[galaxy-user] An error in reporting a tool error...

2012-07-09 Thread leah reshef
Hello all I am working with the LefSe module. Over the last two days, I am gettimg a recurring error in the Plot LefSe result step. LefSe analysis itself is performed OK (I can see the the results in a text browser) but when I want to plot them - I get a red error message. When I do plot

Re: [galaxy-user] An error in reporting a tool error...

2012-07-09 Thread Jennifer Jackson
Hi Leah, It sounds like you are using the Galaxy instance run by the Huttenhower Lab at Harvard? At this link? http://huttenhower.org/galaxy/ If so, then at the bottom of the home page is a link you can use to contact the lab members about issues with the instance. (They probably have the

Re: [galaxy-user] Indexing files everytime - Performance Issue

2012-07-09 Thread Jennifer Jackson
Hi Raj, The GATK tool wrappers are still in Beta and are currently under redesign. Since this question is about a local install, it is probably better for the galaxy-...@bx.psu.edu mailing list. When you write in (new thread, please), could you please clarify a bit more? Do you need help with

[galaxy-user] job is waiting to run forever

2012-07-09 Thread Yehoshua Enuka
Dear Sir/Madam, I am a registered user of the public Galaxy Server (main). Any job I submitted today is labeled as Job is waiting to run forever. Could you please let me know the possible reasons? Sincerely, Enuka ___ The Galaxy User list

Re: [galaxy-user] job is waiting to run forever

2012-07-09 Thread Jennifer Jackson
Hello Eunuka, A job that is grey in color means that it is queued. A job that is yellow is running - and actual run time can vary. Generally, jobs will begin to run (move from grey to yellow) within a short time period or if the public instance is very busy, within 24hrs. I found three jobs

Re: [galaxy-user] job is waiting to run forever

2012-07-09 Thread shamsher jagat
I brought up this issue previously, I guess Galaxy team please look into it your user base is expending the jobs never get fisnished. Fisrt problem of data uplaod and then running jobs. I never had problem but having lot of problem sfrom last 3-4 months so started using other tools too. Thanks