Dear Bjoern, As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is: Admin > Data > Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome, I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.) Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty. Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel? I really appreciate for your help, and thank you so much for your patience! Best, Xiaofei Data Manager Choose your data managing option from below. * Access data managers - get data, build indexes, etc * SnpEff Databases<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4> - Read the list of available snpEff databases * SnpEff Download<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4> - Download a new database * BWA index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1> - builder * BWA Color index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1> - builder * Reference Genome<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1> - fetching * View managed data by manager * SnpEff Databases<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1> - Read the list of available snpEff databases * SnpEff Download<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1> - Download a new database * BWA index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1> - builder * BWA Color index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1> - builder * Reference Genome<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1> - fetching * View managed data by Tool Data Table * snpeff_databases<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases> * snpeff_genomedb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb> * snpeff_regulationdb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb> * snpeff_annotations<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations> * bwa_indexes<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes> * bwa_indexes_color<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color> * all_fasta<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta> * * * * ________________________________________ * From: Björn Grüning [bjoern.gruening@gmail.com] * Sent: Wednesday, April 02, 2014 12:55 PM * To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu * Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors * * Hi, * * that means that the snpeff annotation is missing. You can install it * with the snpeff datamanager under your Admin panel. Have a look at the * wiki page about data-manager and the snpeff wrapper documentation. * You do not need to edit xml files. If so that is an bug in the wrapper * and we should fix it :) * * Cheers, * Bjoern * * Am 02.04.2014 19:34, schrieb Wang, Xiaofei: * >>> When I used SnpEff in local galaxy instance, I got an error: * >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j * > * > * > * > * >> Which Java version do you use. Please make sure you are running Java 1.7. * > * > * > * > * > Yes, it is figured, when I changed the java version to 1.7. Thank you so much! * > * > * > * > * > But, I got another error for snpEff. * > * > * > * > * > java.lang.RuntimeException: Property: 'dm5.30.genome' not found * > at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92) * > at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481) * > at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444) * > at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345) * > at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96) * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245) * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981) * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) * > * > * > * > * > * > * > * > * > What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply. * > * > * > * > * > Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? ) * > * > * > * > * > <param name="genomeVersion" type="select" label="Genome"> * > <option value="hg37">Human (hg37)<option> * > <option value="mm37.61">Mouse (mm37.61)<option> * > <param> * > * > * > * > ________________________________________ * > From: Björn Grüning [bjoern.gruening@gmail.com] * > Sent: Wednesday, April 02, 2014 10:35 AM * > To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu * > Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors * > * > Hi Xiaofei, * > * >> Dear there, * >> * >> When I used SnpEff in local galaxy instance, I got an error: * >> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j * > * > Which Java version do you use. Please make sure you are running Java 1.7. * > * >> Also, when I used the FASTQ Summary Statistics, I got an error like this: * >> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/... * > * > Can you give us the complete error message. The important part is missing. * > * > Ciao, * > Bjoern * > * >> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! * >> * >> * >> * >> * >> ___________________________________________________________ * >> Please keep all replies on the list by using "reply all" * >> in your mail client. 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