/_internal/utils/wheel.py", line 12, in <module>
    from pip._vendor.six import PY2, ensure_str
    ImportError: cannot import name 'ensure_str' from 'six' (/home/parallels/.planemo/gx_venv_3/lib/python3.8/site-packages/six.py)
    Traceback (most recent call last):
    File "/home/parallels/.local/bin/planemo", line 8, in <module>
    sys.exit(planemo())
    File "/usr/lib/python3/dist-packages/click/core.py", line 764, in call
    return self.main(args, kwargs)
    File "/usr/lib/python3/dist-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
    File "/usr/lib/python3/dist-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
    File "/usr/lib/python3/dist-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback,
    ctx.params)
    File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke
    return callback(
    args, kwargs)
    File "/usr/lib/python3/dist-packages/click/decorators.py", line 64, in new_func
    return ctx.invoke(f, obj, *args,
    kwargs)
    File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke
    return callback(args, **kwargs)
    File "/home/parallels/.local/lib/python3.8/site-packages/planemo/cli.py", line 98, in handle_blended_options
    return f(
    args, kwds)
    File "/home/parallels/.local/lib/python3.8/site-packages/planemo/commands/cmd_serve.py", line 43, in cli
    galaxy_serve(ctx, runnables,
    kwds)
    File "/home/parallels/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 25, in serve
    return _serve(ctx, runnables, kwds)
    File "/home/parallels/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 45, in _serve
    with galaxy_config(ctx, runnables,
    kwds) as config:
    File "/usr/lib/python3.8/contextlib.py", line 113, in enter
    return next(self.gen)
    File "/home/parallels/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 215, in galaxy_config
    with c(ctx, runnables, **kwds) as config:
    File "/usr/lib/python3.8/contextlib.py", line 113, in enter
    return next(self.gen)
    File "/home/parallels/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 358, in local_galaxy_config
    _install_galaxy(ctx, galaxy_root, install_env, kwds)
    File "/home/parallels/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 1140, in _install_galaxy
    _install_galaxy_via_git(ctx, galaxy_root, env, kwds)
    File "/home/parallels/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 1158, in _install_galaxy_via_git
    _install_with_command(ctx, galaxy_root, env, kwds)
    File "/home/parallels/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 1203, in _install_with_command
    raise Exception("Failed to install Galaxy via command [%s]" % install_cmd)
    Exception: Failed to install Galaxy via command [if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/parallels/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /usr/bin/virtualenv -p /usr/bin/python3 $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}]
    sorry did not understood the comment from @bgruening
    Björn Grüning
    @bgruening
    @d-salgado can you please clone this repo into a different directory https://github.com/galaxyproject/galaxy
    and then change into this directory and do ./run.sh
    Wolfgang Maier
    @wm75
    @d-salgado by trying to install Galaxy independently of planemo on your VM (this is what @bgruening suggests above), you can get more telling error messages.
    That said, most likely the cause of your issue is Python3.8 or an outdated pip package installer for it.
    It looks as if Galaxy has to go into building some of its Python dependencies from source on your system, then fails to do so.
    d-salgado
    @d-salgado
    Ok thank you both, I am able to have a Galaxy instance runing with the new compilation. No direct links with the planemo compilation. I have tried while the VM was compiling the new galaxy clone on an mac and managed to have planemo and galaxy set up
    Björn Grüning
    @bgruening
    So everything is working now for you?
    d-salgado
    @d-salgado
    Yes thank you, I am working on a schema to illustrate wich steps are more or less completed and which one are missing
    and playing with planemo and galaxy locally with freec
    Björn Grüning
    @bgruening
    ah cool!
    d-salgado
    @d-salgado
    One thing I would like to ask is how to setup a data library for a group of users?
    In fact the dataset that I uploaded to Galaxy was 40GB but gzipped. Unzipped is way more larger … from memory around 140GB
    147.3 exactly for the BAM + few GB for aditional data
    Björn Grüning
    @bgruening
    @d-salgado where can I get this dataset
    can we put it under "Genome and Annotaitons"
    or better under "galaxy courses"?
    Björn Grüning
    @bgruening
    I will care about that. Just let me know where you wanna have it
    d-salgado
    @d-salgado
    this is a link to a tabulated file that contains the ftp link to the bam + to the bai files
    Björn Grüning
    @bgruening
    We can create here a subfolder "Genome in a Bottle"
    d-salgado
    @d-salgado
    yes that will be even better
    and can we imagine having a datalibrary for CNV gold standard files ?
    Björn Grüning
    @bgruening
    yes
    d-salgado
    @d-salgado
    I know for instance that several papers are giving list of CNV that they have validated, so we could imagine runing one analysis and then compare the result of an analysis for sample NA12878( for instance) to a specific set of published Gold standards
    Björn Grüning
    @bgruening
    sure we can do that
    But if the data is small, and from some paper, users can also load them directly
    For big data, like reference genomes, or genome in a bottle I think it makes sense to prepare this and save a lot of time
    working on it now
    d-salgado
    @d-salgado
    ok
    makes sense
    Björn Grüning
    @bgruening
    do you know which version of the human genome that was mapped?
    d-salgado
    @d-salgado
    Yes that was mapped to hg19.
    Screenshot 2020-11-12 at 20.28.34.png
    Here is a screenshot of the link where I obtained this dataset. Here is the link if you need more details to provide in the metadata of the file : https://github.com/genome-in-a-bottle/giab_data_indexes
    it is the last sample on the page