Re: [galaxy-dev] Error when trying to display data on gene track

Hello, The link appears to be one that is generated from this link (link to "GeneTrack"): "view in GeneTrack" Not this link (link to "UCSC Browser", same as in tutorials, and probably the one you want to be using anyway): "display at UCSC main" GeneTrack is no longer supported, although i

Re: [galaxy-dev] FastQC Question

Hello, Min This tool has been stable for a while now and that variable cl is defined as a list in line 52 just above line 63, so this error seems very strange unless you made changes to the source code? It's hard to know where to start helping because there are lots of useful pieces of information

[galaxy-dev] FastQC Question

Hello, When trying to run FastQC, I get this error: Traceback (most recent call last): File "/home/bal/galaxy-dist/tools/rgenetics/rgFastQC.py", line 162, in html,retval,serr = f.run_fastqc() File "/home/bal/galaxy-dist/tools/rgenetics/rgFastQC.py", line 63, in run_fastqc sout.write(

[galaxy-dev] FastQC Question

Hello, When trying to run FastQC, I get this error: Traceback (most recent call last): File "/home/bal/galaxy-dist/tools/rgenetics/rgFastQC.py", line 162, in html,retval,serr = f.run_fastqc() File "/home/bal/galaxy-dist/tools/rgenetics/rgFastQC.py", line 63, in run_fastqc sout.writ

Re: [galaxy-dev] History not updating for multiple instances of Galaxy

Further, when I try "register" I add an email address and password, but the system still doesn't log me in Maybe this is a database configuration issue? I didn't think I'd need to state any specific entries in universe as I am using physically separate directories i.e. /home/galaxy/galaxy-cte/

[galaxy-dev] History not updating for multiple instances of Galaxy

Hi, I have three instances of galaxy running on the same Linux box. My "/etc/apache2/sites-available/default" is: RewriteEngine on RewriteRule ^/galaxy-csiro$ /galaxy-csiro/ [R] RewriteRule ^/galaxy-csiro/static/style/(.*) /home/galaxy/galaxy-csiro/static/june_2007_style/blue

[galaxy-dev] dynamic select problem

I've been tweaking the blast+ tool xml to simplify database selection for our users (we have a lot of databases) and have made it multi-tiered through the use of two select boxen and a filter. Basically, I've added an extra column to blastdb.loc with a group name, then use this as a filter to on

Re: [galaxy-dev] Tool wrappers - Triggering warnings on specific options?

On Wed, Feb 20, 2013 at 11:13 PM, James Taylor wrote: > Peter, I quite like this idea, and I think it might be possible to do as a > simple extension to the validator framework. Basically, a flag indicating > that failing a certain validation would be able to be considered a warning > rather than

Re: [galaxy-dev] Tool wrappers - Triggering warnings on specific options?

Peter, I quite like this idea, and I think it might be possible to do as a simple extension to the validator framework. Basically, a flag indicating that failing a certain validation would be able to be considered a warning rather than an error. Or, allow a validator to return a sentinel indicating

Re: [galaxy-dev] tophat for illumina looking in wrong directory for bowtie2 indexes?

>> But this is what's in my galaxy-dist/tool-data/bowtie2_indices.loc file: >> >> mm10mm10mm10 >> /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index You need: /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome J. >> >> >> Why isn't it lo

Re: [galaxy-dev] Test data for tophat2 with hg19 reference genome

There is some test data for hg19 on the RNA-seq exercise: https://main.g2.bx.psu.edu/rna-seq Best, J. On Feb 20, 2013, at 6:47 AM, Sachit Adhikari wrote: > Hi, > > I need a test_data for Tophat with the hg19 reference genome? The test_data > from this website http://tophat.cbcb.umd.edu/downlo

Re: [galaxy-dev] Installing Prebuilt Indexes for "Tophat for Illumina" - What to do for color space files?

> > I see where I would use the *.ebwt files in the bowtie_index.loc file. > But I'm not sure what to reference in the bowtie_index_color.loc > file? (The same *.ebwt files??) You need to download the colorspace indices separately: http://bowtie-bio.sourceforge.net/index.shtml Good luck, J.___

Re: [galaxy-dev] tophat for illumina looking in wrong directory for bowtie2 indexes?

Just for fun, I updated galaxy-dist/tool-data/bowtie_indices.loc to be: mm10mm10mm10 /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index And ran it again. Now it's looking at the correct directory (Bowtie2Index) but still says: Error: Could not find Bowtie 2 index fil

[galaxy-dev] tophat for illumina looking in wrong directory for bowtie2 indexes?

Hi guys, I'm getting this error when running tophat for Illumina: Error in tophat: [2013-02-20 16:43:50] Beginning TopHat run (v2.0.6) --- [2013-02-20 16:43:50] Checking for Bowtie Bowtie version: 2.0.2.0 [2013-02-20 16:43:50] Checking for Samtools [2

Re: [galaxy-dev] Tool wrapper XSD

Hi, > > If you are going to write one and want a starting point, here is > > the schema I used Thanks John for sharing your XSD. I forked and started to complete it at: I worked on it until my own tool wrapper passed, but it needs more work for any oth

Re: [galaxy-dev] Rendering of < and > in read-me files on Tool Shed

Hi Peter, This one is trickier than it seems, but we;re figuring out the best way to handle it. We'll get the fix out asap and let you know when it's available. Email works well for me with issues like this, but Trello is ok too, so take your pick. I really appreciate your finding and repor

[galaxy-dev] Installing Prebuilt Indexes for "Tophat for Illumina" - What to do for color space files?

Hi, I'm trying to install DM3 from this page (http://tophat.cbcb.umd.edu/igenomes.html) as a pre-built index for "Tophat for Illumina" in our local galaxy install. I'm following the instructions on this page: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup I see where I would use the *.e

Re: [galaxy-dev] Submitting jobs as a real user without using chown, please

Ah...Found what root squashing is and yes, that is turned on our isilon system...So out of luck I take it? We need to chown? we cannot fake the submission name in another way ;)ThanksThonOn Feb 20, 2013, at 10:32 AM, Anthonius deBoer wrote:I cannot run chown even as a sudo command...Same error...W

[galaxy-dev] Error when trying to display data on gene track

Hello, We are running a local instance of galaxy and we get the following error when trying to display genes from our history in the ucsc browser. I got the error as I was following the galaxy 101 video in the galaxy website (last step). Thanks, --Ricardo Perez URL: http://galaxy.tamu.edu/da

Re: [galaxy-dev] Submitting jobs as a real user without using chown, please

I cannot run chown even as a sudo command...Same error...What is root squashing? I am reading on the internet that it is very common not to allow users to change the ownership of files...ThonOn Feb 20, 2013, at 05:52 AM, Nate Coraor wrote:On Feb 19, 2013, at 11:02 PM, Thon de Boer wrote: > Hi, >

[galaxy-dev] Rendering of < and > in read-me files on Tool Shed

Hi Greg, This is probably another minor bug report for your to-do list - would you prefer I try to file Trello issues for things like this directly? Many of the README files on the Tool Shed have an XML snippet in them if they include manual install instructions, but unfortunately the less-than a

Re: [galaxy-dev] galaxy-dev mailing list

Hi Oya, This is the link: http://wiki.galaxyproject.org/MailingLists Thanks for using Galaxy, Dan On Feb 20, 2013, at 8:39 AM, Dannon Baker wrote: > Hi Oya, > > Here's a wiki page detailing how to subscribe and unsubscribe from any > of the galaxy mailing lists: > > -Dannon > > 2013/2/14

Re: [galaxy-dev] environment variables and paths for toolshed tools

On Tue, Feb 19, 2013 at 12:06 PM, Peter Cock wrote: > On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster wrote: >> On Feb 19, 2013, at 5:10 AM, Peter Cock wrote: >> >> Yes, the complete directory hierarchy and content of the original >> repository revision is preserved when it installed into Galax

Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed

It's really hard to say what's going on with those issues without more information about the particular version of galaxy (which unfortunately we'd get from `hg tip`, which won't work on your bio linux install) or proxy configuration, if any. I'm also not sure what the appropriate bio linux update

[galaxy-dev] Tool wrappers - Triggering warnings on specific options?

Hello all, I was wondering if anyone else writing Galaxy tools has wanted to be able to show warning messages conditional on tool options? For example, setting a parameter to a deprecated value could trigger a warning message (with an OK/Cancel dialogue to allow continuation or returning to the t

Re: [galaxy-dev] Tabular file metadata - columns names

Bumping one of my old queries again, with some more use-cases at the end, On Wed, Aug 10, 2011 at 11:28 AM, Peter Cock wrote: > Bumping this old query: > > On Mon, Nov 22, 2010 at 10:11 AM, Peter wrote: >> On Fri, Nov 19, 2010 at 12:20 PM, Peter wrote: >>> Hi all, >>> >>> I'd like to know more

[galaxy-dev] GALAXY LOCAL INSTALLATION: Tools and Data

Hi, I've installed Galaxy in local and following the Tool dependencies manual I installed all necessary tools. However for some of then such as BWA, Bowtie,... it's usually needed to create indexes. Where should I store those indexes?

[galaxy-dev] not enough memory space on my galaxy session

Dear Galaxy manager, I have a problem, I'm actually running my RNA seq project on your galaxy on line program. The matter is I do not have enough space. I'm running 12 times 3 to 4 mega bit of data. I have fews options: 1. running my samples in two times... which is quite difficult because they a

Re: [galaxy-dev] Submitting jobs as a real user without using chown, please

On Feb 19, 2013, at 11:02 PM, Thon de Boer wrote: > Hi, > > I am trying to setup my galaxy system to allow jobs to be submitted as the > real user, since people want to keep an eye on their job on the cluster > sometimes and they have no ideas which ones are theirs… > > I tried the approach

Re: [galaxy-dev] galaxy-dev mailing list

Hi Oya, Here's a wiki page detailing how to subscribe and unsubscribe from any of the galaxy mailing lists: -Dannon 2013/2/14 Oya Uyguner : > I would like to enroll, galaxy-dev mailing list. > Regards, > Z. Oya Uyguner > Department of Medical Genetics > Istanbul Medical Faculty > Istanbul Univer

[galaxy-dev] Tool Shed examples defining datatype conversion

Hello all, I'd like to define 'blastxml' to 'tabular' conversion within Galaxy so that this can be used automatically (e.g. Tools expecting just tabular data would have converted BLAST XML files listed in the drop down). The functionality to do this exists in my Python tool 'blastxml_to_tabular' c

Re: [galaxy-dev] Tool wrapper XSD

Ok, thanks a lot. I'm not sure I will have the time to develop a XSD but after looking at yours I think it would only need a few contributors to get a fully complete and updated one. Thanks again, Pierre Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB)