October 2012 - galaxy-dev - lists.galaxyproject.org

History import returns size zero
by Bossers, Alex 05 Oct '12

05 Oct '12

Dear all, I might have missed it on the list and cannot find it in the archive; When we import a history exported from the same or another galaxy instance it imports ok and all files are there and usuable, only the history size is 0. We are up to latest galaxy-central of October 4th. Is this a bug (or some feature :-) ). Alex

1 0

Mapping input fields in a workflow
by Lukasse, Pieter 05 Oct '12

05 Oct '12

Hi, Is there any way to map an input field from one tool to the input field of another tool in a workflow? E.g. let's say tool A has an input field X which tool B also has. If we use both tool A and B in the same workflow, then we would like to let the user fill in field X only once in tool A and then map that value to the field X in tool B. As far as I can see, there is now only a way to map output files of tool A to input files of tool B. [cid:image001.png@01CDA2E2.20BC4390] Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

1 0

(no subject)
by Alfredo Guilherme Silva Souza 05 Oct '12

05 Oct '12

Hello everyone. Personnel of aid to put my galaxy that is place to be accessed by other machines already setup apache as the galaxy is on wiki, but I'm not getting access to another computer on my network. Does anyone know how to configure Apache to let the galaxy accessible to other machines? Thank you. -- *Alfredo Guilherme* * *

2 2

Issues up/downloading datasets after file_path change
by Josh Nielsen 04 Oct '12

04 Oct '12

Hello all, I recently migrated the location of the Galaxy file_path directory (~/database/files/) along with the temp, job_working_directory, and pbs directory locations (all under ~/database/) to a new storage system mount point and I properly updated the change in the universe_wsgi.ini file but have run into some problems with managing our datasets. I can run Galaxy jobs just fine but I cannot view or download the datasets in the output of the jobs after they have run - when it tries to open it from the new path - and I get an actual browser error when trying to fetch the dataset. On a hunch I created a symbolic link named after the old path in the / directory pointing to the new location (and pointed file_path in the universe_wsgi.ini file back to it - which looks exactly like the old directory path), and sure enough this works as a (temporary) fix to view/download the files. However doing that seems to, in turn, mess with the file uploading function which will fail every time with a "OSError: [Errno 2] No such file or directory" message. So I'm caught between two broken configurations depending on the path I point to (the new path or the symlink alternative). I guess in the latter situation it does not like traversing a symbolic link (which is the only explanation that I can think of). The root of the problem needs to be fixed though in that Galaxy seems to be "remembering" the old path from somewhere (the Galaxy database?) such that it will not let me simply migrate the data to a new location and change the path variables in universe_wsgi.ini. Any suggestions on the proper changes that need to be made to fix this permanently? Thanks, Josh Nielsen

2 3

Galaxy not running
by Hidenori Kage 04 Oct '12

04 Oct '12

Hello. I have been using the Galaxy Main server without any problems until yesterday, when Galaxy suddenly stopped running. I had uploaded 14 files, groomed data, performed quality control, and I was in the middle of trimming. The first 6 files were trimmed without any problems, but on my 7th file, the trimming job has been put on hold. (I ran the first 6 jobs on my regular computer, opened my history on another computer, forgot to logout of the second computer, and tried to run the 7th job on my regular computer). I logged out of both computers, waited 24 hours, and the job still didn't run, so I deleted the dataset and re-ran the job- but still the job does not run. There are no error messages; it's just that the job is kept on hold. Please let me know if you need any more information. Thank you so much for your help. Hide Hidenori Kage, M.D., Ph.D. Postdoctoral Research Associate Division of Pulmonary, Critical Care and Sleep Medicine Keck School of Medicine University of Southern California 2011 Zonal Avenue, HMR 911 Los Angeles, CA 90033

2 1

unhandled exception
by Langhorst, Brad 04 Oct '12

04 Oct '12

(with galaxy-central from a few days ago) URL: http://galaxy/datasets/10385e16ab51958e/display/?preview=True File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 288 in display return data.datatype.display_data(trans, data, preview, filename, to_ext, chunk, **kwd) AttributeError: 'str' object has no attribute 'datatype' looks like the bitbucket "issues" tool has been disabled. Is this the right place to report this sort of thing now? Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com> 978-380-7564

3 2

VCF compression.
by James Boocock 04 Oct '12

04 Oct '12

Hi All, Just a quick question regarding file compression. We have a galaxy instance with limited space and a few people are trying to start working on our server. They will mainly be working with vcfs is there a way to make galaxy keep the vcfs in gz format until they are needed. I know this will slow down operations but it is a requirement as the will be copying the vcfs around etc. Cheers James.

1 0

Uploading composite datatypes.....
by Neil.Burdett＠csiro.au 04 Oct '12

04 Oct '12

Hi, I was under the impression that when a composite datatype (basic) file is uploaded then the files contained within the composite file are also uploaded is this not the case? I was hoping my script would be able to have a file as an input. The file contains multiple files. Each one would then be examined and outputted in turn... my xml file looks like this: <tool id="reorient_studies" name="Reorient images"> <description>for CTE surface</description>  <command interpreter="bash">/usr/local/MILXView.12.08.2/BashScripts/CTESurface/tools/reorient_studies.sh $input $installDir $outputDir </command> <inputs> <param format="mvb" name="input" type="data" label="Input File" /> <param type="text" name="installDir" value="/usr/local/MILXView.12.08.2/" label="Atlas" /> <param type="text" name="outputDir" value="CTE_SURFACE/" label="White Matter" /> </inputs> <outputs> <data format="input" name="output_mvb" from_work_dir="temp.mvb" /> </outputs> (mvb is a new datatype i've added) datatypes_conf.xml : <datatype extension="mvb" type="galaxy.datatypes.data:Mvb" display_in_upload="true"/> data.py : class Mvb( Text ): MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", readonly=True, set_in_upload=True) composite_type = 'basic' file_ext="mvb" allow_datatype_change = False def __init__( self, **kwd ): Text.__init__( self, **kwd ) #self.add_composite_file( '215_T1_MRI_biasCorr.nii.gz', is_binary = True ) #self.add_composite_file( 'VOTE_215_T1_MRI_hard_csf.nii.gz', is_binary = True ) self.add_composite_file( '%s.nii.gz', description = 'Input File', substitute_name_with_metadata = 'base_name', is_binary = True ) However, when I uploaded my backup.mvb file. It uploads the file and contents, but doesn't upload the files listed in the *.mvb file. Should it do this? Otherwise why have a composite datatype, as in this case it's simply acting like a text file Thanks Neil

2 2

Galaxy workflow editor cannot be loaded due to some JS files received 404 not found
by Derrick Lin 04 Oct '12

04 Oct '12

2 4

Galaxy download
by Jennifer Jackson 03 Oct '12

03 Oct '12

Hello Lizex, Are you still having problems? If so, please see below: On 10/2/12 12:34 AM, Lizex Husselmann wrote: > Hi all > I downloaded galaxy om my Mac OS 10.6.8 and have followed the following > steps: > > > Install Galaxy on MacBook Pro OS10.7.4 (08-10-2012) > • Install Mercurial http://mercurial.selenic.com/wiki/ > • Open Applications/Utilities/Terminal.app > • Confirm Mercurial installation by pasting in "hg version", no > quotes and hit return > response = version 2.3+20120807 > • Check Python version by pasting in "python -V", no quotes and hit > return > response = Python 2.7.1 > • Go to your home directory by pasting in "cd", no quotes and hit > return > • Get Galaxy by pasting in "hg clone > http://bitbucket.org/galaxy/galaxy-dist/", no quotes and hit return > • Go to the Galaxy directory by pasting in "cd galaxy-dist", no > quotes and hit return > • Start up Galaxy by pasting in "sh run.sh", no quotes and hit > return > • Open web browser and paste in “http://localhost:8080”, no quotes > and hit return > > > > I started galaxy by pasting sh run.sh and it fetched everything and > updated whats needed. I wonder if the process is actually running or if you need to do an update to incorporate changes first, then run. There is also a newer version of Mercurial (2.3.3) available, but if you are not writing tools for the Tool Shed, this should not be a factor right now. So first, double check that Galaxy is not running, then check to make sure updates are applied, then restart. The "$" in the command strings below represent the terminal prompt, they are not part of what you type. 1. Stop galaxy. With the terminal open to the process running Galaxy (or that you think is still running Galaxy) and use the two keys "Ctrl-c" together from your keyboard. 2. Change back the universe_wsgi.ini file to the default. 3. Still inside the galaxy-dist directory, type this to apply any changes: $ hg update 4. Now start up the Galaxy server: $ sh run.sh Please give this a try and let us know how it goes. I am going to move your question over to the galaxy-dev(a)bx.psu.edu mailing list for better visibility to the development community. This is where you will want to post future questions about your local instance (and consider joining). To keep it updated, following the the News Briefs would be advised. http://wiki.g2.bx.psu.edu/Mailing%20Lists http://wiki.g2.bx.psu.edu/DevNewsBriefs Jen Galaxy team > Upon pasting http://localhost:8080 in my browser > GoogleChrome and Safari respectively, it didn't work. I even changed the > host setting in the universe_wsgi.ini to 0.0.0.0 and still didn't open. > Any suggestions? > > > Kind regards > > > Lizex Husselmann > > This message is confidential and may be covered by legal professional > privilege. It must not be read, copied, disclosed or used in any other > manner by any person other than the addressee(s). Unauthorised use, > disclosure or copying is strictly prohibited and may be unlawful. The > views expressed in this email are those of the sender, unless otherwise > stated. If you have received this email in error, please contact ARC > Service Desk immediately. (mailto:Servicedesk@arc.agric.za) > > To report incidents of fraud and / or corruption in the ARC use our > Ethics Hotline by: > > Phone number : 0800 000 604 > Fax number : 0800 00 7788 > Email address : arc(a)tip-offs.com > Please Call me : 32840 > Website: www.tip-offs.com > > For more information on the ARC Ethics Hotline, please visit our website > at www.arc.agric.za. > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > -- Jennifer Jackson http://galaxyproject.org

1 0