[galaxy-dev] Patch for libxslt and libxml packages

2014-08-04 Thread Jan Kanis
Hi all, I was told that updates to packages owned by devteam should just be sent here, since there is no public repo. I have patches for the libxml2 and libxslt tool_dependency.xml's, that set some more environment variables that my tool needs (specifically, the python lxml package needs some of

[galaxy-dev] creating datatype repository : no module named binary

2014-08-04 Thread Geert Vandeweyer
Hi all, I'm trying to create a new binary datatype in galaxy, but I'm running into troubles. The current installer is available at https://testtoolshed.g2.bx.psu.edu/view/geert-vandeweyer/cuffquant_datatype When I install the repository to a local server, I get the errors below (no module

Re: [galaxy-dev] creating datatype repository : no module named binary

2014-08-04 Thread Björn Grüning
Hi Geert, please include this at the top: from galaxy.datatypes.binary import Binary Cheers, Bjoern Am 04.08.2014 um 15:02 schrieb Geert Vandeweyer: Hi all, I'm trying to create a new binary datatype in galaxy, but I'm running into troubles. The current installer is available at

[galaxy-dev] XLS TO CSV

2014-08-04 Thread Mert Mehnur KIRKALI
Hello, How can i convert xls file to csv file on galaxy ? Is that possible ? Best Regards,Mert. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists,

Re: [galaxy-dev] XLS TO CSV

2014-08-04 Thread Björn Grüning
Hi, not tat I know. But you can export your xls in Excel as tab separated file. Galaxy can handle such tab-delimited files. Cheers, Bjoern Am 04.08.2014 um 14:56 schrieb Mert Mehnur KIRKALI: Hello, How can i convert xls file to csv file on galaxy ? Is that possible ? Best Regards,Mert.

Re: [galaxy-dev] XLS TO CSV

2014-08-04 Thread Peter Cock
Hi Mert, Most of the Galaxy tools dealing with tables of data use tabular format (tab separated variables), not csv (comma separated variables). CVS is a horrible horrible mess of formats, see e.g. http://tburette.github.io/blog/2014/05/25/so-you-want-to-write-your-own-CSV-code/ Also beware that

Re: [galaxy-dev] XLS TO CSV

2014-08-04 Thread Eric Rasche
Hi Peter, On 08/04/2014 09:25 AM, Peter Cock wrote: Hi Mert, Most of the Galaxy tools dealing with tables of data use tabular format (tab separated variables), not csv (comma separated variables). CVS is a horrible horrible mess of formats, see e.g.

Re: [galaxy-dev] XLS TO CSV

2014-08-04 Thread Peter Cock
On Mon, Aug 4, 2014 at 4:28 PM, Eric Rasche rasche.e...@yandex.ru wrote: Hi Peter, On 08/04/2014 09:25 AM, Peter Cock wrote: Hi Mert, Most of the Galaxy tools dealing with tables of data use tabular format (tab separated variables), not csv (comma separated variables). CVS is a horrible

[galaxy-dev] Adding Reference Genomes, builds.txt vs manual_builds.txt

2014-08-04 Thread Lance Parsons
I noticed that the instructions at https://wiki.galaxyproject.org/Admin/DataIntegration direct admins to update the builds.txt file when adding a new reference genome to local Galaxy instances. Up to this point I had been actually modifying the manual_builds.txt file and then rebuilding the

Re: [galaxy-dev] HTTPerror : HTTP error 307 : temporary redirect

2014-08-04 Thread Perley, Danielle
Solved! After finding documentation indicating that changing the URL of the test toolshed from http to https in the tool_sheds_config.xml file solved some redirection issues, I tried the same thing for the URL of the main toolshed. Message: 7 Date: Fri, 1 Aug 2014 20:30:14 + From:

[galaxy-dev] start and end times?

2014-08-04 Thread Evan Bollig
Jobs executed in the workflow appear to have a creation time, but no execution start and end time listed. How does one determine when something executed? I'd like to know exactly where the time is spent computing... -Evan Bollig Research Associate | Application Developer | User Support Consultant

Re: [galaxy-dev] start and end times?

2014-08-04 Thread Dannon Baker
Hi Evan, What you're looking for should be covered by the new Job Metrics plugins. If you'd like to know more, see: https://wiki.galaxyproject.org/Admin/Config/JobMetrics -Dannon On Mon, Aug 4, 2014 at 3:24 PM, Evan Bollig boll0...@umn.edu wrote: Jobs executed in the workflow appear to have

Re: [galaxy-dev] start and end times?

2014-08-04 Thread Evan Bollig
Thanks Dannon. I'll add it to the todo list. Do the metric include time and memory info for the entire history/workflow, or does it only report for individual tools? Max consumed storage during a workflow execution is another data point I'd like to monitor. -E -Evan Bollig Research Associate |

Re: [galaxy-dev] start and end times?

2014-08-04 Thread Dannon Baker
These metrics would only apply to individual jobs and not for the entire history/workflow, though there are plans (https://trello.com/c/XsQdqliU) to expose the data via the API so that one might generate summary metrics, among other things. On Mon, Aug 4, 2014 at 3:40 PM, Evan Bollig

[galaxy-dev] cufflinks suite 2.2.1

2014-08-04 Thread Geert Vandeweyer
Hi all, I've updated the tool wrappers for the cufflinks tools to options supported by cufflinks 2.2.1. I've also added the cuffquant and cuffnorm tools, together with the cxb datatype. As discussed with Jeremy, these updates were welcome :-) Everything is available on the test toolshed,

Re: [galaxy-dev] cufflinks suite 2.2.1

2014-08-04 Thread Björn Grüning
Awesome! Thanks Geert! Bjoern Am 04.08.2014 um 22:37 schrieb Geert Vandeweyer: Hi all, I've updated the tool wrappers for the cufflinks tools to options supported by cufflinks 2.2.1. I've also added the cuffquant and cuffnorm tools, together with the cxb datatype. As discussed with Jeremy,