[galaxy-user] How to do BLAST on Galaxy sever?
Hi, Everybody, I uploaded two complete genome sequences and hope to BLAST homologs from both genome. Does anybody know how to do BLAST search on galaxy? Thanks David ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] How to do BLAST on Galaxy sever?
Hi David, at first you need to predict some genes. In the tool-shed you will find some gene prediction tools. With these gene you can search against local BLAST-databases using the NCBI BLAST+ tools, included in Main-Galaxy. Hope that helps, Bjoern Hi, Everybody, I uploaded two complete genome sequences and hope to BLAST homologs from both genome. Does anybody know how to do BLAST search on galaxy? Thanks David ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] user/groups/roles/permissions ???
Hello Bernd, This wiki explains the organization of roles in Galaxy: http://wiki.g2.bx.psu.edu/Learn/Security%20Features And if you need help with the Admin UI, this wiki can help: http://wiki.g2.bx.psu.edu/Admin/Interface Most administration help located in the wiki organized under this section: http://wiki.g2.bx.psu.edu/Admin The galaxy-...@bx.psu.edu mailing list is a good choice for local instance help. http://wiki.g2.bx.psu.edu/Mailing%20Lists http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing Prior Q/A can also be searched with: http://galaxy.psu.edu/search/mailinglists Hopefully this helps, Best, Jen Galaxy team On 2/8/12 4:13 AM, Bernd Jagla wrote: Hi, I am relatively new to Galaxy and couldn't find an explaination on how you envision the concepts of users/groups/roles etc... I am managing a Galaxy instance and have different groups of biologist (users), who should all are allowed to see the data from that group. Then I have a group of users who are not super users, but still should be able to see data from different groups of biologistl; they should also be able to upload data, other should not... I would like to make sure that my understanding of groups and users is the same as that of Galaxy and also would like to find explaination and possibly example of how to use roles and potentially other tools. Could you please point me to where in the documentation this explained? Kind regards, Bernd ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] How to do BLAST on Galaxy sever?
Hi David, It sounds like you are using the public Galaxy server at http://usegalaxy.org (http://main.g2.bx.psu.edu)? A BLAST service is not available on the public instance. (Megablast is available, but for NGS query data versus a specific set of target native genomes). Bjoern is correct that you will need to obtain a Galaxy BLAST wrapper from the Tool Shed. http://wiki.g2.bx.psu.edu/Tool%20Shed Tools Shed entries can be searched for with: http://galaxy.psu.edu/search/getgalaxy These would be installed into a local or cloud version of Galaxy and set up using the following instructions: http://getgalaxy.org The galaxy-...@bx.psu.edu mailing list is a good choice if you need help/advice with set up: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Prior Q/A can also be searched with: http://galaxy.psu.edu/search/mailinglists Best wishes for your project, Jen Galaxy team On 2/9/12 9:47 AM, David PANG wrote: Hi, Everybody, I uploaded two complete genome sequences and hope to BLAST homologs from both genome. Does anybody know how to do BLAST search on galaxy? Thanks David ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] How to do BLAST on Galaxy sever?
On Thursday, February 9, 2012, Jennifer Jackson j...@bx.psu.edu wrote: Hi David, It sounds like you are using the public Galaxy server at http://usegalaxy.org (http://main.g2.bx.psu.edu)? A BLAST service is not available on the public instance. (Megablast is available, but for NGS query data versus a specific set of target native genomes). Bjoern is correct that you will need to obtain a Galaxy BLAST wrapper from the Tool Shed. http://wiki.g2.bx.psu.edu/Tool%20Shed Tools Shed entries can be searched for with: http://galaxy.psu.edu/search/getgalaxy These would be installed into a local or cloud version of Galaxy and set up using the following instructions: http://getgalaxy.org Hi Jen, The NCBI BLAST wrappers used to be included as standard tools when doing a local Galaxy server installation - and were not in the ToolShed. Has that changed? Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] How to do BLAST on Galaxy sever?
Hi Peter, It looks to me like there are versions both, with the Tool Shed version having the more recent date stamp. But if those extra functions are not needed, then yes, you are correct, the version included in the distribution would be enough. Please send corrections if I have any of this wrong, so that David gets the best information, Thanks Peter! Jen Galaxy team On 2/9/12 1:50 PM, Peter Cock wrote: On Thursday, February 9, 2012, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi David, It sounds like you are using the public Galaxy server at http://usegalaxy.org (http://main.g2.bx.psu.edu)? A BLAST service is not available on the public instance. (Megablast is available, but for NGS query data versus a specific set of target native genomes). Bjoern is correct that you will need to obtain a Galaxy BLAST wrapper from the Tool Shed. http://wiki.g2.bx.psu.edu/Tool%20Shed Tools Shed entries can be searched for with: http://galaxy.psu.edu/search/getgalaxy These would be installed into a local or cloud version of Galaxy and set up using the following instructions: http://getgalaxy.org Hi Jen, The NCBI BLAST wrappers used to be included as standard tools when doing a local Galaxy server installation - and were not in the ToolShed. Has that changed? Peter -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
