Re: [galaxy-dev] Trying to Run MegaBlast
On Monday, December 10, 2012, Jeremy Goecks wrote: Decompress and unpack the file and you'll find the relevant files (though everything now has extensions with p* rather than n*); add an entry to blastdb pointing to the directory with these files and you should be good to go. J. Not quite - blastdb.loc is for nucleotide databases only (needed for megablast), and NR is proteins. For that use blastdb_p.loc and blastp or blastx from the NCBI BLAST+ wrappers. Peter ___ 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/
Re: [galaxy-dev] Trying to Run MegaBlast
Please see the Megablast section on this page for instructions about getting and adding target databases to Galaxy: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Best, J. On Dec 10, 2012, at 2:59 PM, greg wrote: I have a fresh install on our cluster. I'm trying to test out the Megablast tool. The problem is that nothing is listed under against target database. Where do I get the target databases and how do I tell galaxy about them? Thanks, Greg Here's what the tool looks like: Megablast (version 1.2.0) Compare these sequences: against target database: using word size: Size of best perfect match (-word_size) report hits above this identity (-perc_identity): no cutoff if 0 set expectation value cutoff (-evalue): Filter out low complexity regions? (-dust): ___ 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/ ___ 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/
Re: [galaxy-dev] Trying to Run MegaBlast
So I just want to install one target database so that I can simply test whether blast is installed and working correctly. Are there any included with Galaxy, or do I need to download a database? Could you guys point me to a good file to test with? Following the directions you sent I got to the point of downloading a file. I tried download ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.00.tar.gz but I don't see a *.chunk file nor *.nhr, nin, nsq etc that are referenced in the included blastdb.loc Thanks, Greg On Mon, Dec 10, 2012 at 3:35 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: Please see the Megablast section on this page for instructions about getting and adding target databases to Galaxy: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Best, J. On Dec 10, 2012, at 2:59 PM, greg wrote: I have a fresh install on our cluster. I'm trying to test out the Megablast tool. The problem is that nothing is listed under against target database. Where do I get the target databases and how do I tell galaxy about them? Thanks, Greg Here's what the tool looks like: Megablast (version 1.2.0) Compare these sequences: against target database: using word size: Size of best perfect match (-word_size) report hits above this identity (-perc_identity): no cutoff if 0 set expectation value cutoff (-evalue): Filter out low complexity regions? (-dust): ___ 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/ ___ 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/
Re: [galaxy-dev] Trying to Run MegaBlast
Are there any included with Galaxy, or do I need to download a database? You need to download them. Could you guys point me to a good file to test with? Following the directions you sent I got to the point of downloading a file. I tried download ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.00.tar.gz but I don't see a *.chunk file nor *.nhr, nin, nsq etc that are referenced in the included blastdb.loc Decompress and unpack the file and you'll find the relevant files (though everything now has extensions with p* rather than n*); add an entry to blastdb pointing to the directory with these files and you should be good to go. J. ___ 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/
