Am 03.04.2014 04:34, schrieb Wang, Xiaofei:
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.
It's a little bit complicated. If you click on the "SnpEff Download"
under Data Manager a progress ist started that will fetch a list of
available genomes that in a next step is shown under the tool "SnpEff
Databases" there you can choose which genome annotation you want to
install. To sum it up.
1. click "SnpEff Download"
2. choose one genome from "SnpEff Databases" and install 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?
Then there is something missing from your reinstallation. The data
manager is a dependency of the snpeff package and should be installed as
well. Can you check if you need to reinstall the dependency manually
unter the snpeff tool in your admin panel?
Cheers,
Bjoern
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 [[email protected]]
Sent: Wednesday, April 02, 2014 4:17 PM
To: Wang, Xiaofei; Björn Grüning; [email protected]
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 [[email protected]]
* Sent: Wednesday, April 02, 2014 12:55 PM
* To: Wang, Xiaofei; Björn Grüning; [email protected]
* 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 [[email protected]]
* > Sent: Wednesday, April 02, 2014 10:35 AM
* > To: Wang, Xiaofei; [email protected]
* > 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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