galaxy-user March 2011

galaxy-user@lists.galaxyproject.org

75 participants
96 discussions

Re: [galaxy-user] dataflow using Galaxy on Amazon EC2
by Enis Afgan 27 Mar '11

27 Mar '11

Hi Luqman, I was suggesting to visit Galaxy Main to get an idea of what is possible within Galaxy and get familiar with how tools interact with each other, what kind of input/output the expect/provide so that you could draw parallels and get a better idea of how to integrate your own tools in a local instance of Galaxy. As I mentioned earlier, you will have to create a tool wrapper as described on this page https://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial that describes (in terms Galaxy can understand) how to run the tool. Then, if the tool handles multiple steps within itself (i.e., a single command results in multiple transformations of the data), all of the handling of the dataflow will be handled just as if the tool was invoked from the command line. If one command is all that is needed to run multiple java classes (i.e., the tool is equivalent of a workflow), you may now need to create a Galaxy workflow but run your set of java classes a single Galaxy tool. In principle, if a Galaxy workflow is to be created, the data between individual steps within a workflow are passed as files that Galaxy manages. Hope this helps, Enis On Fri, Mar 25, 2011 at 9:24 PM, Luqman Hodgkinson <luqman(a)berkeley.edu>wrote: > > > > > Hi Enis, > > I went to Galaxy Main: there are many built-in tools, but I did not see how > to add my own tools. > > Currently I am using my own custom software to manage a configurable > dataflow through my Java classes. I was interested in transitioning to > Galaxy: however if I remove my custom software for the dataflow, would I > need to create a separate executable for each class? When connecting these > executables into a workflow, how is the data passed from one executable to > the other? In RAM or on disk? > > With best wishes, > Luqman > > > > > On Mar 25, 2011, at 2:27 PM, Enis Afgan wrote: > > Hi Luqman, > Take a look a my comments below. > > On Fri, Mar 25, 2011 at 5:06 PM, Luqman Hodgkinson <luqman(a)berkeley.edu>wrote: > >> >> >> >> >> Hi Enis, >> >> Thank you for your detailed reply. After playing with Galaxy, there are >> some questions I have. >> >> 1. All my Java classes are in the same project. There is only a single >> Main class. In order to use Galaxy, must each class be converted to a .jar >> file individually? If so, the disadvantage to this is then that only >> command-line parameters can be passed in. How does the data flow between the >> classes? Must each class read input from files and write input to files? >> That is, what is the nature of your type system for passing data between >> components. Can data be passed directly through RAM or must it go through >> the file system? >> >> If you are able to perform your complete analysis using a combination of > your Java classes by simply executing a single command (i.e, invoking a > single main class), the same can be achieved through Galaxy. You would > create a galaxy tool wrapper that allows Galaxy to invoke that same command > and the rest (i.e.., executing the tool) is going to be the same (i.e., the > same set of methods will get invoked and you should get the same output). > Once Galaxy invokes a tool, any form of data flow within that tool is up to > the tool itself so if the classes share data between each other, the same > will happen once they are invoked through Galaxy. > > >> 2. Provenance is very important for my workflow. The workflow will be run >> multiple times and a large number of versions will be created. These should >> be organized somewhere on the file system with timestamps and descriptions >> of the versions of the workflows that were used. How much support does >> Galaxy have for this? >> >> Galaxy keeps track of all the parameters and input data used to run a tool > or a workflow so, once the tool is integrated with Galaxy, keeping up with > the details is trivial - that's a big part of why Galaxy exists to begin > with. > > > 3. Have you seen the new Conveyor paper? >> http://www.ncbi.nlm.nih.gov/pubmed?term=21278189 My requirements are very >> similar to those addressed in this paper. However, the current version of >> Conveyor does not seem very stable: I was even unable to get their graphical >> user interface running from their Java files. What are the capabilities of >> Galaxy for this use case? >> >> Unfortunately I have not read this paper yet so I cannot comment much. > If you have not yet, I would suggest you give Galaxy Main (usegalaxy.org) > a shot and try to run some jobs and create a few workflows to get an idea of > what can be done with tools once they are integrated with Galaxy as well as > the type of data and information Galaxy keeps. That should give you a good > indication of whether available functionality can be applied in your > scenario as well. > > Enis > > > >> Sincerely, with best wishes, >> Luqman >> >> >> On Mar 25, 2011, at 10:21 AM, Enis Afgan wrote: >> >> Hi Luqman, >> Were you planning on using Galaxy CloudMan (usegalaxy.org/cloud) and >> integrating your tool (i.e., Java classes) into the Galaxy that it deploys >> or simply starting a new EC2 instance and setting up a Galaxy instance from >> scratch? >> Either way, I would suggest trying the process out on your local system >> first. Adding new tools to Galaxy is pretty straightforward once you have >> the tool installed on the system, see >> https://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial. That >> will also allow you to test the overall functionality offered by Galaxy in >> the context of your own tool before trying to deploy the whole thing on the >> cloud. >> >> Once you transition to the cloud though, you would have to repeat the >> process of installing the tool on the created instance as you have done on >> the local system followed by copying the tool wrapper created to integrate >> it with Galaxy. If you started with a clean instance (i.e., not Galaxy >> CloudMan), after you've installed your tool and integrated it with Galaxy, >> you could simply use the AWS web console to create an AMI automatically. >> Then, you would start the newly created AMI, start Galaxy and start >> processing your data. Note that any data you upload to an instance will be >> lost once you terminate the instance though, unless you associate an EBS >> volume with it and have Galaxy store analysis data there (this is easily >> configured in Galaxy's universe_wsgi.ini file). >> >> Alternatively, you could use CloudMan and add your tool to the set of >> already existing tools as described here: >> https://bitbucket.org/galaxy/galaxy-central/wiki/Cloud/CustomizeGalaxyCloud >> If using CloudMan, all of the details regarding data persistance and >> Galaxy setup are automatically managed for you (excluding the addition of >> your own tool). >> >> Hope this helps, >> Enis >> >> On Mon, Mar 21, 2011 at 6:56 PM, Luqman Hodgkinson <luqman(a)berkeley.edu>wrote: >> >>> >>> >>> >>> >>> Dear Galaxy developers, >>> I have a collection of Java classes linked by a custom dataflow >>> architecture. All classes are in a single project but some of these classes >>> call executables written in languages other than Java. I am investigating >>> the possibility of transitioning to Galaxy. Essentially my desires are to >>> link these Java classes in a DAG representing the dataflow and to execute >>> the dataflow in Amazon EC2. The data flowing along the edges are arbitrary >>> custom Java classes. Additionally it is important to cache intermediate >>> results. The data is acquired from a few web services: iRefIndex, IntAct, >>> UniProt, and Gene Ontology. There are complex software dependencies so after >>> setting up the dataflow I would like to save the entire system as an >>> abstract machine image (AMI). How difficult would this transition be, and >>> would it be worth the effort? >>> Sincerely, with best wishes, >>> Luqman Hodgkinson, >>> Ph.D. student, UC-Berkeley >>> >>> >>> >>> >>> >>> ___________________________________________________________ >>> 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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biomart plugin
by Andrea Edwards 25 Mar '11

25 Mar '11

Hello If i had a local installation of galaxy is it possible to access a biomart database on my local server. It is my understanding that a dataset has to be available on the biomart central server to be accessible via the galaxy biomart plugin. thanks

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Re: [galaxy-user] dataflow using Galaxy on Amazon EC2
by Enis Afgan 25 Mar '11

25 Mar '11

Hi Luqman, Take a look a my comments below. On Fri, Mar 25, 2011 at 5:06 PM, Luqman Hodgkinson <luqman(a)berkeley.edu>wrote: > > > > > Hi Enis, > > Thank you for your detailed reply. After playing with Galaxy, there are > some questions I have. > > 1. All my Java classes are in the same project. There is only a single Main > class. In order to use Galaxy, must each class be converted to a .jar file > individually? If so, the disadvantage to this is then that only command-line > parameters can be passed in. How does the data flow between the classes? > Must each class read input from files and write input to files? That is, > what is the nature of your type system for passing data between components. > Can data be passed directly through RAM or must it go through the file > system? > > If you are able to perform your complete analysis using a combination of your Java classes by simply executing a single command (i.e, invoking a single main class), the same can be achieved through Galaxy. You would create a galaxy tool wrapper that allows Galaxy to invoke that same command and the rest (i.e.., executing the tool) is going to be the same (i.e., the same set of methods will get invoked and you should get the same output). Once Galaxy invokes a tool, any form of data flow within that tool is up to the tool itself so if the classes share data between each other, the same will happen once they are invoked through Galaxy. > 2. Provenance is very important for my workflow. The workflow will be run > multiple times and a large number of versions will be created. These should > be organized somewhere on the file system with timestamps and descriptions > of the versions of the workflows that were used. How much support does > Galaxy have for this? > > Galaxy keeps track of all the parameters and input data used to run a tool or a workflow so, once the tool is integrated with Galaxy, keeping up with the details is trivial - that's a big part of why Galaxy exists to begin with. 3. Have you seen the new Conveyor paper? > http://www.ncbi.nlm.nih.gov/pubmed?term=21278189 My requirements are very > similar to those addressed in this paper. However, the current version of > Conveyor does not seem very stable: I was even unable to get their graphical > user interface running from their Java files. What are the capabilities of > Galaxy for this use case? > > Unfortunately I have not read this paper yet so I cannot comment much. If you have not yet, I would suggest you give Galaxy Main (usegalaxy.org) a shot and try to run some jobs and create a few workflows to get an idea of what can be done with tools once they are integrated with Galaxy as well as the type of data and information Galaxy keeps. That should give you a good indication of whether available functionality can be applied in your scenario as well. Enis > Sincerely, with best wishes, > Luqman > > > On Mar 25, 2011, at 10:21 AM, Enis Afgan wrote: > > Hi Luqman, > Were you planning on using Galaxy CloudMan (usegalaxy.org/cloud) and > integrating your tool (i.e., Java classes) into the Galaxy that it deploys > or simply starting a new EC2 instance and setting up a Galaxy instance from > scratch? > Either way, I would suggest trying the process out on your local system > first. Adding new tools to Galaxy is pretty straightforward once you have > the tool installed on the system, see > https://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial. That > will also allow you to test the overall functionality offered by Galaxy in > the context of your own tool before trying to deploy the whole thing on the > cloud. > > Once you transition to the cloud though, you would have to repeat the > process of installing the tool on the created instance as you have done on > the local system followed by copying the tool wrapper created to integrate > it with Galaxy. If you started with a clean instance (i.e., not Galaxy > CloudMan), after you've installed your tool and integrated it with Galaxy, > you could simply use the AWS web console to create an AMI automatically. > Then, you would start the newly created AMI, start Galaxy and start > processing your data. Note that any data you upload to an instance will be > lost once you terminate the instance though, unless you associate an EBS > volume with it and have Galaxy store analysis data there (this is easily > configured in Galaxy's universe_wsgi.ini file). > > Alternatively, you could use CloudMan and add your tool to the set of > already existing tools as described here: > https://bitbucket.org/galaxy/galaxy-central/wiki/Cloud/CustomizeGalaxyCloud > If using CloudMan, all of the details regarding data persistance and Galaxy > setup are automatically managed for you (excluding the addition of your own > tool). > > Hope this helps, > Enis > > On Mon, Mar 21, 2011 at 6:56 PM, Luqman Hodgkinson <luqman(a)berkeley.edu>wrote: > >> >> >> >> >> Dear Galaxy developers, >> I have a collection of Java classes linked by a custom dataflow >> architecture. All classes are in a single project but some of these classes >> call executables written in languages other than Java. I am investigating >> the possibility of transitioning to Galaxy. Essentially my desires are to >> link these Java classes in a DAG representing the dataflow and to execute >> the dataflow in Amazon EC2. The data flowing along the edges are arbitrary >> custom Java classes. Additionally it is important to cache intermediate >> results. The data is acquired from a few web services: iRefIndex, IntAct, >> UniProt, and Gene Ontology. There are complex software dependencies so after >> setting up the dataflow I would like to save the entire system as an >> abstract machine image (AMI). How difficult would this transition be, and >> would it be worth the effort? >> Sincerely, with best wishes, >> Luqman Hodgkinson, >> Ph.D. student, UC-Berkeley >> >> >> >> >> >> ___________________________________________________________ >> 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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dataflow using Galaxy on Amazon EC2
by Luqman Hodgkinson 25 Mar '11

25 Mar '11

Dear Galaxy developers, I have a collection of Java classes linked by a custom dataflow architecture. All classes are in a single project but some of these classes call executables written in languages other than Java. I am investigating the possibility of transitioning to Galaxy. Essentially my desires are to link these Java classes in a DAG representing the dataflow and to execute the dataflow in Amazon EC2. The data flowing along the edges are arbitrary custom Java classes. Additionally it is important to cache intermediate results. The data is acquired from a few web services: iRefIndex, IntAct, UniProt, and Gene Ontology. There are complex software dependencies so after setting up the dataflow I would like to save the entire system as an abstract machine image (AMI). How difficult would this transition be, and would it be worth the effort? Sincerely, with best wishes, Luqman Hodgkinson, Ph.D. student, UC-Berkeley

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is galaxy down?
by Keith E. Giles 25 Mar '11

25 Mar '11

I keep getting a "SERVER ERROR" message. Is galaxy down, or is this on my end?

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Re: [galaxy-user] history
by Anton Nekrutenko 24 Mar '11

24 Mar '11

Tanita: Histories are saved automatically, but you need to be logged in to your Galaxy account. Thanks, anton On Mar 24, 2011, at 3:13 PM, Fuchs, Tania wrote: > Hi Anton, > > Thanks for the tip. I did not save my history, so I guess it was not saved automatically, since the "saved histories" is empty. I still have everything open at my home computer. Do you think I still can save it there? > > Thanks a lot again for your help, > > Tania > From: Anton Nekrutenko [mailto:anton@bx.psu.edu] > Sent: Thursday, March 24, 2011 12:44 PM > To: Fuchs, Tania > Cc: galaxy-user(a)bx.psu.edu > Subject: Re: [galaxy-user] history > > > Tanita: > > Click "Options" at the top of the history pane and choose "Saved histories". You will see your old history listed in the middle pane. > > Thanks, > > anton > galaxy team > > > On Mar 24, 2011, at 12:15 PM, Fuchs, Tania wrote: > >> 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 >> >> ___________________________________________________________ >> 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/ > > Anton Nekrutenko > http://nekrut.bx.psu.edu > http://usegalaxy.org > > > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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history
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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galaxy-user March 2011