[galaxy-dev] Hidden output files

2012-03-23 Thread Frank Sørensen
Hi, I seem to have some problems with the visibility of tool outputs in my workflows. When I flag any given output as visible, Galaxy sometimes decides to hide it in the resulting history anyway. I can't find any systematic behavior though. It seems to be rather arbitrary weather Galaxy

Re: [galaxy-dev] Hidden output files

2012-03-23 Thread Dannon Baker
Could you share an offending workflow with me? Or is it any workflow? I've not seen this behavior before, but it definitely shouldn't be random. So in your situation the same workflow run multiple times will not consistently hide the same datasets? -Dannon On Mar 23, 2012, at 6:05 AM,

Re: [galaxy-dev] Local Toolshed misbehaviours?

2012-03-23 Thread Greg Von Kuster
Hi Daniel, On Mar 22, 2012, at 11:21 AM, Daniel Sobral wrote: Hi Greg, This is the output I get in the toolshed log: Firefox/10.0.2 172.22.50.249 - - [22/Mar/2012:15:11:50 +0100] GET

Re: [galaxy-dev] Local Toolshed misbehaviours?

2012-03-23 Thread Greg Von Kuster
On Mar 23, 2012, at 10:09 AM, Daniel Sobral wrote: The path I defined on shed_tool_conf.xml should be writable. In fact, I can install repositories from your toolsheds (galaxy main or galaxy test) with no problems. I actually used the galaxy test toolshed to add my own repositories as a

[galaxy-dev] Problem starting toolshed

2012-03-23 Thread Joachim Jacob
Hi all, In order to ease sharing the developed Galaxy tools in our group, we want to launch a private Toolshed. However, upon running ./run_community.sh, I got following error. Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File

[galaxy-dev] Allow dataset with custom build to be displayed in local IGV

2012-03-23 Thread Sarah Diehl
Hi all, is there some way I can allow datasets (specifically bam files) that are annotated with a custom build to be displayed in a local IGV (assuming a genome with the same name was generated for IGV)? I tried some things with display_applications/igv/bam.xml, but I couldn't get it to

Re: [galaxy-dev] Problem starting toolshed

2012-03-23 Thread Greg Von Kuster
You'll need to configure your Python 2.6 to include mercurial. You can do something like easy_install -U mercurial but there are other approaches as well. On Mar 23, 2012, at 10:33 AM, Joachim Jacob wrote: Hi all, In order to ease sharing the developed Galaxy tools in our group, we

Re: [galaxy-dev] Problem starting toolshed

2012-03-23 Thread Joachim Jacob
Thanks for your fast reply! It did the trick and kept me going on a sunny friday afternoon. :-) # easy_install -U mercurial Cheers, Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

[galaxy-dev] Update on Megablast?

2012-03-23 Thread Luobin Yang
Hi, all, Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am wondering if there is an update on megablast web interface and wrapper in Galaxy? Thanks, Luobin ___ Please keep all replies on the list by using reply all

Re: [galaxy-dev] Update on Megablast?

2012-03-23 Thread Peter Cock
On Fri, Mar 23, 2012 at 4:22 PM, Luobin Yang yangl...@isu.edu wrote: Hi, all, Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am wondering if there is an update on megablast web interface and wrapper in Galaxy? Yes, there are wrappers for the main tools from NCBI

Re: [galaxy-dev] Galaxy AMQP listener startup script error

2012-03-23 Thread Greg Von Kuster
Make sure that the Python you're running when you start the server is supported by Galaxy (2.5+) This will tell you what Python version you are using: python -V If that isn't the problem, try deleting the pysam egg and then re-fetching it: python ./scripts/fetch_eggs.py from your Galaxy

Re: [galaxy-dev] Update on Megablast?

2012-03-23 Thread Luobin Yang
Yeah, that's what I was wondering: to update megablast tool to use NCBI BLAST+ . I revised megablast wrapper a bit to use the legacy_blast.pl from NCBI BLAST+, but it seems the output format is not compatible with the tool (Fetch taxonomic representation) in metagenomic analyses anymore. So it

Re: [galaxy-dev] Data source tool doesn't source data

2012-03-23 Thread Mark Johnson
Looks like I'll have to try again. Maybe with a more general question (?) When you're debugging tools, how do you get Galaxy to tell you what the tool is doing? My tool doesn't work properly, but paster.log just shows a line for the request. It doesn't say anything about what tool_runner is

[galaxy-dev] Reference genomes at local instance of Galaxy

2012-03-23 Thread Yang, Yanming
Hi, I have just installed a Galaxy instance at my local machine and uploaded some sequence data into it. But, when I tried to some NGS tools which need reference genome, i found the selection window was empty. I wonder how to get a reference genome data (e.g., hg19) incorporated into the

Re: [galaxy-dev] Data source tool doesn't source data

2012-03-23 Thread Daniel Blankenberg
Hi Mark, Try these changes: tool id=sra-trace-download name=Download SRA data tool_type=data_source and param name=GALAXY_URL type=baseurl value=/tool_runner?tool_id=sra-trace-download/ Although 'GALAXY_URL' should be generated automatically if it is not included explicitly for

Re: [galaxy-dev] refresh_on_change is broken?

2012-03-23 Thread Jeremy Goecks
A final pointer: to see tools that use dynamic options, take a look at Extract GFF features and Filter GFF dataset by feature count Good luck, J. On Mar 22, 2012, at 12:15 PM, Greg Von Kuster wrote: It's always best to look at examples in the code base for technical details like this rather