[galaxy-dev] enable to edit pages

2013-07-31 Thread Philipe Moncuquet
Hi guys, Since the last update of Galaxy. We are enable to edit pages on our local instance. Pages can be viewed without problems but not editing. The server error we get is as foolow, any advice would be greatly appreciated. URL:

[galaxy-dev] job status error in the history panel

2013-07-21 Thread Philipe Moncuquet
Hi all, While in Oslo I heard about the bug that make your job always appeared in queue mod unless you refresh your history. Now that we have updated our own instance I see that bug and was wondering want we can do about it. I haven't seen anything on the mailing list but if I miss the thread

[galaxy-dev] account avatar

2013-06-23 Thread Philipe Moncuquet
Hi, We are running a local instance of Galaxy behind firewall. How can one modify the picture associated with is galaxy account in the configuration ? Regards, Philippe ___ Please keep all replies on the list by using reply all in your mail

[galaxy-dev] removing inputs from a pipeline

2013-04-07 Thread Philipe Moncuquet
Hi Dev, Is there a way to automatically delete inputs in a pipeline ? Let say you don't want to keep your raw data because of quotas issues and you want your pipeline to do it rather than to do it manually. Regards, Philippe ___ Please keep

[galaxy-dev] multiple file output

2013-03-13 Thread Philipe Moncuquet
Hi, I am trying to right a tool that will generate 2 ouptuts, 1 .txt and .gz. Before the tools runs I don't know how many fasta files will be in the .gz file. I have managed to have the perl script writing files like follow : $seqio_obj = Bio::SeqIO-new(-file = $seq_library_name, -format =

[galaxy-dev] Error while installing DESeq-hts

2013-02-28 Thread Philipe Moncuquet
Hi, I have tried to follow instructions provided with this installation a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts. I successfully ran the setup scrip but is there other path and conf that need to be done apart from those done by this script ? b) Inside

[galaxy-dev] tools imported from toolshed stay in waiting to run status

2012-12-13 Thread Philipe Moncuquet
Hi dev, We are running a local instance of Galaxy, last update was the November release (7148:17d57db9a7c0 I think). We are facing problem when trying to run tools that were imported via the toolshed. The never start and the status stays on waiting to run. Other tools work fine, and this generic

[galaxy-dev] tools imported from toolshed stay in waiting to run status

2012-12-12 Thread Philipe Moncuquet
Hi dev, We are running a local instance of Galaxy, last update was the November release (7148:17d57db9a7c0 I think). We are facing problem when trying to run tools that were imported via the toolshed. The never start and the status stays on waiting to run. Other tools work fine, and this generic

Re: [galaxy-dev] Changing interface design

2012-11-30 Thread Philipe Moncuquet
. Changes might only be visible when restarting the instance though! Alex ** ** ** ** *Van:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] *Namens *Philipe Moncuquet *Verzonden:* vrijdag 30 november 2012 5:11 *Aan:* galaxy-dev@lists.bx.psu.edu

[galaxy-dev] Changing interface design

2012-11-29 Thread Philipe Moncuquet
Hi I am not satisfied with some colors of the interface. I am color blind and it's hard to discriminate between job running (light yellow) and job done (light green). Well most of the time I focus on red jobs right but anyway I would like to be able to change these stuff. Can anybody point me the

[galaxy-dev] Multiple language in one tool

2012-11-20 Thread Philipe Moncuquet
Hi dev, I was wondering if the following is possible or not. What if I want to build a tool that that uses Perl and R at the same time ? If I had to do it on my local machine I would create a pipeline but wouldn't it be cool if a wrapper could use different languages. Philippe

Re: [galaxy-dev] Multiple language in one tool

2012-11-20 Thread Philipe Moncuquet
. I've done that sort of thing before with good results. brad On Nov 20, 2012, at 10:03 PM, Philipe Moncuquet philippe.m...@gmail.com wrote: Hi dev, I was wondering if the following is possible or not. What if I want to build a tool that that uses Perl and R at the same time ? If I had

[galaxy-dev] How to get a compressed output in the history

2012-11-11 Thread Philipe Moncuquet
Hi dev, I have written a perl script to perform some complex demultiplexing of reads. It works well on my computer but the integration to Galaxy is a bit tricky since it's the first time for me. At one point my perl script generates a bunch of fasta files, I want all this fasta files to be

[galaxy-dev] How to get a compressed output in the history for my own tool

2012-11-08 Thread Philipe Moncuquet
Hi dev, I have written a perl script to perform some complex demultiplexing of reads. It works well on my computer but the integration to Galaxy is a bit tricky since it's the first time for me. At one point my perl script generates a bunch of fasta files, I want all this fasta files to be

[galaxy-dev] Velvet not working

2012-11-07 Thread Philipe Moncuquet
Hi developers, We have our own instance running and under continuoius development. I installed velvetg and velveth from the toolshed (revision 0:4afe13ac23b6http://toolshed.g2.bx.psu.edu/repository/view_changelog?id=9dca5b8f68c509af) and manually installed binaries for velvet_1.2.08. When I try

Re: [galaxy-dev] Velvet not working

2012-11-07 Thread Philipe Moncuquet
:29 PM, Philipe Moncuquet wrote: Hi developers, We have our own instance running and under continuoius development. I installed velvetg and velveth from the toolshed (revision 0:4afe13ac23b6http://toolshed.g2.bx.psu.edu/repository/view_changelog?id=9dca5b8f68c509af) and manually installed

[galaxy-dev] Output from Barcode splitter

2012-10-21 Thread Philipe Moncuquet
Hi, I am trying to use the Barcode splitter tool as part of a workflow, I am not happy with the html output produce by this tool and would like to have access to fasta files. Any suggestions on how I can modify the tool so that it produces fasta outputs that would appear in the workflow ? Thanks

[galaxy-dev] Error while running freshly installed velvet

2012-10-17 Thread Philipe Moncuquet
Hi galaxy-dev community, I recently installed velevetoptimiser via the toolshed. I copied binaries in the tool directory on our local Galaxy. I wanted to give it a try to confirm installation was correct and get the following error message (see below). I know that the output files are created via