March 2011 - galaxy-user - lists.galaxyproject.org

labeling sections of the history
by Ryan Golhar 31 Mar '11

31 Mar '11

I'm analyzing a bunch of datasets in a single history and the number of history items is getting a little confusing. Is it possible to attached a label a group of history items, or collapse a group of history items on the display? I don't suppose it is, but it would be a nice feature... -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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Re: [galaxy-user] Trouble with RNAseq analysis
by Jeremy Goecks 30 Mar '11

30 Mar '11

Cristian, The ">" is a formatting character; what needs to match is the string after the ">" in the genome file and the entries in the contig column of your GTF. Your GTF is quite different that your genome file; your genome file has 10 contigs labeled by number, but your GTF has many, many contig names labelled by numbers and names. For Cufflinks to work, you can either (a) turn off bias correction or (b) restrict entries in your GTF to those that match your reference genome. Finally, please reply all to emails so that all emails remain on list for archival and community purposes. Thanks, J. On Mar 30, 2011, at 12:02 PM, Cristian Rojas wrote: > Thanks Jeremy. But in genomes fasta files very often any chromosome represents a > sequence followed by ">". Then, it is no possible match contig names in GTF with > ">" names in Genome fasta. What must I do? > Cristian > > > > ----- Mensaje original ---- > De: Jeremy Goecks <jeremy.goecks(a)emory.edu> > Para: Cristian Rojas <cristianrojasbr(a)yahoo.com.ar> > CC: galaxy-user(a)lists.bx.psu.edu > Enviado: miércoles, 30 de marzo, 2011 12:53:50 > Asunto: Re: [galaxy-user] Trouble with RNAseq analysis > > Cristian, > > The contig names in your GTF file don't match those in your reference (fasta) > file. In order for Cufflinks to use a reference GTF, its contigs names must > match those in your reference genome. > > Best, > J. > > On Mar 30, 2011, at 11:31 AM, Cristian Rojas wrote: > >> Thanks Jeremy. I did it. >> Cristian >> >> >> >> ----- Mensaje original ---- >> De: Jeremy Goecks <jeremy.goecks(a)emory.edu> >> Para: Cristian Rojas <cristianrojasbr(a)yahoo.com.ar> >> CC: galaxy-user(a)lists.bx.psu.edu >> Enviado: miércoles, 30 de marzo, 2011 12:02:47 >> Asunto: Re: [galaxy-user] Trouble with RNAseq analysis >> >> Cristian, >> >> Please share your history with me (History Options --> Share/Publish --> Share > >> with User --> my email) and I'll take a look. >> >> Thanks, >> J. >> >> On Mar 30, 2011, at 10:48 AM, Cristian Rojas wrote: >> >>> Hi everybody, I am trying to analyze the differential expression between two >>> RNAseq samples. But I found many troubles aligning my reads. I will describe >>> what I did. First I groomed the FastQ files (2). Then I uploaded the Sorghum >>> genome and aligned the reads to it with Tophat. Aftter that, I tried to use >>> Cufflink with the BAM file of Tophat, using as annotation file an uploaded GTF >> >> >>> file and the Sorghum genome, but I received an error message in the three >>> outputs of Cufflink. I tried to align against new brand Maize genome (now at >>> Galaxy), and the same messages. I also converted the BAM file to SAM, but the > >>> same. Any advice? What was wrong? >>> Thanks in advance. >>> Cristian >>> >>> >>> ___________________________________________________________ >>> 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/

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Re: [galaxy-user] Trouble with RNAseq analysis
by Jeremy Goecks 30 Mar '11

30 Mar '11

Cristian, The contig names in your GTF file don't match those in your reference (fasta) file. In order for Cufflinks to use a reference GTF, its contigs names must match those in your reference genome. Best, J. On Mar 30, 2011, at 11:31 AM, Cristian Rojas wrote: > Thanks Jeremy. I did it. > Cristian > > > > ----- Mensaje original ---- > De: Jeremy Goecks <jeremy.goecks(a)emory.edu> > Para: Cristian Rojas <cristianrojasbr(a)yahoo.com.ar> > CC: galaxy-user(a)lists.bx.psu.edu > Enviado: miércoles, 30 de marzo, 2011 12:02:47 > Asunto: Re: [galaxy-user] Trouble with RNAseq analysis > > Cristian, > > Please share your history with me (History Options --> Share/Publish --> Share > with User --> my email) and I'll take a look. > > Thanks, > J. > > On Mar 30, 2011, at 10:48 AM, Cristian Rojas wrote: > >> Hi everybody, I am trying to analyze the differential expression between two >> RNAseq samples. But I found many troubles aligning my reads. I will describe >> what I did. First I groomed the FastQ files (2). Then I uploaded the Sorghum >> genome and aligned the reads to it with Tophat. Aftter that, I tried to use >> Cufflink with the BAM file of Tophat, using as annotation file an uploaded GTF > >> file and the Sorghum genome, but I received an error message in the three >> outputs of Cufflink. I tried to align against new brand Maize genome (now at >> Galaxy), and the same messages. I also converted the BAM file to SAM, but the >> same. Any advice? What was wrong? >> Thanks in advance. >> Cristian >> >> >> ___________________________________________________________ >> 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/

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Trouble with RNAseq analysis
by Cristian Rojas 30 Mar '11

30 Mar '11

Hi everybody, I am trying to analyze the differential expression between two RNAseq samples. But I found many troubles aligning my reads. I will describe what I did. First I groomed the FastQ files (2). Then I uploaded the Sorghum genome and aligned the reads to it with Tophat. Aftter that, I tried to use Cufflink with the BAM file of Tophat, using as annotation file an uploaded GTF file and the Sorghum genome, but I received an error message in the three outputs of Cufflink. I tried to align against new brand Maize genome (now at Galaxy), and the same messages. I also converted the BAM file to SAM, but the same. Any advice? What was wrong? Thanks in advance. Cristian

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{Disarmed} extra hack to get own database connection to work?
by Perdacher,Martin 30 Mar '11

30 Mar '11

hello galaxy-community, we stored a lot of peak-information in a database. to import these files into galaxy, i read the DataConnectionProtocol (https://bitbucket.org/galaxy/galaxy-central/wiki/DataSources) and i also took a look at the biomart.xml example (https://bitbucket.org/galaxy/galaxy-dist/src/8729d2e29b02/tools/data_source…) biomart does exactly what i want. here is my full tool configuration xml-file: <tool id="regionDb" name="RegionDb-Import"> <description>Import from regionDb</description> <command interpreter="python">../data_source/data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://localhost:8888/index.html" check_values="false" method="get"> <display>Display-Text</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> <param name="tool_id" type="hidden" value="regionDb" /> </inputs> <request_param_translation> <request_param galaxy_name="URL" remote_name="URL" missing=""/> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" /> <request_param galaxy_name="name" remote_name="name" missing="Biomart test query" /> </request_param_translation> <outputs> <data name="regionDb File" format="bed" label="regionDb import" /> </outputs> <help> **What it does** import ... </help> </tool> content of http://localhost:8888/index.html: <form method="POST" type="text" action="http://galaxy/tool_runner/regionDb?type=text&name=new%20history%20entry&URL…" > <input type="submit" value="Send to Galaxy"/> </form> i also tried a different action="http://galaxy/tool_runner?tool_id=regionDb&type=text&name=new%20history%20e…" with the same error message (shown below). what actually works is, if i try to receive biomart data with this request. <form method="POST" type="text" action="http://gen43/galaxy/tool_runner/biomart?type=text&name=ne%20history%20entry…" > <input type="submit" value="Send to Galaxy"/> </form> my question is: was there some extra hack to get the biomart tool to run? i found some lines in the lib/galaxy/web/controllers/tool_runner.py which confirm that assumption: #Hack to get biomart to work, ideally, we could pass tool_id to biomart and receive it back @web.expose def biomart(self, trans, tool_id='biomart', **kwd): """Catches the tool id and redirects as needed""" return self.index(trans, tool_id=tool_id, **kwd) Server Error URL: http://galaxy/tool_runner/regionDb?type=text&name=new%20history%20entry&URL… Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:109 in __call__ >> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:145 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.controllers.tool_runner:27 in regionDb >> return self.index(trans, tool_id=tool_id, **kwd) Module galaxy.web.controllers.tool_runner:75 in index >> template, vars = tool.handle_input( trans, params.__dict__ ) Module galaxy.tools:933 in handle_input >> _, out_data = self.execute( trans, incoming=params ) Module galaxy.tools:1225 in execute >> return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history ) Module galaxy.tools.actions:291 in execute >> wrap_values( tool.inputs, params ) Module galaxy.tools.actions:154 in wrap_values >> input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming ) KeyError: 'GALAXY_URL' extra data CGI Variables CONTENT_LENGTH '-1' CONTENT_TYPE 'application/x-www-form-urlencoded' HTTP_ACCEPT 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET 'ISO-8859-1,utf-8;q=0.7,*;q=0.7' HTTP_ACCEPT_ENCODING 'gzip,deflate' HTTP_ACCEPT_LANGUAGE 'en-us,en;q=0.5' HTTP_CONNECTION 'Keep-Alive' HTTP_COOKIE 'galaxysession=c6ca0ddb55be603af8ffade046cb8ca7fe7a18f326db29b947c846a3b24831e1362e15c491e90b43' HTTP_HOST 'gen43' HTTP_REFERER 'http://localhost:8888/index2.php?GALAXY_URL=http%3A//gen43/galaxy/tool_runn…' HTTP_REMOTE_USER 'perdacher(a)genau.at' HTTP_USER_AGENT 'Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.3) Gecko/20100401 Firefox/3.6.3' HTTP_VIA '1.1 gen43.imp.univie.ac.at' PATH_INFO '/tool_runner/regionDb' QUERY_STRING 'type=text&name=new%20history%20entry&URL=http://localhost:8888/getfile.php' REMOTE_ADDR '10.42.111.27' REQUEST_METHOD 'POST' SCRIPT_NAME '/galaxy' SERVER_NAME 'gen43.imp.univie.ac.at' SERVER_PORT '9191' SERVER_PROTOCOL 'HTTP/1.1' Configuration __file__ '/projects/solexadst/serverData/galaxy-devel/universe_wsgi.webapp.ini' admin_users 'tamir(a)genau.at' apache_xsendfile 'False' brand 'GenAu-Epx Development!!!' cookie_path '/galaxy' debug 'TRUE' enable_api 'True' enable_job_running 'False' enable_pages 'True' here '/projects/solexadst/serverData/galaxy-devel' log_level 'DEBUG' new_user_dataset_access_role_default_private 'True' remote_user_logout_href '/logout' remote_user_maildomain 'genau.at' require_login 'True' set_metadata_externally 'True' static_cache_time '360' static_dir '/projects/solexadst/serverData/galaxy-devel/static/' static_enabled 'True' static_favicon_dir '/projects/solexadst/serverData/galaxy-devel/static/favicon.ico' static_images_dir '/projects/solexadst/serverData/galaxy-devel/static/images' static_scripts_dir '/projects/solexadst/serverData/galaxy-devel/static/scripts/' static_style_dir '/projects/solexadst/serverData/galaxy-devel/static/june_2007_style/blue' upstream_gzip 'False' use_interactive 'False' use_remote_user 'True'

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Combining the paired reads from Illumina run
by Surya Saha 30 Mar '11

30 Mar '11

Hi, I have two fastq files with the forward(/1) and reverse(/2) paired reads. The reads are not in same order in either file, some pairs are absent/missing and the files are 8 GB each with abt 30 mill reads each. I am trying to pull out all the paired reads for which both fwd and rev exist. Can I use a combination of fastq tools in Galaxy to do this? Thanks! -Surya

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Re: [galaxy-user] output file for bowtie suppressed reads (-m/--max)
by karlerhard＠berkeley.edu 30 Mar '11

30 Mar '11

Hi all, I'm running into a problem with the output from bowtie mapping for illumina reads. I've been testing bowtie with a subset of my illumina reads with the intention of estimating the percent of *uniquely* mapping reads represented in my library, ie., non-repetitive reads. I've run bowtie on this small subset (~2000 reads) with and without the -m option specified with n=1 and I get many fewer mappable reads with -m specified, but if I ask galaxy to "Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)", the file always comes up empty. Where did all those suppressed reads go? thanks for any help you can offer, karl

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Re: [galaxy-user] Combining the paired reads from Illumina run
by Surya Saha 29 Mar '11

29 Mar '11

Hi Tony, Yes, that should work too. I have written up a BioPerl hack that indexes the reads and pulls out the pairs that is chugging away right now. If that does not work out somehow, I will give your idea a shot. Thanks! Best, Surya On Tue, Mar 29, 2011 at 4:20 PM, Barbet,Anthony F <barbet(a)ufl.edu> wrote: > Can you not do fastq join on the 2 files, fastq filter for the single (same > max and min bases) full length combined size (and quality if you want), then > fastq splitter? > > Tony > ________________________________________ > From: galaxy-user-bounces(a)lists.bx.psu.edu [ > galaxy-user-bounces(a)lists.bx.psu.edu] On Behalf Of Surya Saha [ > ss2489(a)cornell.edu] > Sent: Tuesday, March 29, 2011 4:00 PM > To: Anton Nekrutenko > Cc: galaxy-user(a)lists.bx.psu.edu > Subject: Re: [galaxy-user] Combining the paired reads from Illumina run > > Hi Anton, > > Thank you for the tip. The sequence names do end in /1 and /2 but that can > be fixed using Manipulate FASTQ tool, right? > > -Surya > > On Tue, Mar 29, 2011 at 3:46 PM, Anton Nekrutenko <anton(a)bx.psu.edu > <mailto:anton@bx.psu.edu>> wrote: > > > > You can try converting fastq to tabular (NGS: QC and Manipulation). > Jointing (Join, Subtract and Group) the two files on ids (provided they do > not have /1 and /2). Splitting into two files with cut (Text manipulation), > and going back into fastq with tabulat-to-fastq (NGS: QC and Manipulation). > With 30 mil reads this will likely take some time though. > > Thanks, > > anton > > > > On Mar 29, 2011, at 11:38 AM, Surya Saha wrote: > > > > These are Illumina reads > > > > -S. > > > > On Tue, Mar 29, 2011 at 11:37 AM, Anton Nekrutenko <anton(a)bx.psu.edu > <mailto:anton@bx.psu.edu>> wrote: > >> > >> Are these illumina or solid reads? > >> > >> Tx, > >> > >> anton > >> > >> > >> On Mar 29, 2011, at 11:29 AM, Surya Saha wrote: > >> > >> > Hi, > >> > > >> > I have two fastq files with the forward(/1) and reverse(/2) paired > reads. The reads are not in same order in either file, some pairs are > absent/missing and the files are 8 GB each with abt 30 mill reads each. > >> > > >> > I am trying to pull out all the paired reads for which both fwd and > rev exist. Can I use a combination of fastq tools in Galaxy to do this? > >> > > >> > Thanks! > >> > > >> > -Surya ___________________________________________________________ > >> > The Galaxy User list should be used for the discussion of > >> > Galaxy analysis and other features on the public server > >> > at usegalaxy.org<http://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/ > >> > >> Anton Nekrutenko > >> http://nekrut.bx.psu.edu > >> http://usegalaxy.org > >> > >> > >> > > > > > > Anton Nekrutenko > > http://nekrut.bx.psu.edu > > http://usegalaxy.org > > > > > >

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Re: [galaxy-user] upload of Zea mays genome to galaxy?
by Kelly Vincent 29 Mar '11

29 Mar '11

Karl, Zea mays is now available as a general database/build label. The full value is "Zea_mays_B73_RefGen_v2", but searching for any part of that or "maize" will bring it up. Thanks for using Galaxy. Regards, Kelly On Mar 6, 2011, at 12:09 PM, karlerhard(a)berkeley.edu wrote: > > Oh, I didn't see your email before I sent that last one. That makes > sense, thanks for the confirmation! > > > >> Karl, >> >> Zea mays is available for use under the NGS tools. I did notice that >> it is not available as one of Galaxy's genome/database labels (such >> as >> on upload), but this is an oversight that will be corrected ASAP. You >> can still use the mapping tools in the meantime. >> >> Regards, >> Kelly >> >> >> On Mar 5, 2011, at 3:49 PM, karlerhard(a)berkeley.edu wrote: >> >>> >>> Hello, >>> >>> I'm interested in using the galaxy tools to analyze some >>> transcriptome >>> libraries I made of maize seedlings. Would it be possible to upload >>> the >>> maize reference genome to the galaxy browser? >>> >>> It's available at the following website: >>> >>> http://ftp.maizesequence.org/current/ >>> >>> Hope this can be done, would be really exciting! >>> >>> Thanks, >>> >>> Karl >>> >>> ___________________________________________________________ >>> 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/ >> >> > >

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HMM tool in Galaxy??
by Surya Saha 29 Mar '11

29 Mar '11

Hi, Are there any tools like HMMER (2.3.2 or 3.0) available on Galaxy to run a HMM on a DNA or protein sequence? I was not able to find any. Thanks -Surya

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