>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.
You mean "SnpEff Download" under Data Manager? But, there is no response when I click on it. Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response. But, when I go to Admin > Data > Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why? When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time? Thank you so much! Best, Xiaofei ________________________________________ From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 4:17 PM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors 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.gruen...@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.gruen...@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/ > * >> > * > > * > > * > * > ___________________________________________________________ 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/
