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
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:
-- 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.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/
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-dev@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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
On Thursday, February 9, 2012, Jennifer Jackson <jen@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
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 <jen@bx.psu.edu <mailto:jen@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
On Thu, Feb 9, 2012 at 9:57 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
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
Hi Jen, I'm not sure which date stamps you are looking at, since I think it is the other way round. The NCBI BLAST+ wrappers shipped with Galaxy are currently at version 0.0.11, both in galaxy-central and galaxy-dist, dated 12 July 2011, e.g. here is the current XML file for the BLASTN wrapper: https://bitbucket.org/galaxy/galaxy-central/src/default/tools/ncbi_blast_plu... https://bitbucket.org/galaxy/galaxy-dist/src/default/tools/ncbi_blast_plus/n... Over on the Tool Shed, Edward Kirton has a forked copy of a much older version of these wrappers at v0.0.1. The push date of 7 Jun 2011 is probably from the toolshed migration, I believe the true date is well before that. Edward added support for using local BLAST databases as a new Galaxy datatype, along with wrappers for makeblastdb and dustmasker. Assuming these have proved useful, it would make sense to merge these changes into the main BLAST+ wrappers. I have CC'd the galaxy-dev mailing list (and Edward) which is probably a better place to discuss this than the galaxy-user list. Peter
David, I think we should go with Peter's advice. I had seen a date of April 2011 in the distribution for the tools I examined, but he knows these tools very well, and I could have easily missed the July 2011 date. Loading from the Tool Shed is not difficult, but perhaps unnecessary. So, for your purposes, starting simple is probably best. This would mean using what is in the distribution, i.e. the http://getgalaxy.org instructions. I didn't cross post this reply to all of the lists to keep the Q & A on topic. However, I do encourage the developers to discuss this further on the galaxy-dev list, separate from your BLAST question, ideally in a brand new thread/subject line. If the wrappers should be updated (sounds like this is worth discussing) - maybe Peter or Ed can start up a new thread? Thanks Peter for getting the most up-to-date information about these tools out to David & other galaxy-user readers, And thanks David, you brought up a good topic, sounds like there might be some small tuning needed on the development side of things, Take care, Jen Galaxy team On 2/10/12 3:19 AM, Peter Cock wrote:
On Thu, Feb 9, 2012 at 9:57 PM, Jennifer Jackson<jen@bx.psu.edu> wrote:
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
Hi Jen,
I'm not sure which date stamps you are looking at, since I think it is the other way round.
The NCBI BLAST+ wrappers shipped with Galaxy are currently at version 0.0.11, both in galaxy-central and galaxy-dist, dated 12 July 2011, e.g. here is the current XML file for the BLASTN wrapper:
https://bitbucket.org/galaxy/galaxy-central/src/default/tools/ncbi_blast_plu... https://bitbucket.org/galaxy/galaxy-dist/src/default/tools/ncbi_blast_plus/n...
Over on the Tool Shed, Edward Kirton has a forked copy of a much older version of these wrappers at v0.0.1. The push date of 7 Jun 2011 is probably from the toolshed migration, I believe the true date is well before that.
Edward added support for using local BLAST databases as a new Galaxy datatype, along with wrappers for makeblastdb and dustmasker. Assuming these have proved useful, it would make sense to merge these changes into the main BLAST+ wrappers.
I have CC'd the galaxy-dev mailing list (and Edward) which is probably a better place to discuss this than the galaxy-user list.
Peter
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
David, I think we should go with Peter's advice. I had seen a date of April 2011 in the distribution for the tools I examined, but he knows these tools very well, and I could have easily missed the July 2011 date. Loading from the Tool Shed is not difficult, but perhaps unnecessary. So, for your purposes, starting simple is probably best. This would mean using what is in the distribution, i.e. the http://getgalaxy.org instructions. I didn't cross post this reply to all of the lists to keep the Q & A on topic. However, I do encourage the developers to discuss this further on the galaxy-dev list, separate from your BLAST question, ideally in a brand new thread/subject line. If the wrappers should be updated (sounds like this is worth discussing) - maybe Peter or Ed can start up a new thread? Thanks Peter for getting the most up-to-date information about these tools out to David & other galaxy-user readers, And thanks David, you brought up a good topic, sounds like there might be some small tuning needed on the development side of things, Take care, Jen Galaxy team On 2/10/12 3:19 AM, Peter Cock wrote:
On Thu, Feb 9, 2012 at 9:57 PM, Jennifer Jackson<jen@bx.psu.edu> wrote:
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
Hi Jen,
I'm not sure which date stamps you are looking at, since I think it is the other way round.
The NCBI BLAST+ wrappers shipped with Galaxy are currently at version 0.0.11, both in galaxy-central and galaxy-dist, dated 12 July 2011, e.g. here is the current XML file for the BLASTN wrapper:
https://bitbucket.org/galaxy/galaxy-central/src/default/tools/ncbi_blast_plu... https://bitbucket.org/galaxy/galaxy-dist/src/default/tools/ncbi_blast_plus/n...
Over on the Tool Shed, Edward Kirton has a forked copy of a much older version of these wrappers at v0.0.1. The push date of 7 Jun 2011 is probably from the toolshed migration, I believe the true date is well before that.
Edward added support for using local BLAST databases as a new Galaxy datatype, along with wrappers for makeblastdb and dustmasker. Assuming these have proved useful, it would make sense to merge these changes into the main BLAST+ wrappers.
I have CC'd the galaxy-dev mailing list (and Edward) which is probably a better place to discuss this than the galaxy-user list.
Peter
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
participants (4)
-
Björn Grüning -
David PANG -
Jennifer Jackson -
Peter Cock