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/
   *   >>
   *   >
   *   >
   *
      *

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