[galaxy-dev] PBSpro Cluster Server possible?

2012-07-24 Thread Stephan Frickenhaus
Hello, I have tried to couple our GALAXY-server (unified, running on a virtual server, ubuntu 12) with our big SGI Cluster-Server uv100 running PBSpro as job system (pbs_version = PBSPro_11.1.1.112253). On the GALAXY-server I have installed ii pbs-drmaa-dev1.0.10-2

Re: [galaxy-dev] PBSpro Cluster Server possible?

2012-07-24 Thread Sascha Kastens
Hi Stephan, I am no expert with PBS but your default_job_runner looks wrong Instead of default_cluster_job_runner = drmaa://uv100.awi.de/slong/ you should use some PBS specific paramters for the drmaa:/// part. I am using SGE an specifiy some of the qsub parameters:

[galaxy-dev] Local instance is running way too slow!!!

2012-07-24 Thread Di Nguyen
Dear All, I successfully install Galaxy onto my new MBP with 16Gb or Ram but when I tried to use Galaxy, it is painfully slow! The first test I did was to create Admin and import data (RNA-seq fastq, about 6Gb in size) into database and then history and it worked fine. The second test was to

Re: [galaxy-dev] Local instance is running way too slow!!!

2012-07-24 Thread Langhorst, Brad
galaxy just wraps existing tools... so it's probably not galaxy that is slow per se, but the fastqgroomer too. Each tool has its own performance characteristics. I don't use fastqgroomer, so I don't know how it can be expected to perform. Are you sure you need it? If you know that your

[galaxy-dev] Build indexes for BWA, Bowtie, and others in local instance

2012-07-24 Thread Di Nguyen
Dear all, I just installed my local instance. In order to use NGS tools, I need indexes. Do I have to build these indexes species by species, program by programs or there is a SHORTCUT for Galaxy compatible readied for download indexes? If I'am not mistaken, building these indexes can take

Re: [galaxy-dev] Local instance is running way too slow!!!

2012-07-24 Thread Kenny Sabir
Hello all, we were having the same issues with groomer taking up to 12 hours for large files. I had a look at the code and saw it was only using the single core. I changed the code to split the fastq input into multiple file parts and process it in parallel and reassemble the results. It also

Re: [galaxy-dev] Local instance is running way too slow!!!

2012-07-24 Thread John Chilton
If you problem really just is that fastq groomer is slower, I implemented several small optimizations for fastq groomer that I think resulted in a big improvement in performance. It seems it is not really used at my institution any more so I never pushed the changes out to our production server or