- galaxy-dev - lists.galaxyproject.org

Sever error while trying to join on genomic intervals
by Bart Pannebakker 27 Oct '11

27 Oct '11

Dear developers, I got the following error on the public server while trying to join to datasets on their genomic intervals: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) I know this is not much information, hope you can help to solve the error. Kind regards, Bart

2 2

Error moving tool-data dir ... bowite indexes missing
by Bossers, Alex 27 Oct '11

27 Oct '11

On our up-to-date galaxy_central version I have successfully moved the database/files directory to mounted storage. After adapting the universe_wsgi.ini it works fine after galaxy restart. Now the tool-data dir becomes bigger and bigger and I wanted to move that to mounted storage as well. I moved the tool-data dir to the other location, made sure file permissions were ok and adapted the universe_wsgi.ini tool_data_path to match the new tool-data location. Galaxy restarts and the loc files are read (since blast recognises its databases). However, the bowtie indexes are not read since they do not show up in the NGS bowtie mapper for illumina..... what could be wrong? When I restore the universe_wsgi.ini it works all fine. I am puzzled. Alex

2 1

BWA wrapper error
by dhivya arasappan 26 Oct '11

26 Oct '11

Hi all, I'm seeing the following error when I try to use the galaxy BWA wrapper for SOLID data : An error occurred running this job:Could not determine BWA version The alignment failed. Error aligning sequence. /bin/sh: bwa: not found Any suggestions in figuring out what this error has to do with would be appreciated. thanks Dhivya

2 1

BWA mapping error on local install
by Christopher Callaway 26 Oct '11

26 Oct '11

Hi, I have Galaxy running locally and when trying to BWA map a set of paired-end reads, the reference genome does not show up (mm9) by selecting either History or Built-in. How do I fix this? Thanks, Christopher W. Callaway University of Utah Dept. of Pediatrics Division of Neonatology 417 Wakara Way #2222 Salt Lake City, UT 84108

2 1

displaying dataset paths in the UI
by Shantanu Pavgi 26 Oct '11

26 Oct '11

I am trying to display dataset paths in the UI when user clicks on the 'view details' icon in the history panel. I was able to display it by adding 'hda.file_name' field in the show_params.mako template file and it seems to be working. Following is a diff for it: {{{ diff --git a/templates/show_params.mako b/templates/show_params.mako index 9f7ad36..58d8108 100644 --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -50,6 +50,8 @@ <tr><td>Dbkey:</td><td>${hda.dbkey}</td></tr> <tr><td>Format:</td><td>${hda.ext}</td></tr> <tr><td>Tool Version:</td><td>${hda.tool_version}</td></tr> + <tr><td>Dataset ID:</td><td>${hda.dataset_id}</td></tr> + <tr><td>Dataset Path:</td><td>${hda.file_name}</td></tr> </table> <table class="tabletip"> }}} It doesn't display any metadata files associated with the dataset. I guess it will need some more changes in the datasets controller to return metadata file paths to this template. But, are these right places to make changes for displaying dataset paths or are there any other files/modules that should be modified? Any comments or suggestions for implementing this will be really helpful. -- Thanks, Shantanu.

2 1

Printing when catching exception get stuck
by Timothy Wu 26 Oct '11

26 Oct '11

Hi, I wrote a Python program which prints something to stdout while catching an exception handling. The code works fine running it standalone. However, when run under Galaxy the code appears to stuck in that printing statement. (At least, as far as I could tell through logging via the logging module). It doesn't actually always gets stuck there since my program run into it multiple times. It enters and exists several times before during the same execution of the program. However, it does always stuck in a particular entry into that exception. Does anyone have a similar experience? I have no idea why that is so. Logging what's printed to stdout to the file encounters zero problem. Timothy

2 1

October 25, 2011 Galaxy Development News Brief
by Jennifer Jackson 26 Oct '11

26 Oct '11

October 25, 2011 Galaxy Development News Brief This release: http://galaxyproject.org/wiki/News%20Briefs/2011_10_25 Release history: http://galaxyproject.org/wiki/News%20Briefs Source: http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 338ead4737ba Highlights: Galaxy is Hiring! Main Data and Job Quotas UI Updates Trackster (GTB) at BioVis Python 2.4 -> 2.7 Official SICER, Trinity, SAMtools rmdup All: What's New Galaxy Main User Interface (UI) Trackster (Galaxy Track Browser) Python and OS Support Galaxy Tool Shed Updated & Improved Tools Quotas and Data Management Source API Scripts Bug Fixes Thanks for using Galaxy!

1 0

Error in using Palmapper
by Fayyaz ul Amir Afsar Minhas 26 Oct '11

26 Oct '11

Hello all, I am using Galaxy to align short reads of length 75 from A. Thaliana (TAIR 9.0) with Palmapper. However, I get the following error: *splice site position (366706) greater than chromosome length (154478)* Can anyone help me in this? Best, -Fayyaz

2 1

Local installation
by Mattia Chiesa 26 Oct '11

26 Oct '11

Hi I'm Chiesa Mattia and I write from an hospital in Milan (ITALY). I want to install Galaxy locally on a CentOS platform. I read in your documentation that Python 2.5/2.6 is required but for some function also Python 2.4 (installed in our CentOS) is okay.What are these functions? Thanks a lot Mattia Il Tuo 5 per Mille a favore della Ricerca del Centro Cardiologico Monzino va dritto al cuore. Tutti coloro che presentano il modello Unico, il modello 730 o piu semplicemente che ricevono dal proprio datore di lavoro il modello CUD, hanno la facolta di scegliere la destinazione del proprio 5 per mille. Nella casella riservata al <a href='http://www.cardiologicomonzino.it/Ricerca/Pages/campagna2010.aspx'>Finanziamento agli Enti della Ricerca Sanitaria</a> inserisci il codice fiscale del CCM (1 3 0 5 5 6 4 0 1 5 8) ed apponi la Tua firma. Questo messaggio � riservato esclusivamente ai destinatari indicati e pu� contenere informazioni di pertinenza o propriet� del Cardiologico Monzino o comunque di carattere privato. Qualora lo riceveste per errore, Vi preghiamo di darcene immediata comunicazione e successivamente di eliminarlo. E' vietato qualunque altro uso del messaggio difforme da quanto indicato. This message is for the designated recipient only and may contain privileged, proprietary, or otherwise private information. If you have received it in error, please notify the sender immediately and delete the original. Any other use of the email by you is prohibited.

2 1

Galaxy Main public instance: data and job quotas
by Jennifer Jackson 26 Oct '11

26 Oct '11

Galaxy Main public instance: data and job quotas October 25, 2011 Dear Galaxy User, Thank you very much for using our free and open public resource. Galaxy has become extremely popular and as a result many people rely on it daily for their analysis needs. Previously our service had no restrictions on usage, which is not sustainable in the long term. To continue providing our open service in a fair manner, we are now implementing quotas at the public Galaxy Main instance http://usegalaxy.org (http://main.g2.bx.psu.edu) The Main quotas are: Data - 250Gb for registered users (with a Galaxy account) - 5Gb for unregistered users Jobs - 8 concurrent jobs running simultaneously (all users) For more details please see: Galaxy Main Wiki http://galaxyproject.org/wiki/Main Data management: accounting and disk quotas http://galaxyproject.org/wiki/Admin/Disk%20Quotas Managing Datasets in Galaxy http://galaxyproject.org/wiki/Learn/Managing%20Datasets#Actions For those users with current account disk usage over the quota limit, we will be implementing a step-down program over the next several weeks. Details for that program will be emailed to those users directly. If you find that you require additional resources, please consider the alternative Galaxy options: http://galaxyproject.org/wiki/Big%20Picture/Choices Thanks for using Galaxy! -- The Galaxy team http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org

1 0