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by Fuchs, Tania 24 Mar '11

24 Mar '11

Hello, I worked on my home computer with Galaxy online and next day when I came to the lab I hoped to be able to access everything I did at home through history, but it does not show up in history. I was logged in both times into my account. What did I do wrong? Thanks! Tania

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Re: [galaxy-user] postgreSQL 9.0.3 / JSONDecodeError error
by Dannon Baker 24 Mar '11

24 Mar '11

Sure, all you need to do is update to at least that revision, you can do that with: % hg pull -u -r 89190bcd1ccf http://bitbucket.org/galaxy/galaxy-central/ On Mar 24, 2011, at 4:58 AM, Vincent Le Texier wrote: > Hello Dannon, > Thanks for your answer. So could you tell me when this issue will be resolved ? Can I apply a patch now and how ? > I am facing problem with galaxy-reports and mysql (date_trunc of Postgresql), so it would be better for me to use postgreSQL 9. > Vincent > > Le 3/22/11 6:13 PM, Dannon Baker a écrit : >> Vincent, >> >> This issue should be resolved after changeset 5074:89190bcd1ccf, available in the galaxy-central repository. This change will also be available in the near future in the galaxy-dist repository. >> >> Thanks! >> >> Dannon >> >> >> >> On Mar 22, 2011, at 12:59 PM, Vincent Le Texier wrote: >> >>> Hello everyone, >>> I am having trouble to save/edit a workflow with postgreSQL 9.0.3. >>> (It works fine if I use MySQL) >>> >>> Any idea of the problem ? >>> >>> I get the following error (JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)) : >>> >>> >>> URL: http://localhost:8080/workflow >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond >>> app_iter = self.application(environ, detect_start_response) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ >>> environ, self.app) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output >>> app_iter = application(environ, replacement_start_response) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ >>> return self.application(environ, start_response) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ >>> return self.application(environ, start_response) >>> File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ >>> body = method( trans, **kwargs ) >>> File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/workflow.py', line 114 in index >>> return self.list( trans ) >>> File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 84 in decorator >>> return func( self, trans, *args, **kwargs ) >>> File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/workflow.py', line 139 in list >>> .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py', line 1267 in all >>> return list(self) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py', line 1422 in instances >>> rows = [process[0](context, row) for row in fetch] >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py', line 2032 in main >>> return _instance(row, None) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1729 in _instance >>> populate_state(state, dict_, row, isnew, only_load_props) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1614 in populate_state >>> populator(state, dict_, row, isnew=isnew, **flags) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py', line 762 in execute >>> dict_[key] = _instance(row, None) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1729 in _instance >>> populate_state(state, dict_, row, isnew, only_load_props) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1614 in populate_state >>> populator(state, dict_, row, isnew=isnew, **flags) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py', line 781 in execute >>> _instance(row, result_list) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1729 in _instance >>> populate_state(state, dict_, row, isnew, only_load_props) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1614 in populate_state >>> populator(state, dict_, row, isnew=isnew, **flags) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py', line 120 in new_execute >>> dict_[key] = row[col] >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py', line 1348 in __getitem__ >>> return self.__parent._get_col(self.__row, key) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py', line 1620 in _get_col >>> return processor(row[index]) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/types.py', line 288 in process >>> return self.process_result_value(value, dialect) >>> File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/model/custom_types.py', line 32 in process_result_value >>> return json_decoder.decode( str( value ) ) >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py', line 402 in decode >>> File '/data-ddn/home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py', line 420 in raw_decode >>> JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0) >>> -- >>> Vincent Le Texier >>> Senior Software Engineer >>> Synergie Lyon Cancer >>> Leon Berard Center, Cheney C >>> 28, rue Laennec >>> 69373 LYON Cedex 08 >>> +33 4 26 55 67 85 >>> >>> letexier(a)lyon.fnclcc.fr >>> ___________________________________________________________ >>> 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/ > > > -- > Vincent Le Texier > Senior Software Engineer > Synergie Lyon Cancer > Leon Berard Center, Cheney C > 28, rue Laennec > 69373 LYON Cedex 08 > +33 4 26 55 67 85 > letexier(a)lyon.fnclcc.fr >

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GFF3 and metagenome data?
by Thomas Haverkamp 24 Mar '11

24 Mar '11

Hi all, has anybody an idea how to do the following in galaxy? I have short (400bp) metagenome reads and I have used meta-Genemark to find protein coding regions in the unassembled reads. Meta-Genemark outputs a GFF3 file (you find a sample at the bottom of the post). I saw that Galaxy has a tool to fetch sequence from a genome file using a GFF format file: "Extract Genomic DNA<http://main.g2.bx.psu.edu/tool_runner?tool_id=Extract+genomic+DNA+1>using coordinates from assembled/unassembled genomes ". I would like to use that tool, if possible. The problem is however that I get the following error: Unspecified genome build, click the pencil icon in the history item to set the genome build. Of course I have no genome, so I am a bit stuck and I have no clue on how to use the coordinates in my GFF file to extract those regions from my metagenome reads. Anybody an idea for a proper workflow? Thomas GFF3 output: ##source-version GeneMark.hmm_PROKARYOTIC 2.7d ##date Thu Mar 24 06:15:18 2011 ##Sequence file name: ghm.mfa ##Model file name: /home/genmark/public_html/metagenome/Prediction/bin_MetaGeneMark/MetaGeneMark_v1.mod FV4B4XA01C8BBF GeneMark.hmm gene 1 513 . + 0 gene_id 1 FV4B4XA01D6PDN GeneMark.hmm gene 2 334 . + 0 gene_id 2 FV4B4XA01DC6SS GeneMark.hmm gene 1 390 . - 0 gene_id 3 FV4B4XA01AOJUF GeneMark.hmm gene 2 400 . - 0 gene_id 4 FV4B4XA01CMP07 GeneMark.hmm gene 1 465 . + 0 gene_id 5 FV4B4XA01CIPQZ GeneMark.hmm gene 1 228 . + 0 gene_id 6 FV4B4XA01DWJZ1 GeneMark.hmm gene 1 459 . - 0 gene_id 7 FV4B4XA01AUE58 GeneMark.hmm gene 237 488 . + 0 gene_id 8 FV4B4XA01C56SJ GeneMark.hmm gene 1 309 . + 0 gene_id 9 FV4B4XA01C56SJ GeneMark.hmm gene 321 422 . + 0 gene_id 10 FV4B4XA01A3DSA GeneMark.hmm gene 3 143 . + 0 gene_id 11

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Re: [galaxy-user] downstream analysis of cuffdiff out put
by Jeremy Goecks 23 Mar '11

23 Mar '11

Jagat, Please send queries such as these to the galaxy-user mailing list (cc'd); there are many users on the list who can contribute to this discussion, and there are many additional users that will benefit from this discussion. > I was wondering if you can point me to a documentation or URL to guide how to perform the downstream analysis once we have cuffdiff out put. In general, I agree that tools are needed to further process cufflinks/compare/diff outputs, but I'm not aware of any that are publicly available. Let's open this issue up for discussion and see if we can reach a consensus about tools might be useful. Everyone, please feel free to contribute ideas/tools; note that the Galaxy Tool Shed is a nice place for sharing tools you've built for Galaxy: http://community.g2.bx.psu.edu/ > Just like any mRNA-seq experiment to achieve following objectives: > > 1. Reconstruct all transcripts of a particular gene and corresponding Cuffdiff significantly expressed transcripts as called by cuffdiff. > 2. What are different isoforms > 3. Location of splicing > > From various output files which unique ID can be matched from one file say Cuffdiff.expr (transcript/ isoform/Splicing) to other file - transcript.gtf corresponding to each sample or combined GTF file. > I've got a script that does this for the cuffdiff isoform expression testing file and a GTF file; I'll wrap it up and add it to Galaxy in the next couple weeks. It would probably be useful to have similar scripts for the other expression testing files as well. Also, it would be nice to be able to take the FPKM values generated by Cuffdiff and attach them to their respective transcripts as attributes. Best, J.

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BED-to-GFF: option for gff3 format
by Karen Tang 23 Mar '11

23 Mar '11

Hi Galaxy developers, Any plans on adding a gff3 format option to BED-to-GFF? I found a BED-to-GFF3 converter at the Rätsch lab's instance of Galaxy (http://galaxy.tuebingen.mpg.de/) Any plans on making this converter more widely available? Karen :) Dept of Plant Biology University of Minnesota

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fastq / nucleotides distribution graph
by Christophe Klopp 22 Mar '11

22 Mar '11

Hi, Nucleotide distribution is much easier to read when it is drawn as lines : http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/good_sequence_short_f… instead of bars : http://main.g2.bx.psu.edu/static/fastx_icons/fastq_nucleotides_distribution… Is there a way to produce a line graph in http://main.g2.bx.psu.edu/ ? Cheers Christophe -- ==================================================================== = Christophe KLOPP BIA INRA Toulouse 31326 Castanet-Tolosan = = Tel: 33 5 61 28 50 36 Email: christophe.klopp(a)toulouse.inra.fr = = http://www.sigenae.org/ = = http://bioinfo.genotoul.fr/ = ====================================================================

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postgreSQL 9.0.3 / JSONDecodeError error
by Vincent Le Texier 22 Mar '11

22 Mar '11

Hello everyone, I am having trouble to save/edit a workflow with postgreSQL 9.0.3. (It works fine if I use MySQL) Any idea of the problem ? I get the following error (*JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)*) : URL: http://localhost:8080/workflow File '/data-ddn/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/workflow.py', line 114 in index return self.list( trans ) File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 84 in decorator return func( self, trans, *args, **kwargs ) File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/workflow.py', line 139 in list .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py', line 1267 in all return list(self) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py', line 1422 in instances rows = [process[0](context, row) for row in fetch] File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py', line 2032 in main return _instance(row, None) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1729 in _instance populate_state(state, dict_, row, isnew, only_load_props) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1614 in populate_state populator(state, dict_, row, isnew=isnew, **flags) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py', line 762 in execute dict_[key] = _instance(row, None) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1729 in _instance populate_state(state, dict_, row, isnew, only_load_props) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1614 in populate_state populator(state, dict_, row, isnew=isnew, **flags) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py', line 781 in execute _instance(row, result_list) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1729 in _instance populate_state(state, dict_, row, isnew, only_load_props) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1614 in populate_state populator(state, dict_, row, isnew=isnew, **flags) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py', line 120 in new_execute dict_[key] = row[col] File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py', line 1348 in __getitem__ return self.__parent._get_col(self.__row, key) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py', line 1620 in _get_col return processor(row[index]) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/types.py', line 288 in process return self.process_result_value(value, dialect) File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/model/custom_types.py', line 32 in process_result_value return json_decoder.decode( str( value ) ) File '/data-ddn/home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py', line 402 in decode File '/data-ddn/home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py', line 420 in raw_decode JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0) -- Vincent Le Texier Senior Software Engineer Synergie Lyon Cancer Leon Berard Center, Cheney C 28, rue Laennec 69373 LYON Cedex 08 +33 4 26 55 67 85 letexier(a)lyon.fnclcc.fr

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Upload file size and user authorization
by Paul-Michael Agapow 22 Mar '11

22 Mar '11

Two questions, either of which may belong more on the developers list. But lets try here first: 1. As we migrate services to Galaxy, a stakeholder expressed concern at uploading large datafiles of "several gigabytes". Given that we can require users to upload from an ftp site or something similar, does anyone have experience with how well this works with gigabyte-size files? I figure I can always write a tool to upload masses of data via a slow but robust method, but it would be good to know if this is required. 2. Similarly, someone else wanted to know if Galaxy authorization could be plugged into another system, such as Active Directory. Any pointers on this, or will I have to cut some code? thanks ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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LASTZ: Controlling Length of Hits
by JASON G. BANKERT 22 Mar '11

22 Mar '11

We're trying to only get hits of certain lengths. Is there a setting to use that sets the minimum length for each hit?

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Recall: Upload file size and user authorization
by Paul-Michael Agapow 22 Mar '11

22 Mar '11

Paul-Michael Agapow would like to recall the message, "[galaxy-user] Upload file size and user authorization". ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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