[galaxy-dev] From NCBI SRA to UCSC viewer pipeline.

2011-07-07 Thread colin molter
Hi all, i am trying to use a local instance of my galaxy to pre-format data stored at sra-ncbi. Does anyone has a working pipeline that (s)he could share. Here is the pipeline I am using, with some questions. 1/ download sra files to my server. 2/ transform them in fastq using the sra toolbox.

[galaxy-dev] custom builds as tool in toolbox panel?

2011-07-07 Thread Michal Stuglik
hi, Would it be possible to build in a Custom builds form user menu to toolbox panel as a tool? Now it is not possible to use this feature in workflow ( as a part of pipeline)... all the best, michal ___ Please keep all replies on

Re: [galaxy-dev] bug or feature :)

2011-07-07 Thread Sarah Diehl
I just also found out about this bug (or feature). It is exactly the same for me and I'm running an older Galaxy version (galaxy-dist from April 8, 2011). On 07/06/2011 09:32 PM, Bossers, Alex wrote: In our local instance (central version) up to changeset (June 28th) I noticed in the admin

Re: [galaxy-dev] From NCBI SRA to UCSC viewer pipeline.

2011-07-07 Thread Peter Cock
On Thu, Jul 7, 2011 at 7:14 AM, colin molter colin.mol...@gmail.com wrote: Hi all, i am trying to use a local instance of my galaxy to pre-format data stored at sra-ncbi. Does anyone has a working pipeline that (s)he could share. Here is the pipeline I am using, with some questions. 1/

Re: [galaxy-dev] How to set java heap size in Galaxy?

2011-07-07 Thread liu bo
Hi Roman, Thanks for your explanation. I'm sorry for this late reply. I think the problem is on my app. I'll further check that. Thanks, Bo Date: Thu, 30 Jun 2011 14:53:08 +0200 From: Roman Valls brainst...@nopcode.org To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How to set java

[galaxy-dev] New version_string tag in tool XML

2011-07-07 Thread Peter Cock
Hi all, This new feature looks very exciting for tracking reproducibility - now in theory both the tool wrapper version (explicit in the XML) and any underlying tool version will both be recorded: https://bitbucket.org/galaxy/galaxy-central/changeset/84b20f29dfdf I have updated the NCBI BLAST+

Re: [galaxy-dev] New galaxy tool shed

2011-07-07 Thread Greg Von Kuster
Hello Marcel, http://usegalaxy.org/community On Jul 7, 2011, at 8:14 AM, Marcel Schumann wrote: Hi Greg, hi Dave, just a shorttrivial question today: ;-) I would like to put a link to the galaxy tool shed on my ISMB poster ... wouldn't it perhaps make sense to setup a (forwarding)

[galaxy-dev] Add Genome

2011-07-07 Thread Somayyeh Fahiminiya
Hello everyone, Could you plz add the genome of *Brachypodium distachyon* to the Galaxy. Thanks in advance ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other

[galaxy-dev] how to reduce Load of galaxy in standalone system by python

2011-07-07 Thread shashi shekhar
Hi All, i have system with single cpu . and have installed galaxy .while running galaxy it will create high load on system. how are you reducing the load of galaxy in system by using the python . Regards shashi ___ Please keep all

Re: [galaxy-dev] BAM display at Trackster

2011-07-07 Thread Kanwei Li
Is this from a recent changeset that you pulled? On Wed, Jul 6, 2011 at 2:19 PM, Vipin TS vipin...@gmail.com wrote: Hi Galaxy team, I am experiencing a problem with visualizing my BAM files through Trackster at my Galaxy instance. Please find the attached image along with this mail. From the

Re: [galaxy-dev] BAM display at Trackster

2011-07-07 Thread Vipin TS
Hi Jeremy, Are you able to visualize any BAM files in Trackster or do all files fail with the same error? Were you able to visualize BAM files before you updated your instance? Do you have SAMTools--which is required by Trackster--installed and available via your path? Yes, all BAM fails

Re: [galaxy-dev] BAM display at Trackster

2011-07-07 Thread Vipin TS
Hi Kanwei, Is this from a recent changeset that you pulled? Yes I pulled on yesterday (6-7-2011) --Vipin ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other

[galaxy-dev] Error when using build_profile_indexes.py on hg19

2011-07-07 Thread Sarah Diehl
Hi everybody, when I run the build_profile_indexes.py script in the scripts/tools/annotation_profiler/ directory on hg19 (downloaded yesterday from UCSC), I get the following error: Created table dir (profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal). ['fileName']

Re: [galaxy-dev] problems with 'Profile Annotations' tool UI

2011-07-07 Thread Daniel Blankenberg
Hi Hans, Very sorry for the delay in response. The sample file that was included was incorrect, but has been updated in changeset 5775:4220f8a5c571 and should now display an interface. If you would like to use or run the tool, you may find

Re: [galaxy-dev] BAM display at Trackster

2011-07-07 Thread Jeremy Goecks
Yes, all BAM fails are failing with the same error message. Before updating my instance I did not try to visualize through Trackster. Samtools path are available to Galaxy. I am not seeing any error/warning message in my log file. Try this in the main interface: (1) click the pencil

Re: [galaxy-dev] Error when viewing data in GeneTrack

2011-07-07 Thread Daniel Blankenberg
Hi Brian, This error is most likely caused by missing HDF libraries and the python Tables module. You should be able to get the exact error of the conversion by looking at the failed conversion history item (its hidden by default; under history options, click 'show hidden datasets'). Please

[galaxy-dev] error showing errors

2011-07-07 Thread Assaf Gordon
Hi, I've encountered a strange error when trying to view a failed job/dataset. I'm using the latest stable revision ( june 23rd, 720455407d1c ). A user executed a job and it failed (bad parameters, so no problem here). The program (bowtie) failed, returned information in STDERR. The peek field

Re: [galaxy-dev] [galaxy-user] Fwd: deleting datasets from history

2011-07-07 Thread Nate Coraor
Sergei Ryazansky wrote: Thanks for reply! set_dataset_sizes.py works fine for me. By the way, what is difference between file_size and total_size fields? It seems that their values are equal. Datasets with external metadata and composite datasets may contain extra files, and total_size will

Re: [galaxy-dev] New version_string tag in tool XML

2011-07-07 Thread Kanwei Li
Hey Peter, Right now the output is stored to a file, so we can do any processing in python, or just keep the multi-line as it is. I agree version_string should be version_cmd... didn't change it since working on it at the Conference ;) On Thu, Jul 7, 2011 at 6:27 AM, Peter Cock