Re: [galaxy-dev] FastQC Tool Errors

2012-06-26 Thread simon andrews
Yes, that's the broken version of gcj. I don't have a Centos machine here at the moment, but I think if you install OpenJDK and use the alternatives system to select that as the default JRE then that should fix things. Simon. On 25 Jun 2012, at 17:19, Josh Nielsen wrote: Hi Simon, I

[galaxy-dev] Tophat Troubles

2012-06-26 Thread Kristen Roop
Hello, I am having an issue on the Galaxy Main server. I had reached my maximum disk space this morning. So I cleaned out some items until my space was down to 61%. I then tried to run Tophat for RNA seq and the tool is doing nothing. I know the datasets aren't too large because I would have

Re: [galaxy-dev] unable to start galaxy

2012-06-26 Thread izmiyati razikin
Re-send From: izmiyati razikin [mailto:izmiy...@novaglobal.com.sg] Sent: Monday, 25 June, 2012 11:01 PM To: 'galaxy-dev@lists.bx.psu.edu' Subject: unable to start galaxy Hello, I'm having problem starting up galaxy. I'm using RHEL 5.3 which comes with python 2.4.3. So I compiled

Re: [galaxy-dev] Tophat Troubles

2012-06-26 Thread Nate Coraor
On Jun 25, 2012, at 5:25 PM, Kristen Roop wrote: Hello, I am having an issue on the Galaxy Main server. I had reached my maximum disk space this morning. So I cleaned out some items until my space was down to 61%. I then tried to run Tophat for RNA seq and the tool is doing nothing. I

Re: [galaxy-dev] Fully Purged Histories and still 30% used

2012-06-26 Thread Jennifer Jackson
Hello, Are you still having this problem? Is this on the public main instance or your own local instance? The display numbers can take up to a few hours to update on the main server, depending on load. The update time on your local install will vary depending on your configuration. If

Re: [galaxy-dev] Fully Purged Histories and still 30% used

2012-06-26 Thread Jennifer Jackson
Hello again, These numbers are in-line with the disk quota limits on Main: http://wiki.g2.bx.psu.edu/Main#User_data_and_job_quotas Just as a reminder, datasets must be 'permanently deleted', not just 'deleted', in order to not count in a quota usage amount. Instructions for reviewing deleted

[galaxy-dev] Complete Genomics CGA Tools� in Galaxy

2012-06-26 Thread Birgit Crain
Dear Community Members Complete Genomics, Inchttp://www.completegenomics.com/. is happy to announce the release of a CGA Tools™ implementation in Galaxy. CGA Tools™ is an open source projecthttp://cgatools.sourceforge.net/ to provide tools for downstream analysis of Complete Genomics Whole

Re: [galaxy-dev] Tophat Troubles

2012-06-26 Thread Anthonius deBoer
The cluster was busy I think, so you just have to wait for the queue to clear...On Jun 25, 2012, at 02:25 PM, Kristen Roop kristen.r...@gmail.com wrote:Hello,I am having an issue on the Galaxy Main server.I had reached my maximum disk space this morning. So I cleaned out some items until my space

[galaxy-dev] Are there any database test scripts?

2012-06-26 Thread Anthonius deBoer
Hi,I am still having serious issues with running galaxy workflows from the API on my installation...I am getting random files on which the workflows are run, rather than the files I select in my script.I am suspecting that my database may be corrupt...Is there any test script that can test my