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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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ngsplotdb.py install not working #93

Open niekwit opened 3 years ago

niekwit commented 3 years ago

I wanted to add mm9 to the ngsplot db, so I downloaded the relevant file from your Google drive and ran:

$ python2 ~/Documents/scripts/ngsplot-2.61/ngsplot/bin/ngsplotdb.py install ~/Downloads/ngsplotdb_mm9_67_3.00.tar.gz

But I get this error: 

Extracting information from package... contains 87 tables.
Will install new genome mm9: Ensembl=> v67.0; ngs.plot=> v3.0. Continue?(y/n): y
Installing new genome...Traceback (most recent call last):
  File "/home/niek/Documents/scripts/ngsplot-2.61/ngsplot/bin/setTableDefaults.py", line 36, in <module>
    in_f = file(sys.argv[1])
NameError: name 'file' is not defined
Error in read.table(default.tbl, header = TRUE, sep = "\t", blank.lines.skip = TRUE,  : 
  no lines available in input
Execution halted
 Done

When I check the db list with:

$ python2 ~/Documents/scripts/ngsplot-2.61/ngsplot/bin/ngsplotdb.py list
ID   Assembly Species      EnsVer   NPVer    InstalledFeatures            
hg19 GRCh37   homo_sapiens 75.0     3.0      cgi,exon,genebody,tss,tes    
hg38 GRCh38   homo_sapiens 76.0     3.0      cgi,exon,genebody,tss,tes    
mm9  NCBIM37  mus_musculus 67.0     3.0

There are no installed features listed with the mm9 genome. It has worked before with other genomes as you can see. How can I fix this? Thank you. (edit I am using ngsplot 2.61)