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[hg] galaxy 3446: Clean up pages:
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/143c920af25c changeset: 3446:143c920af25c user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sun Feb 28 22:19:56 2010 -0500 description: Clean up pages: -remove unused code; -show annotation field when creating a page; -fix bug when filtering pages by sharing status. diffstat: lib/galaxy/web/controllers/page.py | 57 +++++++++---------------------------- 1 files changed, 14 insertions(+), 43 deletions(-) diffs (115 lines): diff -r 5ffd16fb6a12 -r 143c920af25c lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Thu Feb 25 23:20:19 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Sun Feb 28 22:19:56 2010 -0500 @@ -24,13 +24,13 @@ use_panels = True title = "Pages" model_class = model.Page - default_filter = { "published" : "All", "tags" : "All", "title" : "All"} + default_filter = { "published" : "All", "tags" : "All", "title" : "All", "sharing" : "All" } default_sort_key = "-create_time" columns = [ grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -79,40 +79,7 @@ return session.query( self.model_class ).join( model.User.table ) def apply_default_filter( self, trans, query, **kwargs ): return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True ) - -class HistorySelectionGrid( grids.Grid ): - # Custom columns. - class NameColumn( grids.TextColumn ): - def get_value(self, trans, grid, history): - return history.get_display_name() - - # Grid definition. - title = "Saved Histories" - template = "/page/select_histories_grid.mako" - async_template = "/page/select_histories_grid_async.mako" - model_class = model.History - default_filter = { "deleted" : "False" , "shared" : "All" } - default_sort_key = "-update_time" - use_async = True - use_paging = True - num_rows_per_page = 10 - columns = [ - NameColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), - grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), - ] - columns.append( - grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", visible=False, filterable="standard" ) - ) - def apply_default_filter( self, trans, query, **kwargs ): - return query.filter_by( user=trans.user, purged=False ) - + class ItemSelectionGrid( grids.Grid ): """ Base class for pages' item selection grids. """ # Custom columns. @@ -339,12 +306,12 @@ @web.expose @web.require_login( "create pages" ) - def create( self, trans, page_title="", page_slug="" ): + def create( self, trans, page_title="", page_slug="", page_annotation="" ): """ Create a new page """ user = trans.get_user() - page_title_err = page_slug_err = "" + page_title_err = page_slug_err = page_annotation_err = "" if trans.request.method == "POST": if not page_title: page_title_err = "Page name is required" @@ -355,12 +322,14 @@ elif trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first(): page_slug_err = "Page id must be unique" else: - # Create the new stored workflow + # Create the new stored page page = model.Page() page.title = page_title page.slug = page_slug + page_annotation = sanitize_html( page_annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans, page, page_annotation ) page.user = user - # And the first (empty) workflow revision + # And the first (empty) page revision page_revision = model.PageRevision() page_revision.title = page_title page_revision.page = page @@ -381,8 +350,10 @@ public links to this page. A default is generated from the page title, but can be edited. This field must contain only lowercase letters, numbers, and - the '-' character.""" ), - template="page/create.mako" ) + the '-' character.""" ) + .add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err, + help="A description of the page; annotation is shown alongside published pages."), + template="page/create.mako" ) @web.expose @web.require_login( "create pages" ) @@ -432,7 +403,7 @@ must contain only lowercase letters, numbers, and the '-' character.""" ) .add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err, - help="A description of or notes about the page. Annotation is shown alongside published pages."), + help="A description of the page; annotation is shown alongside published pages."), template="page/create.mako" ) @web.expose

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[hg] galaxy 3445: Fixed dbkey's in sam_pileup and sam_to_bam too...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5ffd16fb6a12 changeset: 3445:5ffd16fb6a12 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Thu Feb 25 23:20:19 2010 -0500 description: Fixed dbkey's in sam_pileup and sam_to_bam tools in tests so they will pass diffstat: tools/samtools/sam_pileup.xml | 4 ++-- tools/samtools/sam_to_bam.xml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diffs (42 lines): diff -r 294b1283ea56 -r 5ffd16fb6a12 tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml Thu Feb 25 14:59:43 2010 -0500 +++ b/tools/samtools/sam_pileup.xml Thu Feb 25 23:20:19 2010 -0500 @@ -82,7 +82,7 @@ --> <param name="reference" value="history" /> <param name="input1" value="sam_pileup_in1.bam" ftype="bam" /> - <param name="ownFile" value="chr_m.fasta" ftype="fasta" /> + <param name="ownFile" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> <param name="lastCol" value="no" /> <param name="indels" value="no" /> <param name="mapCap" value="60" /> @@ -96,7 +96,7 @@ chr_m.fasta is the prefix of the index --> <param name="reference" value="indexed" /> - <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="chrM" /> + <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" /> <param name="lastCol" value="no" /> <param name="indels" value="no" /> <param name="mapCap" value="60" /> diff -r 294b1283ea56 -r 5ffd16fb6a12 tools/samtools/sam_to_bam.xml --- a/tools/samtools/sam_to_bam.xml Thu Feb 25 14:59:43 2010 -0500 +++ b/tools/samtools/sam_to_bam.xml Thu Feb 25 23:20:19 2010 -0500 @@ -41,7 +41,7 @@ --> <param name="index_source" value="history" /> <param name="input1" value="3.sam" ftype="sam" /> - <param name="ref_file" value="chr_m.fasta" ftype="fasta" /> + <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> <output name="output1" file="sam_to_bam_out1.bam" /> </test> <test> @@ -53,7 +53,7 @@ should be in the same directory --> <param name="index_source" value="cached" /> - <param name="input1" value="3.sam" ftype="sam" dbkey="chrM" /> + <param name="input1" value="3.sam" ftype="sam" dbkey="equCab2" /> <param name="output1" file="sam_to_bam_out2.bam" /> </test> </tests>

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User customization in the Galaxy tool pane
by H. Mei 02 Mar '10

02 Mar '10

Dear colleagues, We are installing a local Galaxy server for a few groups working on high throughput sequencing. Some users like to customize their tool pane when they log in, e.g., by hiding certain tools that they do not need. I searched through the email list and noticed a somehow similar request: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-January/001619.html Kanwei (Galaxy developer) mentioned that this is possible via user preference table (http://bitbucket.org/galaxy/galaxy-central/issue/286/user-customization-in-…) However, I can't find it in the current Galaxy server. Will this be included in the upcoming releases? Is there a time line? Thanks, Leon

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MySQL database dump import
by Dijk, F van 02 Mar '10

02 Mar '10

Hello, I'm trying to transfer the data from the SQLite database Galaxy uses to a MySQL database we have running locally. I made a database dump from the SQLite database and tried to import into our MySQL database. This results in the following error message: ERROR 1059 (42000) at line 77132: Identifier name 'ix_history_dataset_association_display_at_authorization_history_dataset _association_id' is too long Do you know a way to solve this? Or should I perform an other action to transfer the SQLite database to our own MySQL database? I hope to hear from you soon. Sincerely, Freerk van Dijk University Medical Center Groningen De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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Some data link problems on the wiki
by Iwe Muiser 02 Mar '10

02 Mar '10

Hello Galaxy team, Mainly the wiki on the local setup of NGS is a bit uncomplete. The download links to the built indexes do not seem to function on http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup My box somehow can't make the index files with BWA. This is probably due to memory shortage al though the tool does not specify. The tool just tells me: $ ./bwa index -a bwtsw -p test /home/muiser/data/Human_data/hg18/chromosomes/hg18.fa [bwa_index] fail to open file '/home/muiser/data/Human_data/hg18/chromosomes/hg18.fa'. Abort! Aborted It would be great if the files can be downloaded somewhere. Greetings, Iwe -- Iwe EC Muiser Master student NTNU - Department of Cancer Research and Molecular Medicine Bioinformatics & Gene Regulation Group Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 Trondheim +4594157082

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LIMS Demo stalled
by nsfox＠uwaterloo.ca 01 Mar '10

01 Mar '10

Hi, I have setup up Galaxy on my computer following the instructions and then proceeded to run the LIMS Demo script following the instructions on the wiki. The setup stalled ending with the following: galaxy.jobs INFO 2010-03-01 10:51:36,928 job scheduler policy is galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin galaxy.jobs INFO 2010-03-01 10:51:36,929 job manager started galaxy.jobs INFO 2010-03-01 10:51:37,036 job stopper started Traceback (most recent call last): File "setup_lims_demo.py", line 184, in <module> main() File "setup_lims_demo.py", line 137, in main user_list.append( create_user( app, admin_user_email, 'testuser' ) ) File "setup_lims_demo.py", line 43, in create_user user.flush() AttributeError: 'User' object has no attribute 'flush' The error suggests to me that I missed downloading some methods or something. I have not worked with python before so I am unfamiliar as to where I would look for the flush method or how I would import/use it to make it available. I was wondering if you have any suggestions as to what I could be missing or what I could do to fix the error, please let me know. Any help is greatly appreciated. Thanks, Natalie Fox

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Where to place google analytics tracking code
by Martin Aryee 28 Feb '10

28 Feb '10

Hi, I'd like to use Google Analytics to track visits to our galaxy instance. It involves placing a <script></script> block (example below) on all the site's pages. The recommended location is just before the </body> tag. I'd like to insert the code snippet in one of the mako templates and am wondering which template would be most appropriate? Thanks, Martin. <script type="text/javascript"> var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www."); document.write(unescape("%3Cscript src='" + gaJsHost + " google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E")); </script> <script type="text/javascript"> try{ var pageTracker = _gat._getTracker("UA-xxxxxx-x"); pageTracker._trackPageview(); } catch(err) {} </script>

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Re: [galaxy-dev] Questions about Galaxy!
by WangJun 27 Feb '10

27 Feb '10

Dear Greg Von Kuster, I installed a local Galaxy instance for data submit test for our own GMap project. And I found a question: If I submit from GMap for the first time, then a error page appears. (attached the error information) However, if I use it from "Get Data" in Galaxy for the first time, it works very well. I guess the history_id does not exist when I submit from GMap for the first time. Also I found it's "Server error" if I submit data from UCSC table browser to the public Galaxy instance for the first time. I think I have the same question with them. Can you help to to find a solution? Thanks a lot! Best wishes, Kathleen 2010-01-19 发件人： Greg Von Kuster 发送时间： 2009-11-18 02:10:17 收件人： wangjun 抄送： galaxy-dev 主题： Re: [galaxy-dev] Questions about Galaxy! Kathleen, Please install a local instance of Galaxy and develop a data source tool that works between your Galaxy instance and GMap. You can download Galaxy from http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy. When you have your tool working, please submit it to us for possible inclusion in the public Galaxy instance. Thanks very much for your interest in doing this. Greg Von Kuster On Nov 17, 2009, at 11:27 AM, wangjun(a)mail.cbi.pku.edu.cn wrote: Hello Greg Von Kuster, You can access test GMap at http://202.38.125.5:8383/. Click the big button "search" and submit using the default params, then you can see four tracks. You can click the entry of the second track, for example the red one, then you can see the detail info in the right panel. Click the "view sequence", there is a button "submit to Galaxy", you can try it. Thanks a lot! Kathleen Kathleen, sorry, I thought you had your own local Galaxy instance. Can you give us more information on GMap? Do you have a wiki or something we can access online to read about it? Thanks! On Nov 17, 2009, at 10:37 AM, wangjun(a)mail.cbi.pku.edu.cn wrote: Hello Greg Von Kuster, I am talking about your public Galaxy instance, and we don't have local one. We find that UCSC's data can be saved in your site directly, so we hope that Galaxy can also save our GMap data directly. We use the same post method like UCSC and the data can be saved now, but the data title is wrong. So I am writing to you to hope that you can help us. Thanks you. Kathleen Hello Kathleen, Are you talking about your own local Galaxy instance or our main public Galaxy instance that is hosted here at Penn State University? Greg Von Kuster On Nov 17, 2009, at 10:10 AM, WangJun wrote: Hello Greg Von Kuster, Thanks for your reply, but I think you misunderstood my meaning. I am now working on a genome browser project GMap, and I hope that I can post request from GMap to Galaxy, then Galaxy can retrieve and save the data in the History space like the UCSC request. Untill now, I can post a request, including a url and params, and Galaxy can retrieve the data and save it. However, the title of the data is still "UCSC Main". I think that's because of the tool_id param's value is still "ucsc_table_direct1". I mean whether you can support us by adding a new tool_id named "CBI GMap". Then our post data can be shown with title "CBI GMap", not "UCSC Main". Thanks a lot! Kathleen 发件人： Greg Von Kuster 发送时间： 2009-11-17 21:49:22 收件人： WangJun 抄送：主题： Re: [galaxy-dev] Questions about Galaxy! Kathleen, I'm not sure I understand the question, but if you are simply creating a new tool that is very similar to the "ucsc_table_direct1" tool , and you want the ID of your new tool to be "CBIGMap" ( I would advise against space characters in the tool ID ), then your tools config tag can be something like this: <tool id="CBIGMap" name="CBIG Map" version="1.0.0" hidden="false" tool_type="data_source" URL_method="post"> If you have questions about how to add a new tool to your Galaxy instance, see our wiki at http://bitbucket.org/galaxy/galaxy- central/wiki/AddToolTutorial On Nov 17, 2009, at 8:38 AM, WangJun wrote: Hello Greg Von Kuster, Now I have solved the second problem.:) And for the first one, could you help me to add a new tool_id named "CBI GMap" to support our data source? This is a project in Center for Bioinformatics in Peking University in China. And I am a PhD student working on it. If you have other questions, please email me.:) <tool id="ucsc_table_direct1" name="UCSC Main" version="1.0.0" hidden="false" tool_type="data_source" URL_method="post"> Thanks a lot! Best, Kathleen 20091117 =================================================================== = Hello Greg Von Kuster, Thanks a lot for your reply. But I still have a question: I have a url, and I include three necessary params in the following form. After I post it to Galaxy, I can see that Galaxy fetch the data. However, there are two point that I want to ask: 1. the "tool_id" param. My data's title is still "UCSC Main", I think that's because I use the "ucsc_table_direct1" value for "tool_id", right? Then how do I change this title? Can I adjust it by other param to change the title? 2. If I submit data from UCSC, then I can see a white box containing the data in the History part. However, I can only see the data info without data if I submit from my own site. (You can refer to attachment for detail. The No.20 data is from UCSC, and I can see the sequence. While the No.22 data is from my site, and I can not see the sequence.) And I don't know why. <form method="POST" action="http://main.g2.bx.psu.edu/tool_runner"> <input type="HIDDEN" value="ucsc_table_direct1" name="tool_id"/> <input type="HIDDEN" value="http://202.38.125.5:8383/entry/ rice_nucleotide_frame_galaxy.jsp" name="URL"/> <input type="HIDDEN" value="<%=id%>" name="id"/> <input type="HIDDEN" value="<%=trackName%>" name="trackName"/> <input type="HIDDEN" value="<%=type%>" name="type"/> <input type="HIDDEN" value="rice" name="db"/> <input type="HIDDEN" value="Rice" name="org"/> <input type="SUBMIT" value="Send query to Galaxy" name="submitGalaxy"/> </form> (test data: http://202.38.125.5:8383/entry/ rice_nucleotide_frame_galaxy.jsp? id=LOC_Os02g01370&trackName=MSU_Osa1_Rice_Loci&type=seq ) Thank a lot! Best, Kathleen 20091117 发件人： Greg Von Kuster 发送时间： 2009-11-17 04:50:55 收件人： WangJun 抄送： galaxy-user(a)bx.psu.edu; galaxy-dev(a)bx.psu.edu 主题： Re: [galaxy-dev] Questions about Galaxy! Hello Kathleen, Please see our wiki at http://bitbucket.org/galaxy/galaxy-central/ wiki/DataSources for details about how Galaxy communicates with external data sources. Your "dataset platform" will need to build an url that includes all of the parameters that are needed to retrieve the data, and send that url to Galaxy in the URL parameter so that Galaxy can execute the post. On Nov 16, 2009, at 9:06 AM, WangJun wrote: Hi, This is a question about Galaxy interaction with UCSC data. I hava a dataset platform, and I want to add a button like the UCSC's "Send query to Galaxy". I find that it's actually a form: <form method="POST" action="http://main.g2.bx.psu.edu/ tool_runner"> <input type="HIDDEN" value="ucsc_table_direct1" name="tool_id"/> <input type="HIDDEN" value="http://genome.ucsc.edu/cgi-bin/ hgTables" name="URL"/> <input type="HIDDEN" value="296389734" name="hguid"/> <input type="HIDDEN" value="hg18" name="db"/> <input type="HIDDEN" value="Human" name="org"/> <input type="HIDDEN" value="multiz28way" name="hgta_table"/> <input type="HIDDEN" value="multiz28way" name="hgta_track"/> <input type="HIDDEN" value="range" name="hgta_regionType"/> <input type="HIDDEN" value="primaryTable" name="hgta_outputType"/> <input type="HIDDEN" value="chr3:130734948-130736581" name="position"/> <input type="HIDDEN" value="get output" name="hgta_doTopSubmit"/> <input type="HIDDEN" value="146683120" name="hgsid"/> <input type="SUBMIT" value="Send query to Galaxy" name="hgta_doGalaxyQuery"/> </form> I have a url and three params, and I tried. But I can't see my data in the right-side green box. And what's the tool_id param used for? Thanks in advance! Best, Kathleen 2009-11-16 _______________________________________________ galaxy-dev mailing list galaxy-dev(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev Greg Von Kuster Galaxy Development Team greg(a)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 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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Fwd: create multiple historie items
by Daniel Blankenberg 26 Feb '10

26 Feb '10

Begin forwarded message: > From: Edward Kirton <edward.kirton(a)gmail.com> > Date: February 26, 2010 8:34:19 PM EST > To: Daniel Blankenberg <dan(a)bx.psu.edu> > Subject: Re: [galaxy-dev] create multiple historie items > > unfortunately, no. neither c.s nor c[s] forms work. > > here's a simple test xml file that demonstrates that 2 files are > always created, even when 1 should be filtered by the conditional var. > > <tool id='conditional_filter_test' name='conditional filter test'> > <description>test</description> > <command> > #if $opt.numbfiles == '1': > echo $opt.string1 > $outfile1 > #else: > echo "1: $opt.string2" > $outfile1; > echo "2: $opt.string2" > $outfile2 > #end if > </command> > <inputs> > <conditional name='opt'> > <param name='numbfiles' type='select' label='how many files'> > <option value='1'>1</option> > <option value='2'>2</option> > </param> > <when value='1'> > <param name='string1' type='text' label='enter a string'/> > </when> > <when value='2'> > <param name='string2' type='text' label='Enter a String'/> > </when> > </conditional> > </inputs> > <outputs> > <data name='outfile1' format='txt'/> > <data name='outfile2' format='txt'> > <filter>opt[numbfiles] == 2</filter> > </data> > </outputs> > <help>test</help> > </tool> > > On Fri, Feb 19, 2010 at 6:19 AM, Daniel Blankenberg <dan(a)bx.psu.edu> wrote: >> >> Hello, >> Does e.g. do_full_assembly['create_ace_file'] work? >> Dan >

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Re: [galaxy-dev] [galaxy-bugs] Galaxy tool error report from m.p.villerius@lumc.nl
by Kelly Vincent 26 Feb '10

26 Feb '10

Michel, The newest versions of SAM Tools are on our main public server now. If you could try again, that would be helpful. If it does fail again, please do share your history with me (kpvincent(a)bx.psu.edu) Otherwise, it's good that you were able to get it working locally. The error suppression is actually what we just dealt with with the latest version of the tools. Now it should capture the stderr and output it only if it was an actual error, instead of disrupting successful runs. Galaxy doesn't have any special PATH settings. You just need to make sure that the binary is available on your PATH environment variable when you run Galaxy. Out of the SAM Tools heading tools, only Merge BAM Files and Generate pileup actually rely on the samtools binary, so maybe that's why it seemed like the others were working. I'm not sure on your last question and will forward it to our list for someone else to answer. Regards, Kelly On Thu 25 Feb 2010, at 3:46 AM, vill wrote: > Hi Kelly, > > Yes I tried both places. The test.galaxy server is slow or not > responding right now. 25 Feb. 9:10 am Amsterdam time thus I can't test > samtools there. > The error I got on my local install is solved, I removed in the > sam_to_bam.py the following "2> /dev/null" and the error was can't > find > the path. > I copied samtools to the /usr/local/bin dir and now everything is > working. Strange because the other samtools seemed to work. > How do I add a extra PATH to GALAXY? > > It won't be any problem sharing my History if you need it. > > One other thing when we get data from UCSC main, the data will > become a > history item. When you look at this history item in the info: there > used > to be a link so you could view the data in the UCSC browser: > Info: UCSC Main on Human: > The txt is there but it is not a link, is this something we need to > add > in the configuration? > > //Michel > > > On Wed, 2010-02-24 at 10:38 -0500, Kelly Vincent wrote: >> Michel, >> >> Your other email indicated that you are running a local instance of >> Galaxy, but this error report is from our public server, so I'm >> assuming you tried it both places. Our SAM Tools wrappers have >> recently been slightly rewritten, in changeset 3426:1f05b0c4071f, >> although the changed versions haven't been uploaded to the public >> server yet. You should try rerunning the job with the new version (it >> should be providing more information when something fails). If you >> want to try it on main, I can let you know once it's been updated. >> Also, the new version is already on our test server (http://test.g2.bx.psu.edu/ >> ) if you want to try right away without upgrading your local install. >> If you try it on test and it fails, could you share your history with >> me (kpvincent(a)bx.psu.edu)? >> >> Thanks, >> Kelly >> >> >> On Mon 22 Feb 2010, at 8:40 AM, galaxy-bugs(a)bx.psu.edu wrote: >> >>> >>> GALAXY TOOL ERROR REPORT >>> ------------------------ >>> >>> This error report was sent from the Galaxy instance hosted on the >>> server >>> "main.g2.bx.psu.edu" >>> ----------------------------------------------------------------------------- >>> This is in reference to dataset id 1078127 from history id 322475 >>> ----------------------------------------------------------------------------- >>> You should be able to view the history containing the related >>> history item >>> >>> 4: SAM-to-BAM on data 3 and data 2 >>> >>> by logging in as a Galaxy admin user to the Galaxy instance >>> referenced above >>> and pointing your browser to the following link. >>> >>> main.g2.bx.psu.edu/history/view?id=e9709e1ba7514892 >>> ----------------------------------------------------------------------------- >>> The user 'm.p.villerius(a)lumc.nl' provided the following information: >>> >>> Uploaded a .sam file, uploaded my reference file and tried a sam to >>> bam conversion. >>> I also have an other error on my local Galaxy install -> >>> ################### >>> Traceback (most recent call last): >>> File "/usr/local/galaxy_dist/tools/samtools/sam_to_bam.py", line >>> 113, in >>> if __name__=="__main__": __main__() >>> File "/usr/local/galaxy_dist/tools/samtools/sam_to_bam.py", line >>> 103, in __main__ >>> shutil.move( sorted_bam_file, options.output1 ) >>> File "/usr/lib/python2.6/shutil.py", line 264, in move >>> copy2(src, real_dst) >>> File "/usr/lib/python2.6/shutil.py", line 99, in copy2 >>> copyfile(src, dst) >>> File "/usr/lib/python2.6/shutil.py", line 52, in copyfile >>> fsrc = open(src, 'rb') >>> IOError: [Errno 2] No such file or directory: '/tmp/381.1.all.q/ >>> tmpJzAOLW.bam' >>> ###################### >>> Same file and reference? >>> All works fine on command line. >>> ----------------------------------------------------------------------------- >>> job id: 855615 >>> tool id: sam_to_bam >>> ----------------------------------------------------------------------------- >>> job command line: >>> python /galaxy/home/g2main/galaxy_main/tools/samtools/sam_to_bam.py >>> --input1=/galaxy/home/g2main/galaxy_main/database/files/001/078/ >>> dataset_1078112.dat --dbkey=? --ref_file=/galaxy/home/g2main/ >>> galaxy_main/database/files/001/078/dataset_1078114.dat --output1=/ >>> galaxy/home/g2main/galaxy_main/database/tmp/job_working_directory/ >>> 855615/galaxy_dataset_1078127.dat --index_dir=/galaxy/home/g2main/ >>> galaxy_main/tool-data >>> ----------------------------------------------------------------------------- >>> job stderr: >>> /bin/sh: line 1: 20580 Segmentation fault samtools view -bt / >>> space/g2main/dataset_1078114.dat -o /space/g2main/tmpM7xmZe /galaxy/ >>> home/g2main/galaxy_main/database/files/001/078/dataset_1078112.dat >>> 2> /dev/null >>> /bin/sh: line 1: 20583 Aborted samtools sort /space/ >>> g2main/tmpM7xmZe /space/g2main/tmpmvKLRC 2> /dev/null >>> Traceback (most recent call last): >>> File "/galaxy/home/g2main/galaxy_main/tools/samtools/ >>> sam_to_bam.py", line 113, in <module> >>> if __name__=="__main__": __main__() >>> File "/galaxy/home/g2main/galaxy_main/tools/samtools/ >>> sam_to_bam.py", line 103, in __main__ >>> shutil.move( sorted_bam_file, options.output1 ) >>> File "/usr/lib/python2.5/shutil.py", line 199, in move >>> copy2(src,dst) >>> File "/usr/lib/python2.5/shutil.py", line 91, in copy2 >>> copyfile(src, dst) >>> File "/usr/lib/python2.5/shutil.py", line 46, in copyfile >>> fsrc = open(src, 'rb') >>> IOError: [Errno 2] No such file or directory: '/space/g2main/ >>> tmpmvKLRC.bam' >>> >>> ----------------------------------------------------------------------------- >>> job stdout: >>> >>> ----------------------------------------------------------------------------- >>> job info: >>> None >>> ----------------------------------------------------------------------------- >>> job traceback: >>> None >>> ----------------------------------------------------------------------------- >>> (This is an automated message). >>> _______________________________________________ >>> galaxy-bugs mailing list >>> galaxy-bugs(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-bugs >> > >

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