Re: [galaxy-dev] Trackster and gff file with multiple chromosome annotations

2012-10-31 Thread Yec'han Laizet
I will modify the gff file as you mentioned and update galaxy. Thanks a lot. Yec'han Yec'han LAIZET Ingenieur Plateforme Genome Transcriptome Tel: 05 57 12 27 75 _ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route

Re: [galaxy-dev] Galaxy local install

2012-10-31 Thread Hans-Rudolf Hotz
Hi Vladimir I contacted with this question vendor tech support (Dell), but they could not answer (or did not want to) and directed me to Galaxy developers. I am using RHEL58 and SciLinux55 and want to install a local instance of Galaxy. Both my systems are based on Python 2.4. Question – can I

Re: [galaxy-dev] Parallelism tag and job splitter

2012-10-31 Thread Peter Cock
On Wednesday, October 31, 2012, Edward Hills wrote: Thanks Peter. My next question is, I have found that VCF files don't get split properly as the header is not included in the second file as is usually required by tools (such as vcf-subset). I have read the code and am happy to implement

[galaxy-dev] Resend: Unnamed histories proliferating, can't get to my data

2012-10-31 Thread Karger, Amir
Hi. Resending because I got no response. Can anybody suggest anything that might explain this, or tell me how I can troubleshoot? Where to look in the Python code? Whether anybody has seen anything like this? Our beta tester can't actually test anything. This occurs whether he does the FTP-style

[galaxy-dev] Incorrect chain order for SSL certificates on Galaxy main

2012-10-31 Thread Brad Chapman
Hi all; I ran into SSL certification errors when using Java to connect to Galaxy main via the API. My knowledge of this stuff is minimal, but I did some searching and discovered that the certificate chain on Galaxy main is a problem:

Re: [galaxy-dev] Incorrect chain order for SSL certificates on Galaxy main

2012-10-31 Thread Nate Coraor
On Oct 31, 2012, at 8:55 AM, Brad Chapman wrote: Hi all; I ran into SSL certification errors when using Java to connect to Galaxy main via the API. My knowledge of this stuff is minimal, but I did some searching and discovered that the certificate chain on Galaxy main is a problem:

[galaxy-dev] Amazon

2012-10-31 Thread Scooter Willis
Started up a cluster on Amazon using the Launch a Galaxy Cloud Instance and got the following message. Since I don't have any control over where the instances are run not sure how I can control this. The last 4 or 5 times I have started up an existing instance has worked with no problem.

Re: [galaxy-dev] Amazon

2012-10-31 Thread Scooter Willis
Tried it again and same error message. The volume was originally created in us-east-1b and newly created instances are being started in us-east-1a. Shouldn't the availability zone be set to us-east-1b when the instance is requested or that info stored in the properties file in the S3 bucket?

Re: [galaxy-dev] Amazon

2012-10-31 Thread Dannon Baker
For this instance, you'll need to restart using the old method for launching via the console, specifying the zone 1b. Detection of the zone volumes are in for existing clusters and specifying those for launch is on the short list of things coming up for cloud launch. On Oct 31, 2012, at

[galaxy-dev] which .loc file for SAM to BAM?

2012-10-31 Thread Andreas Kuntzagk
Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try SAM to BAM for a BAM file that has hg18 set as build I get a message that Sequences are not currently available for the specified build. I guess that I have either to manipulate one of the .loc

[galaxy-dev] output name of downloaded datasets

2012-10-31 Thread julie dubois
Hello, My goal is to introduce, in the xml file of one tool like MACS for example, a supplementary command to redirect the output in another directory (+ creating link between this and the directory of galaxy outputs). But I want to rename my output with the same name that the downloading tools

Re: [galaxy-dev] which .loc file for SAM to BAM?

2012-10-31 Thread Carlos Borroto
On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try SAM to BAM for a BAM file that has hg18 set as build I get a message that Sequences are not currently

[galaxy-dev] November 2012 Galaxy Update

2012-10-31 Thread Dave Clements
Hello all, The November 2012 Galaxy Update is now availablehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_11. *Highlights:* - 44 new papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_11#New_Papers, and *500 total papers in the Galaxy CiteULike group.* - Galaxy's new issue

[galaxy-dev] Error trying to run functional tests on a single tool

2012-10-31 Thread Dan Tenenbaum
Hi, I'm trying to test out the functional testing mechanism by running it on an existing Galaxy tool. First I ran ./run_functional_tests.sh -list which produced a list of tools I can test. I chose 'vcf_annotate' and tested it as follows: ./run_functional_tests.sh -id vcf_annotate This

Re: [galaxy-dev] Accessing Galaxy API from Java

2012-10-31 Thread Brad Chapman
Scooter; (cc'ing the dev list and updating the subject line in case others are interested) I have been looking for Java related API's to run workflows externally and haven't found anything searching message forums etc. Would like to automate data coming off up hiseq uploaded to Amazon S3 and

Re: [galaxy-dev] output name of downloaded datasets

2012-10-31 Thread Jeremy Goecks
Downloading data is handled in lib/galaxywebapps/galaxy/controllers/dataset.py, method display(), which in turn calls this line: -- return data.datatype.display_data(trans, data, preview, filename, to_ext, chunk, **kwd) -- Which, in most cases, calls display_data in

Re: [galaxy-dev] Galaxy processing

2012-10-31 Thread Jeremy Goecks
Where do I find info if the installed applications make use of multiple nodes via MPI(etc) which would indicate the benefit of starting up X number of nodes for faster processing? You'll need to look at the individual tool documentation. In general, many tools uses multiple cores, few use

[galaxy-dev] user management problem

2012-10-31 Thread Jordi Vaquero
Hello, I am trying to configure my galaxy instance and I have two problem. The first one is that I cannot delete users, I created some users for testing, I enabled the option on the universe_wsg.ini, and the button appears, but the users set only marked as deleted but they didn't disappear

[galaxy-dev] Join version 1.0.0 error

2012-10-31 Thread Scooter Willis
Using large amazon instance Trying to do an interval join of SNPs as output from pileup 120,000 regions(5.5Mb) with with snp135Common 12,000,000(425Mb) and get the following errors. The goal is to pickup rs id's for known SNPs in the list of SNPs. Is this a memory issue? I was able to do the

Re: [galaxy-dev] Join version 1.0.0 error

2012-10-31 Thread Scooter Willis
Did a subtract first to get a known list of rs SNPs that will be found in the tumor SNPs. That ran without error. Doing a join of the subtracted list of rs SNPs and the tumor SNPs. So something different in the join code then in the subtract code. From: Scooter Willis

Re: [galaxy-dev] Empty TopHat output

2012-10-31 Thread Mohammad Heydarian
We are still getting empty TopHat output files on our Galaxy instance on the cloud. We see that TopHat is generating data while the tool is running (by monitoring our disk usage on the Amazon cloud), but the output is empty files. Is anyone else having this issue? Does anyone have any

Re: [galaxy-dev] Empty TopHat output

2012-10-31 Thread Jeremy Goecks
Given that this doesn't seem to be happening on our public server or on local instances, my best guess is that the issue is old code. Are you running the most recent dist? J. On Oct 31, 2012, at 7:37 PM, Mohammad Heydarian wrote: We are still getting empty TopHat output files on our Galaxy

Re: [galaxy-dev] Empty TopHat output

2012-10-31 Thread Jeremy Goecks
In this case, it's useful to differentiate between (i) the AMI that Galaxy Cloud uses and (ii) the Galaxy code running on the cloud. I suspect that (ii) is out of data for you; this is not (yet) automatically updated, even when starting a new instance. Try using the admin console to update to

Re: [galaxy-dev] Parallelism tag and job splitter

2012-10-31 Thread Edward Hills
Hi Peter, thanks again. Turns out that it has been implemented by the looks of it in lib/galaxy/datatypes/tabular.py under class Vcf. However, despite this, it is always the Text class in data.py that is loaded and not the proper Vcf one. Can you point me in the direction of where the type is

[galaxy-dev] (no subject)

2012-10-31 Thread Sachit Adhikari
Hello Everyone, I am about to write a syncing tool for Galaxy like Dropbox using Python with the progress bar. How do I integrate it with galaxy? It would be easy for client to upload files using the syncing tool. Are there any syncing tools available for Galaxy? Thanks

[galaxy-dev] Dataset upload fail

2012-10-31 Thread Vladimir Yamshchikov
Local install of Galaxy on SciLinux55. Fails to upload 5.2 GB fastq file from local HD, while normally loading smaller fastq and fasta datasets (less than 1 GB). Chunks of 1.2 GB size remain in */database/tmp, which all represent beginning of the file that fails to upload. Several attempts to