October 2011 - galaxy-dev - lists.galaxyproject.org

moving the galaxy-dist folder structure
by Joseph Hargitai 14 Oct '11

14 Oct '11

Hi, we moved the /home/galaxy/galaxy-dist structure to another fs. Some tools, like fastqc, stopped working. Are there internal links that we possibly ignored? Is there a way to adjust the installation via a download or update? joe

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Re: [galaxy-dev] [galaxy-user] Problem with new tool shed
by Greg Von Kuster 13 Oct '11

13 Oct '11

Hello Florent, Sorry for the confusion on this - we are preparing a new Galaxy distribution, and the tool shed wiki has been written in preparation for it. The new distribution will be available fairly soon, and the Galaxy News Brief will include information about these new tool shed features. In any case, you have already discovered that you can use in if you update your Galaxy instance to the latest Galaxy development repository ( Galaxy central ). The problem you see is most likely caused by your not having configured an additional tool_config_file setting in your universe_wsgi.ini. Look for something like following in your latest version of the universe_wsgi.ini.sample that you got when you updated from Galaxy central. # Locally installed tools and tools installed from tool sheds tool_config_file = tool_conf.xml,shed_tool_conf.xml If you add a new additional file name like shed_tool_conf.xml, you should not have a problem installing from a tool shed. I'll have a fix for the bug you've discovered shortly, but making this change will fix the behavior until then. Let me know if you bump into any additional problems. Thanks for finding this! Greg Von Kuster On Oct 4, 2011, at 2:53 AM, Florent Angly wrote: > Hi all, > > I tried the latest stable version of Galaxy: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30. This page has links to how to use the new tool shed including how to automatically deploy tools from the shed in a local Galaxy server. > The documentation mentioned some tool shed options available from the the admin section of Galaxy but I could not locate these options in my instance of galaxy. So my question is: Can one only take advantage of the tool deployment from the shed in the development version of Galaxy? If so, I think the Tool shed wiki should be more clear about this. > > Then I tried the latest development version of Galaxy and could locate the tool shed deployment options. I attempted to install the Grinder wrapper (http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&webapp… <http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&webapp…>) but ran into an error that I am pasting below: >> URL: http://localhost:8080/admin/install_tool_shed_repository?tool_shed_url=tool… >> File '/home/floflooo_mint/Software/galaxy-central/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond >> app_iter = self.application(environ, detect_start_response) >> File '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ >> environ, self.app) >> File '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output >> app_iter = application(environ, replacement_start_response) >> File '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ >> return self.application(environ, start_response) >> File '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ >> return self.application(environ, start_response) >> File '/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__ >> body = method( trans, **kwargs ) >> File '/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/framework/__init__.py', line 173 in decorator >> return func( self, trans, *args, **kwargs ) >> File '/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/controllers/admin.py', line 805 in install_tool_shed_repository >> shed_tool_conf = trans.app.toolbox.shed_tool_confs.keys()[0].lstrip( './' ) >> IndexError: list index out of range > > I get the same problem with other wrappers such as FastQC. Am I doing something wrong? > > Thanks, > > Florent > > > ___________________________________________________________ > 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/ Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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The need for wrappers
by Timothy Wu 13 Oct '11

13 Oct '11

Hi, Looking under the tools directory I realized that some tools comes with *_wrapper.py. I wonder under what circumstances is this needed? I'm trying to do a quickie for RepeatMasker. It looks to me like the tool does not allow one to specify the name of the output files. It also appears to me that tools should have an $output variable specifies within the <command> tag. So I was wondering if this is one case where a wrapper.py is needed. Thanks. Timothy

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Re: [galaxy-dev] Accept-Ranges: bytes for
by Kip Bodi 13 Oct '11

13 Oct '11

Perhaps this is a distribution issue. For those who have gotten the "Display at UCSC" link to work on a local server or workstation, what linux distribution and version did you use? Has anyone used this successfully with Red Hat Enterprise Linux 6.1? Best, -Kip On Fri, Oct 7, 2011 at 6:28 PM, Bodi, Kip <Kip.Bodi(a)tufts.edu> wrote: > Hi all, > > I have a local galaxy instance, proxied by Apache, and am trying to get the > 'display at UCSC' link to work. I've followed all of the instructions and am > nearly there, but now I'm getting this response from UCSC when it tries to > load the track: > > "Byte-range request was ignored by server. Expected Partial Content 206." > etc. > > I think the error is because the PasteWSGIServer isn't allowing byte-range > requests. When I look at the header, "Accept-Ranges: bytes" is not present: > [galaxy@galaxy galaxy_dist]$ curl --head localhost > HTTP/1.1 200 OK > Date: Fri, 07 Oct 2011 22:23:49 GMT > Server: PasteWSGIServer/0.5 Python/2.6.6 > content-type: text/html; charset=UTF-8 > Set-Cookie: > galaxysession=c6ca0ddb55be603a4e98b4f13a4db8bfb8635f0aa576697114d40b13a8355efe2cf7a075ef81d769; > expires=Thu, 05-Jan-2012 17:23:49 GMT; Max-Age=7776000; Path=/; Version=1 > Vary: Accept-Encoding > Connection: close > > Whereas on another server, "Accept-Ranges: bytes" appears in the header: > [galaxy@galaxy galaxy_dist]$ curl --head apollo.med.tufts.edu< > http://apollo.med.tufts.edu> > HTTP/1.1 403 Forbidden > Date: Fri, 07 Oct 2011 22:22:42 GMT > Server: Apache/2.2.21 (Fedora) > Accept-Ranges: bytes > Content-Length: 4609 > Connection: close > Content-Type: text/html; charset=UTF-8 > > I'm running RHEL6 with the latest version of galaxy-dist. I've tried > manually enabling 'accept-ranges' but haven't had any luck. Any suggestions? > Can I enable it somehow in universe_wsgi.ini? > > Best, > > -Kip > -- Kip Lord Bodi Jr. Tufts University School of Medicine 136 Harrison Avenue, South Cove 502 Boston, MA 02118 617-636-3763 kip.bodi(a)tufts.edu www.tucf.org | genomics.med.tufts.edu

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Re: [galaxy-dev] Some changes to tophat and cufflinks wrappers for indexing loc files
by Chorny, Ilya 12 Oct '11

12 Oct '11

I made some changes to the cufflinks and tophat wrapper to pull gtf files from an indexed loc file as opposed to from history. The diff's are attached. I made it an optional feature. Please let me know if this makes its way into galaxy-central. Best, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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samtools mpileup update
by David Hoover 12 Oct '11

12 Oct '11

Is there any good reason why Galaxy can't use a more recent version of samtools? The only difference I can see is the mpileup command. The algorithm by which mpileup finds SNPs is a little different. Does anyone know if the file format has changed? The only files that need to change are sam_pileup.py and sam_pileup.xml. David Hoover Helix Systems Staff http://helix.nih.gov

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Re: [galaxy-dev] Possible to browse local filesystem
by Greg Von Kuster 12 Oct '11

12 Oct '11

Allesandro, Are your users making the correct selection in the Copy data into Galaxy? select list? If they choose "Link to files without copying into Galaxy" as shown below, you should see the behavior you want. The default selection is "Copy files into Galaxy", so if they leave the default selection, copies of the files will be made. On Oct 12, 2011, at 12:10 PM, alessandro albiero wrote: > Dear Greg, > > thank you for your answer. I followed the wiki but I did not solve my problem. > I setted these parameters on the universe_wsgi.ini: > > user_library_import_dir = /u/galaxy/userimport > > Then I created the /u/galaxy/userimport directory with a series of sub-dirs named as the login users. > I done this to allow our user to load into galaxy their files. In this case every user put its data in its dir on /u/galaxy/userimport (or using symlinks) and then load them on galaxy. > > My problem is that galaxy duplicate the files; for example: > > 1) User "A" place a file "FILE1" on its dir and it load the dir on galaxy. On galaxy he sees "FILE1" > 2) The user "A" place another file in its dir ("FILE2") and re-load the dir on galaxy. On galaxy he sees "FILE1", "FILE1", "FILE2" > > It seems that galaxy re-loads all the files of the user dir without checking the duplications. > We would like to avoid this duplications. > > We found that removing the old files from the user directory solves the problem. Is there a simpler way to do this (without removing the files) ? > > > All the best > > Alessandro > > > > 2011/10/11 Greg Von Kuster <greg(a)bx.psu.edu> > Hello Alessandro, > > You can upload files from filesystem paths to a Galaxy data library without copying the files into Galaxy's configured file directory. This approach should provide what you're looking to do. See our wiki at http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files for all of the details. > > Greg Von Kuster > > On Oct 11, 2011, at 6:45 AM, alessandro albiero wrote: > >> Dear all, >> >> I have a problem with galaxy and I have already tried to write on ther user list.... >> My problem concern the upload on galaxy of new files. >> >> We are setting up a galaxy istance on our server (HPC Cluster with torque and PBS) for internal use. >> Our problem is that we manage only NGS data (SOLiD and Illumina Data) that are already stored on the server. >> We tried to set up the user directory in the universe_wgsi.ini file to allow to any user tu upload their local files, but adding new file and re-uploading the dir we found duplicated files (it seems that galaxy re-upload every time all the files ignoring if some are already present). This method is OK for us but how can we avoid the file duplications ? >> >> In a presentation found on web (blankenberg_pittsburg_2001), we saw that there is the possibility to automatically upload the sequenced reads on Galaxy (and let them available to all our user). Where can we find information for doing this ? >> >> >> Thank in advance >> >> All the best >> >> Alessandro >> >> >> >> >> -- >> ****************************** >> Alessandro Albiero >> Bioinformatics Lab >> CRIBI-Padua University >> Viale G. Colombo, 3 >> 35121 Padova-Italy >> >> http://genomics.cribi.unipd.it >> http://genomics.cribi.unipd.it/index.php/User:Albiero >> Phone. +39. 049 827-6165 >> Fax. +39. 049 827-6159 >> ******************************** >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > Greg Von Kuster > Galaxy Development Team > greg(a)bx.psu.edu > > > > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Trasfering Galaxy workflows to other instances
by Chorny, Ilya 12 Oct '11

12 Oct '11

Is there a way of uploading workflows by saving the workflow to a file and copying the workflow files to a directory or editing a database file to point to them. When external authentication is invoked linking to workflows does not seem to work and copy and pasting from a file is very tedious. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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Specifying data types for workflow inputs
by Ann Black 12 Oct '11

12 Oct '11

I am developing a custom workflow in galaxy. I have 4 input files that need to be fed into various steps of the workflow. I would like to be able to specify a data type for the inputs such that the pre-populated drop downs are filtered to datasets of the appropriate type as well as being able to do some simple validation before the workflow begins. Is there someway to do this? Thanks much, Ann

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strange history error
by Chorny, Ilya 12 Oct '11

12 Oct '11

I am getting a strange error that I cannot figure out how to debug. It's from a second instance we have running on the same server. When I upload data it does not show me my history. I get the following messages from the log file. Thoughts? galaxy.web.framework DEBUG 2011-10-11 15:47:50,259 Error: this request returned None from get_history(): http://ussd-dev-swim02.illumina.com/galaxy2/history/list galaxy.web.framework DEBUG 2011-10-11 15:47:50,261 Error: this request returned None from get_history(): http://ussd-dev-swim02.illumina.com/galaxy2/history/list galaxy.web.framework DEBUG 2011-10-11 16:34:25,717 Error: this request returned None from get_his tory(): http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-10-11 16:34:25,717 Error: this request returned None from get_his tory(): http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned None from get_his tory(): http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned None from get_his tory(): http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned None from get_his tory(): http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-10-11 16:34:25,718 Error: this request returned None from get_his tory(): http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-10-11 16:34:25,719 Error: this request returned None from get_his tory(): http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-10-11 16:34:25,719 Error: this request returned None from get_his tory(): http://ussd-dev-swim02.illumina.com/galaxy2/tool_runner/upload_async_create Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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