July 2010 - galaxy-dev - lists.galaxyproject.org

workflow empty input dataset
by Jorge.DUARTE＠biogemma.com 29 Jul '10

29 Jul '10

Hi, I managed to install galaxy from the source available on the bitbucket website and i was able use it and to create a simple workflow, but then even if i have loaded data from the menu Get data > Upload file when i run the workflow the drop down list for input data set stays empty !? Can you help ? Thanks Jorge. --- Jorge Duarte Bioinformatics Research Engineer BIOGEMMA - Upstream Genomics Group Z.I. Du Brézet 8, Rue des Frères Lumière 63028 CLERMONT FERRAND Cedex 2 FRANCE Tel : +33 (0)4 73 39 60 73 Fax : +33 (0)4 73 42 79 81 E-mail : jorge.duarte(a)biogemma.com ***************************************************************** Pour toute demande de support merci d'inclure BIOGEMMA_BioInfo_Service ou bioinfo(a)biogemma.com dans les destinataires lors du premier contact ***************************************************************** BIOGEMMA S.A.S. au capital social de 48.335.652,00 ?. 1, Rue Edouard Colonne - 75001 PARIS. RCS PARIS 412 514 366 This message and any attachments are confidential and intended solely for the use of the addressee(s) named above. The information contained in this email may also be legally privileged. If you have received this email in error, please notify us immediately by reply email or by fax and then delete it. Any use, distribution or reproduction of this message is strictly prohibited. The integrity or authenticity of this message cannot be guaranteed. We therefore shall not be liable for the message if altered, changed or falsified. Thank you. Cet email et ses pièces jointes sont strictement confidentiels et destinés uniquement à l'usage du (des) destinataire(s) sus-indiqué(s). Les informations contenues dans cet email sont légalement protégées. Si vous avez reçu cet email par erreur, merci de nous le retourner immédiatement par courrier électronique ou télécopie avant de le supprimer. Toute utilisation ou reproduction de cet email est strictement interdite. La véracité et l'authenticité de cet email et de son contenu ne peuvent être garanties et nous ne pouvons être tenus responsables de leur altération, modification ou falsification. Merci.

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Re: [galaxy-dev] Eucalyptus genome in Galaxy
by Reddy.Thumma＠csiro.au 29 Jul '10

29 Jul '10

Hi, Could you please include Eucalyptus genome (http://eucalyptusdb.bi.up.ac.za/) in the public version of Galaxy. It is being sequenced at JGI and recently 8x assembly was completed. Thank you, Regards, Bala Thumma

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does anyone have Galaxy running with PBS Pro (not torque)?
by Michael Pheasant 28 Jul '10

28 Jul '10

If so, i'm interested to hear how that went. Cheers Mike. -- Michael Pheasant Software Engineer Queensland Facility for Advanced Bioinformatics Level 5, QBP University of Queensland, QLD 4072 T: +61 (0)7 3346 2070 F: +61 (0)7 3346 2101 www.qfab.org

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check_galaxy.py with external user authentification
by Michael Siebauer 28 Jul '10

28 Jul '10

Hi, is there a way to run the check_galaxy script when external user authentification through apache is enabled? I get the following error: |root@bioapp07:/home/galaxy/galaxy_dist/scripts# python check_galaxy.py 127.0.0.1:8080 ==> at http://127.0.0.1:8080/user Traceback (most recent call last): File "check_galaxy.py", line 358, in <module> if b.check_if_logged_in(): File "check_galaxy.py", line 278, in check_if_logged_in self.get("/user") File "check_galaxy.py", line 128, in get tc.code(200) File "/usr/lib/pymodules/python2.6/twill/commands.py", line 133, in code should_be)) twill.errors.TwillAssertionError: code is 403 != 200 | Bytheway, there is no hint in the documentation that a package "python-twill" is required to run the script ;-) Thx, Michael

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Help about zip upload (esd files)
by Eric Aguiar 28 Jul '10

28 Jul '10

Dear, I followed all steps in the galaxy tutorial, but I didn't have success. I'm trying to create a datatype for megabase chromatograms (.esd) very similar to the Ab1 ones. Here is my configurations. *1 - Creating datatypes in datatypes_conf.xml* <datatype extension="zip" type="galaxy.datatypes.binary:Esd" mimetype="application/zip" display_in_upload="true"/> <datatype extension="esd" type="galaxy.datatypes.binary:Esd" mimetype="application/octet-stream" display_in_upload="true"/> *2 - Defining types in lib/galaxy/datatypes/binary.py* class Esd( Binary ): """Class describing an ab1 binary sequence file""" file_ext = "esd" def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = "Binary chromatograms sequence file" dataset.blurb = data.nice_size( dataset.get_size() ) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' def display_peek( self, dataset ): try: return dataset.peek except: return "Binary esd sequence file (%s)" % ( data.nice_size( dataset.get_size() ) ) class Zip( Binary ): """Class describing a zip archive of binary sequence files""" file_ext = "zip" def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: zip_file = zipfile.ZipFile( dataset.file_name, "r" ) num_files = len( zip_file.namelist() ) dataset.peek = "Archive of %s binary sequence files" % ( str( num_files ) ) dataset.blurb = data.nice_size( dataset.get_size() ) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' def display_peek( self, dataset ): try: return dataset.peek except: return "Binary sequence file archive (%s)" % ( data.nice_size( dataset.get_size() ) ) def get_mime( self ): """Returns the mime type of the datatype""" return 'application/zip' When I'm going to send the file in zip format (.esd files compressed),it shows me the following error: *"An error occurred running this job: Invalid 'File Format' for archive consisting of binary files - use 'Binseq.zip'"* I tried somethings, but I don't have success. Thank you, --

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Running galaxy as an unprivileged user
by simon andrews (BI) 28 Jul '10

28 Jul '10

I'm in the process of setting up a multi-user galaxy server and am trying to sort out permissions and am having some problems. What I'd like to end up with ideally would be: * A galaxy-dist folder owned by a normal user * The galaxy server running as an unprivileged user 'galaxy' and bound to port 80 At the moment I'm having to have the galaxy user own the galaxy-dist directory and bound to port 8080. So I have a couple of questions: 1) Within galaxy-dist is there are list of locations which the owner of the server process will need to read and write to so I can open up permissions on just these files/directories? 2) Is there any way to have the server be launched as root so it can bind to port 80, but then drop privileges to run as an unprivileged user after that? I found a bug on the paster.py trac site saying this wasn't something they were going to implement (there is a --user option but it drops its privileges too early), but that individual servers could implement it. Thanks Simon.

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Re: [galaxy-dev] Dynamically adding tools to Galaxy
by Sumedha Ganjoo 26 Jul '10

26 Jul '10

Great! I am glad to hear that.. Regards, Sumedha On Mon, Jul 26, 2010 at 8:22 PM, Minh Bui <buiduyminh(a)gmail.com> wrote: > it works great. Thank you for the tool. > > On Mon, Jul 26, 2010 at 7:31 PM, Sumedha Ganjoo <sumedha.coep(a)gmail.com> > wrote: >> >> refreshTool.py is an empty file currently...u can just create an empty >> file called refreshTool.py at '/home/minh/galaxy_dist/tools/mystuff/' >> >> Then execute the tool.It should work >> >> Please let me know if you have any questions, >> >> Regards, >> Sumedha >> >> On Fri, Jul 23, 2010 at 10:22 AM, Minh Bui <buiduyminh(a)gmail.com> wrote: >> > Hi Sumedha, >> > I got this error when i execute the Refresh tool >> > An error occurred running this job: python: can't open file >> > '/home/minh/galaxy_dist/tools/mystuff/refreshTool.py': [Errno 2] No such >> > file or directory >> > Look like its missing refreshtool.py or Am I doing something wrong? >> > Where to >> > do place that refreshTool.xml? >> > Thank you, >> > >> > On Thu, Jul 22, 2010 at 6:40 PM, Sumedha Ganjoo <sumedha.coep(a)gmail.com> >> > wrote: >> >> >> >> Hello, >> >> >> >> We here at the Universoty of Georgia have developed a suite of tools >> >> to enable accessing >> >> Web services through Galaxy's interface, one time and also in >> >> workflows. We do this by reading >> >> the descriptions of the Web services (from WSDLs and WADLs) and adding >> >> tools dynamically to >> >> Galaxy that are able to take correct inputs from the user and invoke >> >> these services. >> >> >> >> Though most of this functionality was added by adding tools, we had to >> >> make minimal change in Galaxy's >> >> source code to support the capability of refreshing Galaxy toolbox >> >> without restarting the server. >> >> This is hardly 5 lines of code that was added to Galaxy's code base. >> >> These tools will be available shortly >> >> on the community page. I was wondering if it will be possible to add >> >> the support for dynamic tool addition >> >> to the main instance of Galaxy. Please find the details below: >> >> >> >> >> >> Changes to Galaxy to add refresh toolbox ability: >> >> 1. change the execute method of the class tool in >> >> lib/galaxy/tools/__init__.py to >> >> >> >> def execute( self, trans, incoming={}, set_output_hid=True ): >> >> """ >> >> Execute the tool using parameter values in `incoming`. This just >> >> dispatches to the `ToolAction` instance specified by >> >> `self.tool_action`. In general this will create a `Job` that >> >> when run will build the tool's outputs, e.g. >> >> `DefaultToolAction`. >> >> """ >> >> >> >> ############# >> >> #add code to verify if user has administrative privileges >> >> #added by sumedha ganjoo, sganjoo(a)uga.edu: line 1104 to 1109 - >> >> to refresh toolbox >> >> if self.id == 'REFRESH_ID': >> >> self.app.refreshToolBox() >> >> ############# >> >> >> >> return self.tool_action.execute( self, trans, >> >> incoming=incoming, set_output_hid=set_output_hid ) >> >> >> >> 2. add refreshToolBox method (find below) to UniverseApplication class >> >> in lib/galaxy/app.py >> >> >> >> ########### >> >> # added by sumedha ganjoo,sganjoo(a)uga.edu, line 86-90 >> >> def refreshToolBox( self): >> >> self.toolbox = tools.ToolBox( self.config.tool_config, >> >> self.config.tool_path, self ) >> >> ########### >> >> >> >> >> >> 3. Add Refresh tool. Attached. >> >> >> >> Thanks, >> >> Sumedha >> >> >> >> >> >> On Tue, May 4, 2010 at 10:37 AM, Nate Coraor <nate(a)bx.psu.edu> wrote: >> >> > Sumedha Ganjoo wrote: >> >> >> >> >> >> Hello, >> >> >> >> >> >> I am a student at the University Of Georgia. We had developed a tool >> >> >> for >> >> >> Galaxy 1.3 that enables accessing >> >> >> various web services as tools from Galaxy. >> >> >> >> >> >> We are currently working on a similar tool for the current version >> >> >> of >> >> >> Galaxy. This requires adding a tool dynamically >> >> >> without having to restart Galaxy. I was wondering if someone has >> >> >> already >> >> >> implemented that feature? We do have most >> >> >> of the code for this in place. Is there a way, once complete, this >> >> >> code >> >> >> can be added to the main Galaxy source code? >> >> > >> >> > Hi Sumedha, >> >> > >> >> > This is on our to-do list - if you already have it implemented and it >> >> > fits >> >> > our design goals, we would likely add it to the source. Please send >> >> > along a >> >> > patch or create a fork in Bitbucket once it's ready. >> >> > >> >> >> Also I would really appreciate if someone could tell me where can I >> >> >> find >> >> >> the older versions ( v 1.3 ) of Galaxy? >> >> > >> >> > Galaxy 1 is about 5 or 6 years old now and was basically unrelated >> >> > sourcewise to Galaxy 2. I'm not sure where the source is now, >> >> > although >> >> > I >> >> > might be able to find it if necessary. Do you need something in >> >> > specific >> >> > from it? >> >> > >> >> >> Thanks in advance. >> >> >> >> >> >> Regards, >> >> >> Sumedha >> >> >> >> >> >> Sumedha Ganjoo >> >> >> Graduate Assistant >> >> >> Computer Science Department >> >> >> University Of Georgia >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> >> >> _______________________________________________ >> >> >> galaxy-dev mailing list >> >> >> galaxy-dev(a)lists.bx.psu.edu >> >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> > >> >> > >> >> >> >> >> >> >> >> -- >> >> Sumedha Ganjoo >> >> Graduate Assistant, >> >> Department Of Computer Science, >> >> University Of Georgia, >> >> Athens, GA , USA >> >> >> >> _______________________________________________ >> >> galaxy-dev mailing list >> >> galaxy-dev(a)lists.bx.psu.edu >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> >> > >> > >> >> >> >> -- >> Sumedha Ganjoo >> Graduate Assistant, >> Department Of Computer Science, >> University Of Georgia, >> Athens, GA , USA > > -- Sumedha Ganjoo Graduate Assistant, Department Of Computer Science, University Of Georgia, Athens, GA , USA

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Conf files?
by Minh Bui 26 Jul '10

26 Jul '10

Hi, I am running local galaxy and I just wrote a script that allowed me to create a config file for Gbrowse (*.conf) but I dont think Galaxy supports *.conf files. I tried to save the file but Galaxy saved it under "Download" name without extension . What can I do to make Galaxy supports *.conf files? Thank you, Minh.

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Dynamically adding tools to Galaxy
by Sumedha Ganjoo 26 Jul '10

26 Jul '10

Hello, I am a student at the University Of Georgia. We had developed a tool for Galaxy 1.3 that enables accessing various web services as tools from Galaxy. We are currently working on a similar tool for the current version of Galaxy. This requires adding a tool dynamically without having to restart Galaxy. I was wondering if someone has already implemented that feature? We do have most of the code for this in place. Is there a way, once complete, this code can be added to the main Galaxy source code? Also I would really appreciate if someone could tell me where can I find the older versions ( v 1.3 ) of Galaxy? Thanks in advance. Regards, Sumedha Sumedha Ganjoo Graduate Assistant Computer Science Department University Of Georgia

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Question about galaxy
by Simon Lank 26 Jul '10

26 Jul '10

Hi. We have a new server and are planning to dedicate it exclusively to Galaxy. We've previously set up galaxy on OS X, and Ubuntu. I'm wondering if you guys have a preferred linux distribution that you know works well for galaxy. We'd like to spend as little time configuring the dependencies as possible (we already spent a while getting things working in os x), so any advice on the most streamlined distribution (from galaxy's perspective) would be appreciated. Regards, Simon Simon Lank Associate Research Specialist O'Connor Lab, WNPRC 555 Science Dr. Madison WI (608) 265-3389

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