[galaxy-user] Trouble with BLAST+ and .loc file
Dear Galaxy users, I have been trying to upload a blastable database in my local instance of galaxy. I have used the nr database and generated all the nhr, nin, nsq, and nal files. I have also edited the blastdb.loc file in the galaxy-dist/tool-data/ directory and it looks like this: database [build data] path nr_01_Mar_2012 nr 15 Mar 2012 /home/user/Desktop/nr.00/nr Nevertheless when i start galaxy the megablast tool can't recognise the database. Am I missing something? Thank you in advance Makis Ladoukakis ___ 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] Trouble with BLAST+ and .loc file
2012/3/21 Makis Ladoukakis makis4e...@hotmail.com: Dear Galaxy users, I have been trying to upload a blastable database in my local instance of galaxy. I have used the nr database and generated all the nhr, nin, nsq, and nal files. I have also edited the blastdb.loc file in the galaxy-dist/tool-data/ directory and it looks like this: database [build data] path nr_01_Mar_2012 nr 15 Mar 2012 /home/user/Desktop/nr.00/nr Nevertheless when i start galaxy the megablast tool can't recognise the database. Am I missing something? The NR database comes split up into many parts, 00 to 06 currently, and you need to download them all. They are linked by the nr.pal file, which you should also have downloaded. The database is then used via the full name of the nr.pal file (but without the .pal extension). If you are running Galaxy on a server, it is likely your systems administrator can/has setup a shared set of NCBI BLAST databases for all the system users (including Galaxy), to avoid unnecessary copies under /home Note that queries about local Galaxy installations are normally handled via the galaxy-dev mailing list (although perhaps the project needs three lists now given local Galaxy installations are getting more common and not everyone wants to follow the Galaxy development itself). 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] Trouble with BLAST+ and .loc file
On Wed, Mar 21, 2012 at 10:21 AM, Peter Cock p.j.a.c...@googlemail.com wrote: 2012/3/21 Makis Ladoukakis makis4e...@hotmail.com: Dear Galaxy users, I have been trying to upload a blastable database in my local instance of galaxy. I have used the nr database and generated all the nhr, nin, nsq, and nal files. I have also edited the blastdb.loc file in the galaxy-dist/tool-data/ directory and it looks like this: database [build data] path nr_01_Mar_2012 nr 15 Mar 2012 /home/user/Desktop/nr.00/nr Nevertheless when i start galaxy the megablast tool can't recognise the database. Am I missing something? The NR database comes split up into many parts, 00 to 06 currently, and you need to download them all. They are linked by the nr.pal file, which you should also have downloaded. The database is then used via the full name of the nr.pal file (but without the .pal extension). If you are running Galaxy on a server, it is likely your systems administrator can/has setup a shared set of NCBI BLAST databases for all the system users (including Galaxy), to avoid unnecessary copies under /home Note that queries about local Galaxy installations are normally handled via the galaxy-dev mailing list (although perhaps the project needs three lists now given local Galaxy installations are getting more common and not everyone wants to follow the Galaxy development itself). Peter Sorry, I missed something else which is vitally important: The NCBI NR database is a protein database, and should be listed in blastdb_p.loc (which is used by the BLASTP wrapper etc) while blastdb.loc is for nucleotide databases only (and used for the BLASTN/megablast wrapper etc). As you were asking about megablast, you probably want the NCBI NT BLAST database instead (although sometimes confusingly the NCBI can use the names ambiguously, for the file names this is very important). 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] Trouble with BLAST+ and .loc file
Dear Peter, Thank you for your reply. You are right I do have all 6 parts of the nr database on the server plus the .pal file in the same directory. The .loc file still is: database [build data] path nr_01_Mar_2012 nr 15 Mar 2012 /path/on/the/server/nr_directory/nr but the megablast tool still doesn't recognise the database. Am I missing something? Thank you in advance, Makis Ladoukakis Date: Wed, 21 Mar 2012 10:21:16 + Subject: Re: [galaxy-user] Trouble with BLAST+ and .loc file From: p.j.a.c...@googlemail.com To: makis4e...@hotmail.com CC: galaxy-user@lists.bx.psu.edu 2012/3/21 Makis Ladoukakis makis4e...@hotmail.com: Dear Galaxy users, I have been trying to upload a blastable database in my local instance of galaxy. I have used the nr database and generated all the nhr, nin, nsq, and nal files. I have also edited the blastdb.loc file in the galaxy-dist/tool-data/ directory and it looks like this: database [build data] path nr_01_Mar_2012 nr 15 Mar 2012 /home/user/Desktop/nr.00/nr Nevertheless when i start galaxy the megablast tool can't recognise the database. Am I missing something? The NR database comes split up into many parts, 00 to 06 currently, and you need to download them all. They are linked by the nr.pal file, which you should also have downloaded. The database is then used via the full name of the nr.pal file (but without the .pal extension). If you are running Galaxy on a server, it is likely your systems administrator can/has setup a shared set of NCBI BLAST databases for all the system users (including Galaxy), to avoid unnecessary copies under /home Note that queries about local Galaxy installations are normally handled via the galaxy-dev mailing list (although perhaps the project needs three lists now given local Galaxy installations are getting more common and not everyone wants to follow the Galaxy development itself). 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] Bowtie Seed length (-l) and non-unique reads mode (m=-1)
Hi Eric, On 3/19/12 4:13 PM, Eric Guo wrote: Hi there, I have two questions regarding alignment using Bowtie: 1. Is there a way to set the Seed Length (-l) to the full length of each read instead of using a single Seed Length for all reads? The seed length is a single input value for all sequences in any particular job. 2. When using m = -1 mode (Suppress all alignments for a read if more than n reportable alignments exist (-m): OFF), will a read be randomly assigned to one of the alignment positions in the genome? Or, will all the alignments for one single read be reported in the final output .bam file. If alignment are not suppressed, then all reportable hits are in the output. More about Bowtie can be found here: http://bowtie-bio.sourceforge.net/index.shtml Best, Jen Galaxy team Thanks in advance for your help. -Eric ___ 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/ ___ 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 add alignment to the MAF
Hello Lyni, Are you still having problems with your analysis? If so, then I can point you to a few tools that can help. - FASTA manipulation - Tabular-to-FASTA and FASTA-to-Tabular - Text Manipulation - Concatenate datasets - Filter and Sort - Sort I am not sure how many RNA-seq transcripts you have, if just one, then concatenate that fasta sequence with the others into a single fasta file. If you have several, then they are likely named already (by the Extract MAF process) so that they can be grouped together by sorting. Convert the fasta data to tabular, concatenate, sort, then convert back to fasta. Thanks for using Galaxy, Jen Galaxy team On 3/2/12 10:03 AM, chengyuyan wrote: Hi galaxy, I'm trying to know the coding potential of my RNA-seq transcripts by phylogeny analysis. So I want to generate a FASTA file that includes ORF of my sequence and 29 other mammalian species. I usedExtract MAF blocks and Stitch MAF blocks using my RNA-seq data(gtf file from cuffcompare) as intervals. But the final FASTA file doesn't include my sequence. How can I add my sequence to the final FASTA so that it includes both the 29 mammalian genome and my sequence? Thanks in advance. Lyni. ___ 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/ ___ 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/
[galaxy-user] Deploying a tool
Hi, This is a simple question, but I couldn't find an explicit explanation online. How do I deploy a tool from the Galaxy toolshed to my local version of Galaxy? Do I have to download the package and move the files into the tools/ directory, and update the tool list, or is there an automatic way to deploy through the browser interface? Thanks, Mark ___ 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/
[galaxy-user] Job is waiting to run
Dear Sir/Madam, I am a registered user of the public Galaxy Server (main). Any job I submitted today is labeled as Job is waiting to run forever. The total volume of my files is 249 mb, which is far below the quota limit of 250 gb, and I am trying to run less than 8 jobs. Could you please let me know the possible reasons? Sincerely, Shisheng ___ 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/
[galaxy-user] Drosophila yakuba reference genome
Hi, Could galaxy include the Drosophila yakuba reference genome for use with Tophat? It's not listed. ___ 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] Bowtie Seed length (-l) and non-unique reads mode (m=-1)
Hello Eric, I apologize, but I made a mistake, please see below On 3/21/12 5:42 AM, Jennifer Jackson wrote: Hi Eric, On 3/19/12 4:13 PM, Eric Guo wrote: Hi there, I have two questions regarding alignment using Bowtie: 1. Is there a way to set the Seed Length (-l) to the full length of each read instead of using a single Seed Length for all reads? The seed length is a single input value for all sequences in any particular job. 2. When using m = -1 mode (Suppress all alignments for a read if more than n reportable alignments exist (-m): OFF), will a read be randomly assigned to one of the alignment positions in the genome? Or, will all the alignments for one single read be reported in the final output .bam file. If alignment are not suppressed, then all reportable hits are in the output. This is incorrect. If alignments are not suppressed, then reporting -a (all) is not the default. Rather, there are several 'reporting options', and they are used in combination and with 'alignment options' to achieve different output results. It is probably best to show you the documentation, so that you can compare different parameters and output they produce. Please see: http://bowtie-bio.sourceforge.net/manual.shtml#reporting Hopefully this clears up any confusion my original reply may have caused! Jen Galaxy team More about Bowtie can be found here: http://bowtie-bio.sourceforge.net/index.shtml Best, Jen Galaxy team Thanks in advance for your help. -Eric ___ 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/ ___ 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/ ___ 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] Drosophila yakuba reference genome
Hello, The quickest way to use a genome that is not already indexed is to load it into you history and select it as a custom genome from the TopHat tool form with the option: Will you select a reference genome from your history or use a built-in index?: - Use one from the history Instructions are included in this wiki: http://wiki.g2.bx.psu.edu/Learn/CustomGenomes This genome is sourced from UCSC and is available here: http://hgdownload.cse.ucsc.edu/downloads.html Best, Jen Galaxy team On 3/21/12 2:07 PM, Evgeny Brud wrote: Hi, Could galaxy include the Drosophila yakuba reference genome for use with Tophat? It's not listed. ___ 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/ ___ 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/
