blacktie icon indicating copy to clipboard operation
blacktie copied to clipboard

blacktie/scripts/cummerbund.py doesn't import errors

Open xguse opened this issue 11 years ago • 0 comments

blacktie --prog all ../../config_files/tophat_cufflinks_Cq_0-4-6-8-10.gtf_strict.hpc.yaml --mode qsub_script
[Note] Starting tophat step.

[Note] Starting cufflinks step.

[Note] Starting cuffmerge step.

[Note] Starting cuffdiff step.

sh: R: command not found
Traceback (most recent call last):
  File "/data/users/dunnw/py273/bin/blacktie", line 8, in <module>
    load_entry_point('blacktie==0.2.1qf1', 'console_scripts', 'blacktie')()
  File "/data/users/dunnw/py273/lib/python2.7/site-packages/blacktie/scripts/blacktie_pipeline.py", line 236, in main
    from blacktie.scripts import cummerbund
  File "/data/users/dunnw/py273/lib/python2.7/site-packages/blacktie/scripts/cummerbund.py", line 37, in <module>
    raise errors.BlacktieError('Importing required module "rpy2" failed because no R application could be found on your system. Try again after instaling R.')
NameError: name 'errors' is not defined

xguse avatar May 22 '13 03:05 xguse