jianxinwang
commented
5 years ago Hi Simon,
Thank you for your interest in using GenESysV. My first impression for the trouble you are having is that you need to create a virtual environment for python version 3. Please refer to the documentation on how to do this.
Jianxin
On Thu, Jun 13, 2019 at 2:38 AM Simon Thompson notifications@github.com wrote:
really keen to get this working but when i follow the documentation get an error loading data
root@debian-template:~/GenESysV# python utils/load_vcf.py --vcf test_data/test_4families_annovar.vcf.gz --tmp_dir /tmp --annot annovar --hostname 127.0.0.1 --port 9200 --index test_4families_annovar --study_name test_4families_annovar --dataset_name test_4families_annovar --num_cores 4 --assembly hg19 --ped test_data/test_4families.ped --cleanup File "utils/load_vcf.py", line 686 gene, refseq, exon, *cdna_aa = subval.split(':') ^ SyntaxError: invalid syntax
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tekkisse
really keen to get this working but when i follow the documentation get an error loading data
root@debian-template:~/GenESysV# python utils/load_vcf.py --vcf test_data/test_4families_annovar.vcf.gz --tmp_dir /tmp --annot annovar --hostname 127.0.0.1 --port 9200 --index test_4families_annovar --study_name test_4families_annovar --dataset_name test_4families_annovar --num_cores 4 --assembly hg19 --ped test_data/test_4families.ped --cleanup File "utils/load_vcf.py", line 686 gene, refseq, exon, *cdna_aa = subval.split(':') ^ SyntaxError: invalid syntax