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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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Problem loading class GenerateEnselmbDataCache while running gene-utils #306

Closed FrancescaMiccolis closed 2 years ago

FrancescaMiccolis commented 2 years ago

Hi, I'm trying to use LINX to obtain fusions from GRIDSS output. In order to run LINX I have to generate the required Enselmb data files. To create these files I would use gene-utils, so I run the following command: java -cp gene-utils.jar com.hartwig.hmftools.geneutils.ensembl.GenerateEnsemblDataCache -ensembl_db mysql://ensembldb.ensembl.org:3337/homo_sapiens_core_89_37 -ensembl_user anonymous -ensembl_pass -ref_genome_version 37 -output_dir ensemble_cache/ as stated in gene-utils documentation. However when I run this command an error occurs:

Error: Could not find or load main class com.hartwig.hmftools.geneutils.ensembl.GenerateEnsemblDataCache Caused by: java.lang.ClassNotFoundException: com.hartwig.hmftools.geneutils.ensembl.GenerateEnsemblDataCache

Have you ever had this problem? Do you know how I can fix this error? It's possible that the error is related to the java version?

charlesshale commented 2 years ago

I will look into that issue, but in the meantime I would recommend using the Ensembl data cache files for both v37 and v38 from our HMF Tools-Resources page here:

https://resources.hartwigmedicalfoundation.nl/ - see Ensembl-Data-Cache

These have been generated to match the HGNC gene names, and we've ensure that consistent gene names are used between the 2 ref genome versions.

charlesshale commented 2 years ago

Here is a release for gene-utils:

https://github.com/hartwigmedical/hmftools/releases/tag/gene-utils-v1.0

I have checked that the command to generate the Ensembl data cache works as per the read-me. It requires Java 11. Could you give it a try?

FrancescaMiccolis commented 2 years ago

Thanks a lot for your help. Actually I'm not at home, but as soon as I get to work I’ll give it a try and update you about the outcome.

FrancescaMiccolis commented 2 years ago

I’m sorry it took so long but I finally got to try. I download the release of gene-utils and try to generate the ensembl cache directory with Java 11 and it works! Thanks a lot for your support.