[galaxy-dev] Deseq2 wrapper question

2013-09-10 Thread ruiwang.sz
Hi All, we are making a wrapper for deseq2, and there is a step where control/experimental conditions need to be determined. For example, it would be a column like the following in the input file Type CTC CTC LM LM PT PT and we want the select list to contain CTC LM PT In other words, we want

Re: [galaxy-dev] Deseq2 wrapper question

2013-09-11 Thread ruiwang.sz
Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.**php/about/80-teamhttp://www.bits.vib.be/index.php/about/80-team On 09/11/2013 01:15 AM, ruiwang.sz wrote: Hi All, we are making a wrapper for deseq2, and there is a step where control/experimental conditions

Re: [galaxy-dev] Deseq2 wrapper question

2013-09-11 Thread ruiwang.sz
/deseq2 Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/11/2013 01:15 AM, ruiwang.sz wrote: Hi All, we are making a wrapper for deseq2, and there is a step where control/experimental conditions need to be determined

[galaxy-dev] puzzle: tool result always set dataset state to ERROR

2013-09-29 Thread ruiwang.sz
Hi Guys, I'm doing a very simple test about deseq2...there is a weird situation always happening: It looks like the deseq2 tool executed just fine, without any error, and the result files were created, but after the set_metadata, galaxy always 'set dataset state to ERROR'. The xml file for this

Re: [galaxy-dev] puzzle: tool result always set dataset state to ERROR

2013-09-29 Thread ruiwang.sz
to suppress them as well -- but how come they are on stderr not stdout? Thanks, Rui On Sun, Sep 29, 2013 at 3:36 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Sun, Sep 29, 2013 at 8:47 PM, ruiwang.sz ruiwang...@gmail.com wrote: Hi Guys, I'm doing a very simple test about deseq2

Re: [galaxy-dev] puzzle: tool result always set dataset state to ERROR

2013-09-30 Thread ruiwang.sz
Hi Peter, Thanks! I got it working by putting a suppressMessages() around the function call. I might have some questions on how to generate output file names on the fly...let me make some attempts first. :-) Best, Rui On Sun, Sep 29, 2013 at 10:54 PM, ruiwang.sz ruiwang...@gmail.com wrote

[galaxy-dev] wigTobigwig error: broken pipe and len file not found

2013-11-16 Thread ruiwang.sz
Hi All, I‘m seeing some weird error messages...I googled but didn't see anything useful: So, it is during the wigToBigwig conversion: Dataset generation errors Dataset 47: Wig/BedGraph-to-bigWig on data 43 Tool execution generated the following error message: grep: writing output: Broken

Re: [galaxy-dev] wigTobigwig error: broken pipe and len file not found

2013-11-19 Thread ruiwang.sz
, Rui On Mon, Nov 18, 2013 at 10:40 AM, Nate Coraor n...@bx.psu.edu wrote: On Sat, Nov 16, 2013 at 12:27 PM, ruiwang.sz ruiwang...@gmail.com wrote: Hi All, I‘m seeing some weird error messages...I googled but didn't see anything useful: So, it is during the wigToBigwig conversion

[galaxy-dev] wigToBigwig error

2014-01-14 Thread ruiwang.sz
Hi All, I'm having an error at this: *Dataset 18: Wig/BedGraph-to-bigWig on data 12* Tool execution generated the following error message: grep: writing output: Broken pipe grep: writing output: Broken pipe grep: writing output: Broken pipe grep: writing output: Broken pipe .. put: Broken

Re: [galaxy-dev] wigToBigwig error

2014-01-15 Thread ruiwang.sz
this tool run successfully, in Galaxy, on the type without span included. If you find that the span variable is problematic after correcting any other format issue issues, switch to the format without span. Good luck, Jen Galaxy team On 1/14/14 9:52 PM, ruiwang.sz wrote: Hi All, I'm having

[galaxy-dev] a question regarding galaxy 'workflow'

2014-02-11 Thread ruiwang.sz
Hi All, A quick question on the indices. Here is the information provided by the sample file: #Your bowtie_indices.loc file should include an entry per line for each #index set you have stored. The file in the path does not actually #exist, but it is the prefix for the actual index files. For

[galaxy-dev] universe_wsgi.ini question for Cistrome

2014-02-26 Thread ruiwang.sz
Hi Guys, Are there anyone who is using Cistrome? I tried to merge Cistrome's setting into our own galaxy instance. A new entry is # Path to the static library files for assembly, ceaslib, chromLen, conservation, liftOver and MAT-lib # Then in other tool configuration xml file, we can use 'from

[galaxy-dev] upload error

2014-02-27 Thread ruiwang.sz
Hi Guys, Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen

[galaxy-dev] tool_shed question on multiple tool versions

2014-03-07 Thread ruiwang.sz
Hi Guys, Sorry for the duplicate posting...nobody saw my original one seems and I'm still wondering what the proper way is. I searched around the wiki but didn't find much. Originally, I installed macs dependency for galaxy myself. The version is 1.4.2. It worked well. Now, after galaxy

[galaxy-dev] how to manage multiple tool versions

2014-03-07 Thread ruiwang.sz
Hi Guys, I'm sorry to post multiple times for the same question. Now I removed all the specifics of my problem and I only want someone to point me to the right documentation. Admins, I know you are busy, but don't you want more people to benefit from this platform? When galaxy upgraded it

Re: [galaxy-dev] how to manage multiple tool versions

2014-03-08 Thread ruiwang.sz
now for testing Am 08.03.2014 00:48, schrieb ruiwang.sz: Hi Guys, I'm sorry to post multiple times for the same question. Now I removed all the specifics of my problem and I only want someone to point me to the right documentation. Admins, I know you are busy, but don't you want more people

Re: [galaxy-dev] upload error

2014-03-08 Thread ruiwang.sz
Hi John, Thanks for the note. Please see inline. On Fri, Mar 7, 2014 at 7:18 PM, John Chilton jmchil...@gmail.com wrote: Hmm... I am not certain but it sounds like the migration script ripped something out of your Galaxy tool panel that you did not want it to? This is unfortunate - but I

[galaxy-dev] nginx configuration question

2014-05-16 Thread ruiwang.sz
Hi All, I have been trying to get the visualization through ucsc main working, thus I installed the nginx on our ubuntu(the one comes with update), then I configured it according to the wiki https://wiki.galaxyproject.org/Admin/Config/nginxProxy Here is the section in my nginx.conf

Re: [galaxy-dev] nginx configuration question

2014-05-17 Thread ruiwang.sz
is not effective. But why is this? btw I'm using the 1.1.19 version of nginx that comes with ubuntu. Could anyone give me a hint? I'll be really grateful. Thanks, Rui On Fri, May 16, 2014 at 12:29 PM, ruiwang.sz ruiwang...@gmail.com wrote: Hi All, I have been trying to get the visualization through

Re: [galaxy-dev] nginx configuration question

2014-05-17 Thread ruiwang.sz
, at least redirect works, but I don't know why there is only one server block in use at a time. How do I solve this? Any help would be greatly appreciated. Thanks, Rui On Sat, May 17, 2014 at 7:36 PM, ruiwang.sz ruiwang...@gmail.com wrote: Hi Guys, I did a little further investigation. I found

Re: [galaxy-dev] nginx configuration question

2014-05-17 Thread ruiwang.sz
Just to answer myself... Those 2 location blocks should be in the same server block! Hope this could help someone else... :) Rui On Sat, May 17, 2014 at 8:54 PM, ruiwang.sz ruiwang...@gmail.com wrote: Hi Guys, I just switch to 1.6.0 of nginx, but the behavior is the same. I also tried

[galaxy-dev] error: flexbar dependency is not installed by the toolshed

2014-05-19 Thread ruiwang.sz
Hi Guys, I tried to install flexbar from toolshed, but upon running, error said it could not find it. I checked and found idtoolshed.g2.bx.psu.edu/repos/jtilman/flexbar/flexbar/2.4/id in the config file, but this path does not exist. Is it that I need to install the dependency on my own? I