[galaxy-user] Trouble with BLAST+ and .loc file

2012-03-21 Thread Makis Ladoukakis
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:

Re: [galaxy-user] Trouble with BLAST+ and .loc file

2012-03-21 Thread Peter Cock
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

Re: [galaxy-user] Trouble with BLAST+ and .loc file

2012-03-21 Thread Peter Cock
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,

Re: [galaxy-user] Trouble with BLAST+ and .loc file

2012-03-21 Thread Makis Ladoukakis
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

Re: [galaxy-user] Bowtie Seed length (-l) and non-unique reads mode (m=-1)

2012-03-21 Thread Jennifer Jackson
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

Re: [galaxy-user] How to add alignment to the MAF

2012-03-21 Thread Jennifer Jackson
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

[galaxy-user] Deploying a tool

2012-03-21 Thread Mark Maienschein-Cline
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

[galaxy-user] Job is waiting to run

2012-03-21 Thread Shisheng Li
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

[galaxy-user] (no subject)

2012-03-21 Thread Moein Farshchian
hi to all Would you please someone help me to remove my email from galaxy users list? Thanks. Moein ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.

[galaxy-user] Drosophila yakuba reference genome

2012-03-21 Thread Evgeny Brud
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.

Re: [galaxy-user] Bowtie Seed length (-l) and non-unique reads mode (m=-1)

2012-03-21 Thread Jennifer Jackson
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

Re: [galaxy-user] Drosophila yakuba reference genome

2012-03-21 Thread Jennifer Jackson
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