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namphuon / ViFi

Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
GNU General Public License v3.0
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I got an error: File "/data/program/ViFi/ViFi/scripts/run_vifi.py", line 118, in <module> reference_dir = os.environ['REFERENCE_REPO'] File "/usr/lib/python2.7/UserDict.py", line 40, in __getitem__ raise KeyError(key) KeyError: 'REFERENCE_REPO' #20

Open byeonggill opened 5 years ago

byeonggill commented 5 years ago

Hi I install docker and execute setup_linux_mac.sh my cmd: sudo python $VIFI_DIR/scripts/run_vifi.py --cpus 2 --hmm_list $VIFI_DIR/data/hbv/hmms/hmms.txt -f $VIFI_DIR/test/data/test_R1.fq.gz -r $VIFI_DIR/test/data/test_R2.fq.gz -o $VIFI_DIR/tmp/docker/ --docke but, I got the following error File "/data/program/ViFi/ViFi/scripts/run_vifi.py", line 118, in reference_dir = os.environ['REFERENCE_REPO'] File "/usr/lib/python2.7/UserDict.py", line 40, in getitem raise KeyError(key) KeyError: 'REFERENCE_REPO'

I confirmed my environmental variables.

byeonggill commented 5 years ago

I resolve above issue. but, Even command -v hbv, vifi run hpv in docker version. why ?