bcbio_dir undefined in utils.py

[johnziniti]

Version info

• bcbio version (bcbio_nextgen.py --version): 1.2.3
• OS name and version: Red Hat Enterprise Linux Server release 6.10 (Santiago)

To Reproduce

• Exact bcbio command you have used: bcbio_nextgen.py /proj/regeps/regep00/studies/COPDGene/analyses/rejpz/bcbio_ea/rnaseq_snp_concordance/bcbio_system.yaml ../config/301898_accepted_hits_merged_markeddups_recal.yaml
• Your sample configuration file

details:
- algorithm:
    aligner: bwa
    variantcaller: freebayes
  analysis: variant2
  description: 301898.accepted_hits.merged.markeddups.recal
  files:
  - /proj/regeps/regep00/studies/COPDGene/data/rna/mrna/nasal_shortread/data/raw/TOPMED_11.19.2019/301898.accepted_hits.merged.markeddups.recal.bam
  genome_build: hg38
fc_name: 301898_accepted_hits_merged_markeddups_recal
upload:
  dir: ../final

Observed behavior
Error message or bcbio output.

File "/proj/regeps/regep00/studies/COPDGene/analyses/rejpz/bcbio_ea/.snakemake/conda/2460f313/lib/python3.7/site-packages/bcbio/utils.py", line 55, in wrapper
    return f(*args, **kwargs)
  File "/proj/regeps/regep00/studies/COPDGene/analyses/rejpz/bcbio_ea/.snakemake/conda/2460f313/lib/python3.7/site-packages/bcbio/distributed/multitasks.py", line 323, in concat_variant_files
    return vcfutils.concat_variant_files(*args)
  File "/proj/regeps/regep00/studies/COPDGene/analyses/rejpz/bcbio_ea/.snakemake/conda/2460f313/lib/python3.7/site-packages/bcbio/variation/vcfutils.py", line 370, in concat_variant_files
    input_file_list = _get_file_list(orig_files, out_file, regions, ref_file, config)
  File "/proj/regeps/regep00/studies/COPDGene/analyses/rejpz/bcbio_ea/.snakemake/conda/2460f313/lib/python3.7/site-packages/bcbio/variation/vcfutils.py", line 416, in _get_file_list
    exist_files = _fix_gatk_header(exist_files, out_file, config)
  File "/proj/regeps/regep00/studies/COPDGene/analyses/rejpz/bcbio_ea/.snakemake/conda/2460f313/lib/python3.7/site-packages/bcbio/variation/vcfutils.py", line 454, in _fix_gatk_header
    (utils.get_java_clprep(), header_file, base_file, base_fix_file, " ".join(ropts)),
  File "/proj/regeps/regep00/studies/COPDGene/analyses/rejpz/bcbio_ea/.snakemake/conda/2460f313/lib/python3.7/site-packages/bcbio/utils.py", line 776, in get_java_clprep
    return "%s && export PATH=%s:\"$PATH\"" % (clear_java_home(), get_java_binpath(cmd))
  File "/proj/regeps/regep00/studies/COPDGene/analyses/rejpz/bcbio_ea/.snakemake/conda/2460f313/lib/python3.7/site-packages/bcbio/utils.py", line 758, in get_java_binpath
    cmd = Rscript_cmd()
  File "/proj/regeps/regep00/studies/COPDGene/analyses/rejpz/bcbio_ea/.snakemake/conda/2460f313/lib/python3.7/site-packages/bcbio/utils.py", line 697, in Rscript_cmd
    rscript = which(os.path.join(get_bcbio_bin(), "Rscript"))
  File "/proj/regeps/regep00/studies/COPDGene/analyses/rejpz/bcbio_ea/.snakemake/conda/2460f313/lib/python3.7/site-packages/bcbio/utils.py", line 657, in which
    for path in get_all_conda_bins():
  File "/proj/regeps/regep00/studies/COPDGene/analyses/rejpz/bcbio_ea/.snakemake/conda/2460f313/lib/python3.7/site-packages/bcbio/utils.py", line 832, in get_all_conda_bins
    return [bcbio_bin] + list(glob.glob(os.path.join(conda_dir, "envs", "*", "bin")))
NameError: name 'bcbio_bin' is not defined

Expected behavior
get_all_conda_bins() should successfully return a list of paths.

Log files
Please attach (10MB max): bcbio-nextgen.log, bcbio-nextgen-commands.log, and bcbio-nextgen-debug.log.

Additional context
It's seems clear to me that the function get_all_conda_bins is referring to a variable that is not defined within the function. I was able to work around this error by adding:

bcbio_bin = get_bcbio_bin()

immediately before this line.

[naumenko-sa]

Thanks for reporting @johnziniti !
We have fixed it. Feel free to reopen if you still experience issues.