GATK v4.0.8.1 conda set up error: Command "python setup.py egg_info" failed with error code 1

shleeshlee CambridgeMember, Broadie, Moderator admin

When creating the gatk conda environment using conda env create -f gatkcondaenv.yml for GATK v4.0.8.1 on my Mac, I run into the following error.

...
Collecting pysam==0.13 (from -r /Applications/genomicstools/gatk/gatk-4.0.8.1/condaenv.E6OfWe.requirements.txt (line 17))
  Using cached https://files.pythonhosted.org/packages/31/17/31d317006a74941d2caddac97c5106601fe4da467653d0f061702e9ead95/pysam-0.13.tar.gz
    Complete output from command python setup.py egg_info:
    checking for gcc... gcc
    checking whether the C compiler works... no
    configure: error: in `/private/var/folders/z0/s2h6193s3nb_75fsv36m5xldw34_0r/T/pip-build-_0t_kf9d/pysam/htslib':
    configure: error: C compiler cannot create executables
    See `config.log' for more details
    checking for gcc... gcc
    checking whether the C compiler works... no
    configure: error: in `/private/var/folders/z0/s2h6193s3nb_75fsv36m5xldw34_0r/T/pip-build-_0t_kf9d/pysam/htslib':
    configure: error: C compiler cannot create executables
    See `config.log' for more details
    xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
    # pysam: no cython available - using pre-compiled C
    # pysam: htslib mode is shared
    # pysam: HTSLIB_CONFIGURE_OPTIONS=None
    # pysam: htslib configure options: None
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/z0/s2h6193s3nb_75fsv36m5xldw34_0r/T/pip-build-_0t_kf9d/pysam/setup.py", line 220, in <module>
        htslib_make_options = run_make_print_config()
      File "/private/var/folders/z0/s2h6193s3nb_75fsv36m5xldw34_0r/T/pip-build-_0t_kf9d/pysam/setup.py", line 63, in run_make_print_config
        stdout = subprocess.check_output(["make", "-s", "print-config"])
      File "/Users/shlee/anaconda2/envs/gatk/lib/python3.6/subprocess.py", line 336, in check_output
        **kwargs).stdout
      File "/Users/shlee/anaconda2/envs/gatk/lib/python3.6/subprocess.py", line 418, in run
        output=stdout, stderr=stderr)
    subprocess.CalledProcessError: Command '['make', '-s', 'print-config']' returned non-zero exit status 1.

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/z0/s2h6193s3nb_75fsv36m5xldw34_0r/T/pip-build-_0t_kf9d/pysam/

CondaValueError: pip returned an error

I've been successful in setting up the gatk conda environment for prior versions of GATK4. I recently updated my Mac to High Sierra.

Best Answer

  • shleeshlee Cambridge admin
    edited September 2018 Accepted Answer

    I solved this with help from a developer. The relevant error line is:

    xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
    

    If we ls /Library/Developer/CommandLineTools/usr/, I only see one item, share and no item bin.

    I updated my Mac's Xcode to v9.4.1, which is the latest from App Store. Then I installed Xcode Command Line Developer Tools with xcode-select --install. After this install, ls /Library/Developer/CommandLineTools/usr/ shows a bunch of folders including bin.

    Finally, I removed the previous erring install with rm -r /Users/shlee/anaconda2/envs/gatk and ran conda env create -f gatkcondaenv.yml within the GATK directory. We see the installation is successful because of the following message:

    #
    # To activate this environment, use:
    # > source activate gatk
    #
    # To deactivate an active environment, use:
    # > source deactivate
    #
    

    See this external article for some entertaining comments about the error.

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator admin
    edited September 2018 Accepted Answer

    I solved this with help from a developer. The relevant error line is:

    xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
    

    If we ls /Library/Developer/CommandLineTools/usr/, I only see one item, share and no item bin.

    I updated my Mac's Xcode to v9.4.1, which is the latest from App Store. Then I installed Xcode Command Line Developer Tools with xcode-select --install. After this install, ls /Library/Developer/CommandLineTools/usr/ shows a bunch of folders including bin.

    Finally, I removed the previous erring install with rm -r /Users/shlee/anaconda2/envs/gatk and ran conda env create -f gatkcondaenv.yml within the GATK directory. We see the installation is successful because of the following message:

    #
    # To activate this environment, use:
    # > source activate gatk
    #
    # To deactivate an active environment, use:
    # > source deactivate
    #
    

    See this external article for some entertaining comments about the error.

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