snpEff installation, unable to download reference genome

Question

[swethabiochem]

Hello All, I am trying to install snpEff installation and getting the following errors could you help me regarding this.

1.

./snpEff.config


./snpEff.config: line 17: data.dir: command not found
./snpEff.config: line 22: database.repository: command not found
./snpEff.config: line 27: versions.url: command not found
./snpEff.config: line 35: database.clinvar.GRCh38: command not found
./snpEff.config: line 36: database.repository.clinvar: command not found
./snpEff.config: line 38: database.dbsnp.GRCh38: command not found

2.

java -jar snpEff.jar download GRCh38.76


java.lang.RuntimeException: Property: 'GRCh38.76.genome' not found
    at org.snpeff.interval.Genome.<init>(Genome.java:106)
    at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
    at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
    at org.snpeff.snpEffect.Config.init(Config.java:480)
    at org.snpeff.snpEffect.Config.<init>(Config.java:117)
    at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:80)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)
    at org.snpeff.SnpEff.main(SnpEff.java:162)

[Kevin Blighe]

I think that your command should be:

java -Xmx4g -jar snpEff.jar download -c snpEff/snpEff.config -v GRCh38.76

?

[Matteo Schiavinato]

The snpEff.config file is not an executable file. Did you follow these guidelines closely? http://snpeff.sourceforge.net/download.html#install

Is your /data/ directory properly set within the snpEff.config file?