[galaxy-dev] new_file_path vs $TMP

2011-03-29 Thread Louise-Amélie Schmitt
Hello We managed to install Galaxy according to the unified method, with the runner and the web application running on separate machines sharing by NFS the same storage space where the Galaxy files are. The thing is, the data must be saved in another NFS storage space so we had to define the

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread Peter Cock
On Tue, Mar 29, 2011 at 1:31 AM, Assaf Gordon gor...@cshl.edu wrote: Hello all, We're developing alternative bowtie tools that more closely suit our needs, are we're happy to share (and get comments). The main differences are: 1. separate tools for paired-end and single-end Sounds sensible

Re: [galaxy-dev] new_file_path vs $TMP

2011-03-29 Thread Nate Coraor
Louise-Amélie Schmitt wrote: Hello We managed to install Galaxy according to the unified method, with the runner and the web application running on separate machines sharing by NFS the same storage space where the Galaxy files are. The thing is, the data must be saved in another NFS

Re: [galaxy-dev] Sequencer Configuration

2011-03-29 Thread Greg Von Kuster
Hello Joe, Yes, our documentation is lacking here, and what is available is very outdated. On Mar 28, 2011, at 4:11 PM, Joe Cruz wrote: Hello, Where can I find information on setting up Galaxy to communicate directly with a sequencer? I know of this place:

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread Assaf Gordon
Hi Peter, Peter Cock wrote, On 03/29/2011 05:39 AM: 2. the tools accepts FASTA, FASTQ in both Sanger and Illumina format (no more need for grooming). Illumina is the default for newly uploaded FASTQ files. I think that's a bad idea - use Sanger FASTQ as the default to be consistent with

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread Daniel Blankenberg
Hi Assaf, Just a quick note that the standard bowtie tool in Galaxy was enhanced in changeset 5157:7a9476924daf to work on 'fastqillumina' and 'fastqsolexa' variants in addition to the already possible 'fastqsanger'. In general, it is not a good idea to have a tool accept dataset.ext=='fastq'

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread Assaf Gordon
Hi Dan, Daniel Blankenberg wrote, On 03/29/2011 10:55 AM: When files are added to Galaxy, the datatype can be directly set to any of the fastq variants (e.g. fastqillumina), which removes the requirement of grooming (but should only be done when users know what they are doing). I'm not using

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread Peter Cock
On Tue, Mar 29, 2011 at 4:46 PM, Assaf Gordon gor...@cshl.edu wrote: Hi Dan, Daniel Blankenberg wrote, On 03/29/2011 10:55 AM: When files are added to Galaxy, the datatype can be directly set to any of the fastq variants (e.g. fastqillumina), which removes the requirement of grooming (but

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread Ryan Golhar
Note about multithreaded bowtie: currently the tools use 10 threads (hard-coded in the XML files) - easily changeable. If possible, have the user indicate as a parameter how many threads they wish to use. -- CONFIDENTIALITY NOTICE: This email communication may contain private,

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread Daniel Blankenberg
The Grooming step is currently very time consuming and can be quite wasteful in disk space if the source and target fastq files are the same, but I have seen many occasions where Grooming has 'saved the day' by e.g. detecting truncated files that may have gone undetected by downstream tools or

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread Assaf Gordon
Ryan Golhar wrote, On 03/29/2011 12:26 PM: Note about multithreaded bowtie: currently the tools use 10 threads (hard-coded in the XML files) - easily changeable. If possible, have the user indicate as a parameter how many threads they wish to use. This will never happen, at least not

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread Assaf Gordon
Dan and Peter, Peter Cock wrote, On 03/29/2011 12:08 PM: Why not do the Illumina to Sanger conversion as part of your pipeline that gets the data into Galaxy (and mark the files as fastqsanger)? As Glen said, with a C tool that isn't really so slow. That future proofs you for the pending

[galaxy-dev] Wiki bug for updating local galaxy?

2011-03-29 Thread Ryan Golhar
Hi all - I was about to update my local Galaxy installation, and went back to the wiki to refer to how to do this (https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy), and noticed a mistake. Step 1 says to use hg clone https://bitbucket.org/galaxy/galaxy-dist/; Step 5 says If you

[galaxy-dev] plotting/statistics tools suggestion

2011-03-29 Thread Marshall Hampton
I've just started seriously looking at Galaxy, and I already have a suggestion (everyone's a critic...): switch from using rpy or even rpy2 to scipy/numpy/matplotlib for basic statistics and plots. I wrestled a bit with getting rpy to work on my local setup and decided it would be quicker to

Re: [galaxy-dev] Can't save BAM file from Galaxy

2011-03-29 Thread Ryan Golhar
On 3/22/11 12:06 PM, Nate Coraor wrote: Liisa Koski wrote: Hello, I have a local instance of galaxy and after successfully running an NGS analysis I am trying to save my BAM file to my local machine. When I click on the save icon my Galaxy instance crashes with the following error. This also

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread James Taylor
I would humbly guess that most of those truncated files are due to problematic HTTP uploads - so it saves the day from another problem, which should be avoided all together. Maybe most, but definitely not all. We see all kinds of strange corruption. However, I have been thinking about