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.gruening@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 Databaseshttp://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 Downloadhttp://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 indexhttp://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 indexhttp://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 Genomehttp://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 Databaseshttp://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 Downloadhttp://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 Color indexhttp://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 Genomehttp://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_databaseshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases
snpeff_genomedbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb
snpeff_regulationdbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb
snpeff_annotationshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations
bwa_indexeshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes
bwa_indexes_colorhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color
all_fastahttp://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!
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