/bin folder inside your conda package is executable with a single command. Usually people install these files with a setup.py script.
@JasonYangShadow , sorry I have never worked with those packages you mentioned... :)
But this looks like working:
$ conda create -n for_trinity -c bioconda trinity # create environment "for_trinity" for the "trinity" package
$ conda create -n for_picard -c bioconda picard # create environment "for_picard" for the "picard" package
Then you will have 2 environments, where different openjdk versions are present. To run picard and trinity you need to activate their corresponding environments first (e.g. in separate terminals if you want to use them at the same time). Or use "conda run" command.
I'm not sure, maybe this was what you wanted to sort out...
rust_dev as an alternative label to ensure it is not a problem specific to broken.
@DerKevinRiehl the first step is to learn how to write a setup.py and a proper python package (that is completely orthogonal to conda packaging).
If you want to hack something, then you need to learn a little bit of bash or cmd.exe scripting and just copy your script into $PREFIX/bin (inside your conda meta.yaml).
e.g.
script: cp myscript.py $PREFIX/bin/myscript.py # [unix]
script: COPY myscript.py %PREFIX%\Library\bin\myscript.py # [win]but this is really hacky and should be avoided. But at this point you're asking really general questions and you should read some tutorials, e.g. the python packaging ones
{install_dir}\Library\bin isn't on the PATH after loading into an embedded Python, but {install_dir}\Library\usr\bin is on the PATH twice. The PATH is correct when sitting on the command line and running Python directly. So I'm wondering how PATH is built and/or modified by the conda environment manager and/or the shipped python executable (or libpython package? good lord...). I'm not sure how all the pieces of conda work together and who I should be reporting this bug to.
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conda activate operation? For me it is taking 90 seconds. I looked at etc/conda/activate.d/*.sh scripts, and all they do is check file/directory existence and set environment variables. I can’t figure out what is taking so long.
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- https://MY_USER:MY_LONG_API_KEY@myserver.com/mychannel
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conda env create -f envfile.yaml
.condarc via the create_default_packages key
