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