galaxy-dev January 2014

galaxy-dev@lists.galaxyproject.org

86 participants
131 discussions

Share history (or change history ownership) through the Galaxy API?
by Daniel Sobral 15 Jan '14

15 Jan '14

Hello, Is it possible to share a history with a user (by user name) or change ownership through the Galaxy API? I didn't see any example doing this. Thanks. Cheers, Daniel -- Daniel Sobral, Bioinformatics Unit Instituto Gulbenkian de Ciência

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Re: [galaxy-dev] after update unable to login
by John Chilton 15 Jan '14

15 Jan '14

On Wed, Jan 15, 2014 at 11:30 AM, Briand, Sheldon <Sheldon.Briand(a)ssc-spc.gc.ca> wrote: > Hi John, > > Thanks for getting back to me. > > My use_remote_user is set to false. Yes nginx is setup as you suggest. My proxy setup worked before I updated. I have already tested talking to galaxy directly and the problem remains. I meant to mention that in my first message. I tried putting use_pbkdf2 in my configuration file and the galaxy server will not start. > > I noticed there is activation code for user accounts in the new the universe_wsgi.ini file. Could this be buggy? Have you enabled the activation stuff - is user_activation_on set in universe_wsgi.ini? What database are you using. When you added "use_pbkdf2=False" to the configuration file - did you add it to the app:main section? -John > > Thanks, > -Sheldon > > -----Original Message----- > From: jmchilton(a)gmail.com [mailto:jmchilton@gmail.com] On Behalf Of John Chilton > Sent: Wednesday, January 15, 2014 11:50 AM > To: Briand, Sheldon > Subject: Re: [galaxy-dev] after update unable to login > > This is unfortunate, sorry about the problems. > > There were some changes to the authentication stuff as part of that update - but this is the first report of problems I think. Just to understand your setup - Galaxy is doing the authentication right - ( use_remote_user is not set to true in your universe_wsgi.ini )? > > So likely your nginx is setup to proxy requests say from port 80 to > 8080 or something like that? Did you configure this? The one thing I would try is to talk to Galaxy directly by pointing your web browser at port localhost:8080 or whatever (you may need to setup SSH tunnels if this is a remote server and not your desktop). I would like to be sure this is a problem with Galaxy and not the nginx configuration - this would confirm that. > > If it works to talk to Galaxy directly, somehow your proxy is misconfigured I think - not sure how to resolve that but it would be good to know. Otherwise the problem is with Galaxy's configuration - again not sure how to resolve that but it would be good to know. In this second case, the next I would try is setting use_pbkdf2 to False in universe_wsgi.ini restart and see if you an login then - this shouldn't matter but this problem shouldn't be occurring at all :(. > > Let me know if you make any progress. > > -John > > > On Tue, Jan 14, 2014 at 12:20 PM, Briand, Sheldon <Sheldon.Briand(a)ssc-spc.gc.ca> wrote: >> Hi, >> >> >> >> I've tried reinstalling from scratch in case there was a problem when >> I updated the last time. I am still having trouble logging in. The >> "broken pipe" error message has nothing to do with the failed logins. >> >> >> >> The logins are successful as far as authentication goes ( I get no >> error message, if I put in the wrong password I do get an error message ). >> However, after login the user is redirected to the last page they were >> on and does not appear to be logged in (no history, clicking on user >> gives the login or register options). >> >> >> >> If I sent logins so that anonymous logins are not allowed I always get >> sent back to the login page. >> >> >> >> I've looked through the archives for a similar problem and not found >> anything relevant. I've tried using the stable version of the latest >> build as well as the development version. No joy on either. >> >> >> >> Is there something I've missed? >> >> >> >> Thanks, >> >> -Sheldon >> >> >> >> >> >> >> >> From: Briand, Sheldon >> Sent: Thursday, January 09, 2014 2:26 PM >> To: 'galaxy-dev(a)lists.bx.psu.edu' >> Subject: after update unable to login >> >> >> >> Hi, >> >> >> >> I had a working local install of galaxy. I wanted to install gatk2 >> and wasn't able to install it. I upgraded and I am now unable to log >> in to galaxy. >> >> >> >> I should note that I am relatively new to galaxy. I had a previously >> logged in admin session (before the update). So I am able to see that >> galaxy (after the update) believes, by checking the manage users admin >> page, I have newly logged in on another browser. The session, >> however, shows no indication that I am logged in other than not showing an error. Usually I >> end up back at the last page I was viewing before I logged in. Clicking on >> user doesn't show me as logged in, I have no history, and there is no >> admin tab. >> >> >> >> I have a nginx proxy setup. >> >> >> >> Paster.log shows a "Broken pipe" error when I login from nginx. I show no >> error when I log in directly via the galaxy server. The results are >> the same. I upgraded from database version 115 to version 117. >> >> >> >> Is there an easy fix? >> >> >> >> Thanks, >> >> -Sheldon >> >> >> >> Sheldon Briand >> >> NRC Research Computing Support Analyst >> >> Research Computing Support / Soutien Informartique a la Recherche >> >> Operations, Science Portfolio / Operations, Portefeuil des sciences >> >> SSC-NRC / SPC-CNRC >> >> Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford >> >> Halifax, NS B3H 3Z1 >> >> 902 426-1677 >> >> sheldon.briand(a)ssc-spc.gc.ca >> >> >> >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/

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after update unable to login
by Briand, Sheldon 15 Jan '14

15 Jan '14

Hi, I had a working local install of galaxy. I wanted to install gatk2 and wasn't able to install it. I upgraded and I am now unable to log in to galaxy. I should note that I am relatively new to galaxy. I had a previously logged in admin session (before the update). So I am able to see that galaxy (after the update) believes, by checking the manage users admin page, I have newly logged in on another browser. The session, however, shows no indication that I am logged in other than not showing an error. Usually I end up back at the last page I was viewing before I logged in. Clicking on user doesn't show me as logged in, I have no history, and there is no admin tab. I have a nginx proxy setup. Paster.log shows a "Broken pipe" error when I login from nginx. I show no error when I log in directly via the galaxy server. The results are the same. I upgraded from database version 115 to version 117. Is there an easy fix? Thanks, -Sheldon Sheldon Briand NRC Research Computing Support Analyst Research Computing Support / Soutien Informartique a la Recherche Operations, Science Portfolio / Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS B3H 3Z1 902 426-1677 sheldon.briand(a)ssc-spc.gc.ca

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Linking Data Files
by Cantarel, Brandi L. 15 Jan '14

15 Jan '14

I am a total galaxy newbie who is setting up a galaxy server for a group of internal researchers in order to do RNASeq analysis. I can see where I can upload libraries from the galaxy server, but I can’t figure out how to load the “available” data (fastqs) — to clarify instead of asking users to upload 5GB fastq files, which are already on the galaxy server, I would like for users to be able to “see” that data when setting up their pipeline without having to upload the data (ie use Get Data). Is this possible? When I search, I can only see how to do this for “Data Libraries”. Many Thanks! Brandi ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Brandi Cantarel, PhD Bioinformatics Research Scientist Baylor Institute for Immunology Research Baylor Health Care System 214-818-8673 (office) ********************************************************************** This e-mail may contain confidential and/or privileged information. This information is intended only for the use of the individual(s) and entity(ies) to whom it is addressed. If you are the intended recipient, further disclosures are prohibited without proper authorization. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden and possibly a violation of federal or state law and regulations. Baylor Health Care System, its subsidiaries, and affiliates hereby claim all applicable privileges related to this information.

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wigToBigwig error
by ruiwang.sz 15 Jan '14

15 Jan '14

Hi All, I'm having an error at this: *Dataset 18: Wig/BedGraph-to-bigWig on data 12* Tool execution generated the following error message: grep: writing output: Broken pipe grep: writing output: Broken pipe grep: writing output: Broken pipe grep: writing output: Broken pipe .. put: Broken pipe grep: writing output: Broken pipe grep: writing output: Broken pipe .. grep: writing output: Broken pipe grep: write error Error running wigToBigWig. The tool produced the following additional output: hashMustFindVal: '1' not found I searched and found this link: http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10745&S=2a335135e76c… which says that there is a naming convention difference. I followed what he did and replaced chrom=1 to chrom=chr1 etc, now it goes further, but still dies with error: line 18020168 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276760 line 18020169 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276770 line 18020170 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276780 line 18020171 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276790 line 18020172 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276800 line 18020173 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276810 line 18020174 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276820 line 18020175 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276830 line 18020176 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276840 line 18020177 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276850 line 18020178 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276860 line 18020179 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276870 line 18020180 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276880 Unrecognized line 18020181 of /tmp/t3: variableStep chr10 span=10 Error running wigToBigWig. The command line is: wigToBigWig /tmp/t3 /home/bioinfoadmin/app/galaxy-dist/tool-data/shared/ucsc/chrom/ucsc_gg4.len /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_769.dat -clip 2>&1 || echo "Error running wigToBigWig." >&2 Quite puzzled...wondering if anyone has seen it before and could give me a hand. :-) I'll really appreciate! Thanks, Rui

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Tophat2 Output file error
by Bankers, Laura A 15 Jan '14

15 Jan '14

To whom it may concern, I am a grad student at the University of Iowa using Galaxy to analyze data from an RNA-seq experiment. I have been using Tophat2 and noticed that it is not longer providing an alignment summary text file in the output, which it used to do. I was wondering if this was an error, or if there was a way to obtain that output file (as the information is incredibly useful). Thanks, Laura

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Re: [galaxy-dev] referring to tool_data_tables[] structure (John Chilton)
by Dooley, Damion 15 Jan '14

15 Jan '14

Hi John, Thansk for the feedback. Righto, I saw abundant use of "trans" in core galaxy code; and problem is I'd wanted access from a tool wrapper's python code. Basically I'm trying to get more out of .loc files, for example this field specification for blast report data: #value type subtype sort filter default min max choose name # Remember to edit tool_data_table_conf.xml for column spec! length numeric int 1 1 1 Alignment length qstart numeric int 1 1 1 Alignment start in query qend numeric int 1 1 1 Alignment end in query sstart numeric int 1 1 1 Alignment start in subject send numeric int 1 1 1 Alignment end in subject qseq text atgc 0 1 1 Aligned part of query sequence sseq text atgc 0 1 1 Aligned part of subject sequence mseq text atgc 0 1 1 Alignment, matched part pident numeric float 1 1 97 90 100 1 Percentage of identical matches ... This data is being accessed in our tool xml code via a too_data_table entry and is handily providing field lists for sorting, filtering, and searching input data. In our python code I'd like to just say blastfieldspec = app.tool_data_tables[ 'blast_report_fields' ] And then go to town on sorting, filtering, validation etc. as desired in python, using this spec. I don't want the python code to be specifying the .loc path directly (which I have to do now), I'd much rather take advantage of what tool_data_tables could provide. Our second desired use of tool_data_tables info is a case where some tools would be making use of 3rd party datasets that another tool manages. We want to set up a tool/system that manages 3rd party reference databases (e.g. for particular specialized gene "universal target" databases like Chaperonin cpn60 or Legionella mip). This system would periodically get and process fasta data online from sources listed in a .loc file. We'd process and use these databases in pulldown menus, but each of these reference database will need management through a Galaxy interface via a plugin tool I guess. Someone has done a prototype for this for database specific to NCBI. We'd target other niche data sources. I realise another hurdle is getting modified .loc file info refreshed back into galaxy without having to stop/restart the server. Hoping an extension to the tool_data_tables class could do this too. Regards, Damion ---------------------------------------------------------------------- Message: 1 Date: Fri, 10 Jan 2014 16:56:56 -0800 From: "Dooley, Damion" <Damion.Dooley(a)bccdc.ca> To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> Subject: [galaxy-dev] referring to tool_data_tables[] structure Message-ID: <7891813F3C8F424B97D8BF2E5600E51903301B88EFFD(a)VEXCCR02.phsabc.ehcnet.ca> Content-Type: text/plain; charset="us-ascii" I've seen $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] in tool xml templates. Is there a way I can access the tool_data_tables structure from python code too? I see all the initialization stuff happening in https://bitbucket.org/abrenner/galaxy-central/src/f3e736fe03df3a6dd5438c12b… But not seeing where one can access any of these app variables? Regards, Damion ------------------------------ Message: 2 Date: Fri, 10 Jan 2014 20:42:50 -0600 From: John Chilton <chilton(a)msi.umn.edu> To: "Dooley, Damion" <Damion.Dooley(a)bccdc.ca> Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> Subject: Re: [galaxy-dev] referring to tool_data_tables[] structure Message-ID: <CANwbokeUZ4KfB0+9Z9RVk0rtdMtE1iwmg+e3uo8yTUOXfbLj9w(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Just to clarify do you want to access them from Galaxy web server code or from a Galaxy tool wrapper written in Python? Nearly every part of the Galaxy source code has access to app and everything inside of it, for instance all controller methods take in a trans variable that contains a reference to app (trans.app). I suspect you want to access it from a tool wrapper though? This is not possible. If this is the case - what are you hoping to accomplish? Do you want to access to the all_fasta data table information in the example? -John

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Modifying shed_tool_conf.xml
by Cristian Alejandro Rojas 15 Jan '14

15 Jan '14

Hello All, I'm trying to personalize my own galaxy instance, I'd like to know if editing the file shed_tool_conf.xml will make inestable my galaxy instance, I'd like to move tools from one to another section but I don't know if this will affect future updates of the tools. Best, -- *Cristian Alejandro Rojas Quintero* *Estudiante Ingeniería de Sistemas * *Universidad Distrital Francisco José de Caldas* Bogotá - Colombia

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Change Tool Shed owner
by Philip Mabon 14 Jan '14

14 Jan '14

Is it possible to permanently change the owner of a Tool in the Tool Shed? Really want to transfer responsibility of my tools to others. Thanks!

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Create user error
by Nikos Sidiropoulos 14 Jan '14

14 Jan '14

Hi all, Although users were able to create accounts till recently, now the following error pops up whenever someone is trying to register as a new user after filling the fields and clicking submit. "Select the user's type and information" Is anyone familiar with this error? Bests, Nikos

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galaxy-dev January 2014