Hi Xiaofei,
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.
After SnpEff Databases > Execute you still need to pick genome of interest and run "SnpEff Download". SnpEff Databases just downloads a list of available genomes. Hope that will help! Bjoern
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. To manage your subscriptions to this * >> and other Galaxy lists, please use the interface at: * >> http://lists.bx.psu.edu/ * >> * >> To search Galaxy mailing lists use the unified search at: * >> http://galaxyproject.org/search/mailinglists/ * >> * > * > * *