Re: [galaxy-dev] Splitting large jobs over multiple nodes/CPUs?

2012-02-20 Thread Bram Slabbinck
Hi Dannon, If I may further elaborate on this issue, I would like to mention that this kind of functionality is also supported by the Sun Grid Engine in the form of 'array jobs'. With this functionality you can execute a job multiple times in an independent way, only differing for instance in

Re: [galaxy-dev] Using Galaxy as a Framework

2012-02-20 Thread Peter Cock
On Sat, Feb 18, 2012 at 10:40 PM, Mikal Ustad mikal.e.us...@gmail.com wrote: Hello, I am part of a senior project group at Northern Arizona University.  We are interested in adapting Galaxy for a project related to building image processing workflows.  The existing system that we are working

Re: [galaxy-dev] Splitting large jobs over multiple nodes/CPUs?

2012-02-20 Thread Peter Cock
On Mon, Feb 20, 2012 at 8:08 AM, Bram Slabbinck br...@psb.vib-ugent.be wrote: Hi Dannon, If I may further elaborate on this issue, I would like to mention that this kind of functionality is also supported by the Sun Grid Engine in the form of 'array jobs'. With this functionality you can

[galaxy-dev] How to learn about new tools in the official Tool Shed

2012-02-20 Thread Sarah Diehl
Hello, one quick question: is there a way to get news about new tools in the Tool Shed? I saw that I can subscribe to get news about already existing tools, but how about newly created ones? I would also be fine with some subscription to any changes in the Tool Shed in general. Best

Re: [galaxy-dev] How to learn about new tools in the official Tool Shed

2012-02-20 Thread Björn Grüning
Hi Sarah, if you have an account you can use New repository alert under your personal preferences. That should work. Kind regards, Bjoern Hello, one quick question: is there a way to get news about new tools in the Tool Shed? I saw that I can subscribe to get news about already

[galaxy-dev] Functional tests

2012-02-20 Thread Frank Sørensen
Hi Guys, Sorry if this is a stupid question, but in order to find out which external reference files (.loc - list files etc.) we need for our newly installed Galaxy server, and to get an overview of which tools are in working order, I have tried for a couple of days now, to run the script

Re: [galaxy-dev] Splitting large jobs over multiple nodes/CPUs?

2012-02-20 Thread Dannon Baker
Peter has it right in that we need to do this internally to ensure functionality across a range of job runners. A side benefit is that it gives us direct access to the tasks so that we can eventually do interesting things with scheduling, resubmission, feedback, etc. If the overhead looks to

Re: [galaxy-dev] Functional tests

2012-02-20 Thread Greg Von Kuster
Hello Frank, see my inline comments. On Feb 20, 2012, at 6:56 AM, Frank Sørensen wrote: Hi Guys, Sorry if this is a stupid question, but in order to find out which external reference files (.loc - list files etc.) we need for our newly installed Galaxy server, and to get an overview of

[galaxy-dev] BWA empty output and failed alignment

2012-02-20 Thread Praveen Baskaran
Hi, I have a problem running BWA in my local instance of galaxy. When I try to align the short reads in bwa, sometimes it gives empty file otherwise it throws the following error BWA Version: 0.6.1-r104 The alignment failed. The output file is empty. You may simply have no matches, or there

Re: [galaxy-dev] advanced parameters: all or nothing?

2012-02-20 Thread Andrew Warren
Thanks for the pointer to the updated wrapper and the optional tag. So is the behavior of the optional=true tag that if the field form is left empty for that parameter then it will not be passed to the tool? I am wondering if a more sophisticated behavior on the UI side of things for the optional

[galaxy-dev] functional test failures

2012-02-20 Thread Anne Pajon
Hello, I am trying to have all functional tests on our production server (galaxy-dist 6621:26920e20157f) run successfully but I do still have failures that I do not know how to solve. Theses failures are related to unexpected differences probably due to versions of software that have been

[galaxy-dev] Setup questions

2012-02-20 Thread Brami, Daniel
Hi folks, I am trying to setup a local copy of Galaxy and I am running into a few issues with which I would greatly appreciate some help. 1. I am trying to setup my built-in indices for bowtie mapping and I have been following the instructions given at

Re: [galaxy-dev] anyone using SFTP?

2012-02-20 Thread Dave Clements
Hi Mattias, Posting to Galaxy-Dev, so others can see the question and response. Is there anyone using SFTP in a local Galaxy installation? I read that FTP is insecure because it sends the data and user credentials in plaint text. The short answer is yes. See.

[galaxy-dev] Extracting the metrics files from a composite file such as Picard

2012-02-20 Thread Thon Deboer
Hi, Is there a way to extract the individual files from a composite file, such as the HTML files created by the picard tools? I would like to take the metrics files and use them further down in some workflow, but I only get an HTML file... While these HTML files are nice for quickly looking at

Re: [galaxy-dev] Extracting the metrics files from a composite file such as Picard

2012-02-20 Thread Ross
Hi, Thon, On Tue, Feb 21, 2012 at 6:47 AM, Thon Deboer thondeb...@me.com wrote: Hi, Is there a way to extract the individual files from a composite file, such as the HTML files created by the picard tools? The decision to hide multiple outputs in a single history html object has this as a

Re: [galaxy-dev] Extracting the metrics files from a composite file such as Picard

2012-02-20 Thread Anthonius deBoer
Hi Ross,Thanks for the reply...It is indeed as I feared...I'll probably refactor the code so the user is able to get the actual output files.ThonOn Feb 20, 2012, at 01:29 PM, Ross ross.laza...@gmail.com wrote:Hi, Thon,On Tue, Feb 21, 2012 at 6:47 AM, Thon Deboer thondeb...@me.com wrote:Hi,Is there

Re: [galaxy-dev] Extracting the metrics files from a composite file such as Picard

2012-02-20 Thread Ross
Thon, I just had an idea - write a new tool that takes an Html dataset from the user's history and a file specification (eg foo.xls) and 'promotes' the file(s) in the extra_files_path that match the file specification into new history items? That way you can automate the process - of course,

Re: [galaxy-dev] anyone using SFTP?

2012-02-20 Thread Fields, Christopher J
Yes, we are using this locally (sftp and scp). Basically follow the same rules as for FTP on the wiki, but leave out the ProFTP setup; this was per Nate's instructions, whom I believe is to change the FTP-specific documentation at some point. Basically, any mechanism that transfers data to