raydai
commented
4 years ago Hi @biocai , I had the same problem before, and I found some issues for the root module under python=2.7. Thus I decided to create a new environment with python=3.8, and after that, I let the environment solver do the work of determining the remaining dependencies.
time conda create -n cnvn_env -c conda-forge python=3.8 --yes --quiet #took ~1 minute
source activate cnvn_env
time conda install -c pwwang root=6.20.4 cnvnator=0.4.1 --yes --quiet #took 4min 20sec cnvnator
Not enough parameters.
CNVnator v0.4.1
Usage: cnvnator -root out.root [-genome name] [-chrom 1 2 ...] -tree file1.bam ... [-lite] cnvnator -root out.root [-genome name] [-chrom 1 2 ...] -merge file1.root ... cnvnator -root file.root [-genome name] [-chrom 1 2 ...] -vcf [file.vcf.gz | file.vcf] [-rmchr] [-addchr] cnvnator -root file.root [-genome name] [-chrom 1 2 ...] -idvar [file.vcf.gz | file.vcf] [-rmchr] [-addchr] cnvnator -root file.root [-genome name] [-chrom 1 2 ...] -mask strict.mask.file.fa.gz [-rmchr] [-addchr] cnvnator -root file.root [-genome name] [-chrom 1 2 ...] [-d dir | -fasta file.fa.gz] -his bin_size cnvnator -root file.root [-genome name] [-chrom 1 2 ...] -baf bin_size [-hap] [-useid] [-nomask] cnvnator -root file.root [-chrom 1 2 ...] -stat bin_size cnvnator -root file.root -eval bin_size cnvnator -root file.root [-chrom 1 2 ...] -partition bin_size [-ngc] cnvnator -root file.root [-chrom 1 2 ...] -call bin_size [-ngc] cnvnator -root file.root -genotype bin_size [-ngc] cnvnator -root file.root -view bin_size [-ngc] cnvnator -pe file1.bam ... -qual val(20) -over val(0.8) [-f file] cnvnator-root file.root [-chrom 1 2 ...] -cptrees newfile.root cnvnator-root file.root -ls
Valid genomes (-genome option) are: NCBI36, hg18, GRCh37, hg19, mm9, hg38, GRCh38
I install cnvnator using command conda install cnvnator -c bioconda -c conda-forge. It reports an error "cnvnator: error while loading shared libraries: libreadline.so.8: cannot open shared object file: No such file or directory". When I search for libreadline.so, only libreadline.so.7 is found. The system is Ubuntu 18.04.
How to fix this?