December 2013 - galaxy-dev - lists.galaxyproject.org

How to get an API key during execution?
by Neil.Burdett＠csiro.au 10 Dec '13

10 Dec '13

Hi, I know that if I put : ${ __app__.model.User.get( $__user_id__ ).api_keys[0].key } in my tools xml file I am able to get the current api key. The xml calls my python script with this value, which i then use to execute workflows via the API. However, if this is value empty/blank is there a way I can generate an api key it from within my python script. i.e. is there a method I can call which would generate this for me? Thanks Neil

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The latest galaxy-dist run.sh failed
by zong-pei.han＠imm.ox.ac.uk 10 Dec '13

10 Dec '13

Hi, We've just installed the latest galaxy-dist: hg clone https://bitbucket.org/galaxy/galaxy-dist/ cd galaxy-dist hg -v update stable The server runs: CentOS release 6.5, python 2.6.8, and mysql-5.1.71-1.el6.x86_64 "sh run.sh" has failed: ...... migrate.versioning.repository DEBUG 2013-12-10 09:35:51,145 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2013-12-10 09:35:51,145 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}} galaxy.model.migrate.check DEBUG 2013-12-10 09:35:51,152 MySQL_python egg successfully loaded for mysql dialect galaxy.model.migrate.check INFO 2013-12-10 09:35:51,309 No database, initializing Traceback (most recent call last): File "/wwwdata/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/wwwdata/galaxy/lib/galaxy/app.py", line 54, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "/wwwdata/galaxy/lib/galaxy/model/migrate/check.py", line 64, in create_or_verify_database db_schema = schema.ControlledSchema( engine, migrate_repository ) File "/wwwdata/galaxy/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py", line 32, in __init__ self.load() File "/wwwdata/galaxy/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py", line 44, in load self.table = Table(tname, self.meta, autoload=True) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 318, in __new__ table._init(name, metadata, *args, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 381, in _init self._autoload(metadata, autoload_with, include_columns) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 408, in _autoload self, include_columns, exclude_columns File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2425, in run_callable return conn.run_callable(callable_, *args, **kwargs) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1968, in run_callable return callable_(self, *args, **kwargs) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 260, in reflecttable return insp.reflecttable(table, include_columns, exclude_columns) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 350, in reflecttable tbl_opts = self.get_table_options(table_name, schema, **table.kwargs) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 178, in get_table_options **kw) File "<string>", line 1, in <lambda> File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 47, in cache ret = fn(self, con, *args, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2064, in get_table_options parsed_state = self._parsed_state_or_create(connection, table_name, schema, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2163, in _parsed_state_or_create info_cache=kw.get('info_cache', None) File "<string>", line 1, in <lambda> File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 47, in cache ret = fn(self, con, *args, **kw) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2188, in _setup_parser full_name=full_name) File "/wwwdata/galaxy/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/mysql/base.py", line 2275, in _show_create_table raise exc.NoSuchTableError(full_name) DatabaseNotControlledError: `migrate_version` Your help is much appreciated. Zong-Pei Han

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hmmer install
by Karen Miga 08 Dec '13

08 Dec '13

Hello, I would like to use hmmer on our cloudman instance. However, when I install I am only finding a wrapper for hmmpress. There was some conversation about this back in 2012 ( http://gmod.827538.n3.nabble.com/Missing-tool-previews-in-tool-shed-e-g-hmm…) I installed the hmmer package 3.0 and 3.1 from the toolshed as well, however, I am not seeing a wrapper for these tools - perhaps I am missing something? Best wishes, Karen

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FTP Problem: Users cannot see their uploads files.
by Misharl mon 07 Dec '13

07 Dec '13

Hi everybody, I have managed to get proftpd to work, it can connect to the galaxy sql database, and users can log to upload files in their directory. But there is a problem, when a galaxy user logs in the galaxy web platform, the user can't see his upload files since Galaxy doesn't have the rights to open the directory. How can i change the permissions in proftpd so that galaxy can open the user directory? Thanks in advance to all. Mish

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Announcing the Galaxy Community Log Board
by Dave Clements 06 Dec '13

06 Dec '13

Hello all, I am pleased to announce the *Galaxy Community Log Board <http://wiki.galaxyproject.org/Community/Logs>.* The Log Board is a place to share how you addressed a particular task in your Galaxy deployment. Log entries describe specific solutions to particular tasks, such as the details of what steps were taken to deploy Galaxy on particular platforms<http://wiki.galaxyproject.org/Community/Log/2013/URGIVirtualisation>, or specific stumbling blocks when configuring Galaxy<http://wiki.galaxyproject.org/Community/Log/2013/Example>. Solutions can be described on this wiki<http://wiki.galaxyproject.org/Community/Log/2013/Example>, or just some metadata and a link to the description elsewhere<http://wiki.galaxyproject.org/Community/Log/2013/UsingBioServicesWithGalaxy>. Log entries are an easy way to help others (and learn from others) by sharing what you've already done. If you have figured out or documented how to do something, then this is the ideal forum for sharing that information with the community. Share your experience<http://wiki.galaxyproject.org/Community/Logs#Add_a_Log_Page> *now <http://wiki.galaxyproject.org/Community/Logs#Add_a_Log_Page>.* The Galaxy Community Log Board<http://wiki.galaxyproject.org/Community/Logs> describes how things can be done, and it complements the (also recently announced <http://wiki.galaxyproject.org/News/GalaxyDeploymentCatalog>) *Galaxy Deployments Catalog <http://wiki.galaxyproject.org/Community/Deployments>*, which describes different Galaxy installations. Both the Log Board<http://wiki.galaxyproject.org/Community/Logs> and the Deployments Catalog<http://wiki.galaxyproject.org/Community/Deployments> came out of discussions at the GCC2013 GalaxyAdmins Birds-of-a-Feather gathering <http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins>. Thanks to everyone who attended that BoF. Dave Clements -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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ClustalW
by Sheri Zada 06 Dec '13

06 Dec '13

Hi there, I think there is an error with ClustalW. I uploaded a fasta file containing two sequences of the luciferin gene from two different organisms. This site: http://www.ch.embnet.org/software/ClustalW.html works for the same files, but I would like to keep everything on galaxy because I want to produce a workflow for a page I am creating with a project partner. The error that comes up is : "clustalw2 not found", and the file is empty. Any help would be much appreciated. Thanks! Sheri Zada

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phyloviz: save visualization error
by Karen Miga 06 Dec '13

06 Dec '13

Hello, I am trying to use phyloviz on the cloud/Galaxy cloudman. Unfortunately, I am unable to save the visualization using the save/disk icon on the right hand side of the banner. Any help would be appreciated. Karen

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cloudman FTP upload: localhost?
by Arno, Matthew 06 Dec '13

06 Dec '13

Hi - Question from a biologist on thin ice here... I've setup a galaxy instance on cloudman AWS, and I'd like to upload some data using FTP. When I used the public galaxy server previously I used 'usegalaxy.org' as the host in FileZilla FTP program; what do I use for the host in the cloud instance? It just says 'localhost' on the galaxy upload page...which doesn't work? I presume the instance has some specific/temporary host/server ID, somewhere...where would I find it? Cheers, Matt ---------------------- Matthew Arno, Ph.D. Genomics Centre Manager Franklin-Wilkins Building (Waterloo Campus) King's College London T +44 (0) 207 848 4286 www.kcl.ac.uk/genomics The contents of this email are strictly confidential. It may not be transmitted in part or in whole to any other individual or groups of individuals. This email is intended solely for the use of the individual(s) to whom they are addressed and should not be released to any third party without the consent of the sender. -----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: 06 December 2013 16:00 To: Arno, Matthew; galaxy-bugs(a)bx.psu.edu Subject: Re: [galaxy-bugs] Galaxy tool error report from matthew.arno(a)kcl.ac.uk Hi Matt, Using a cloud galaxy is intended to be as simple as possible, and once it is going, really is in most ways the same exact experience as using the public Main server, except that your jobs will run quicker (if you allocate resources to them) and you will have much more space. This is the only way to get more processing power. Please see: http://usegalaxy.org/cloud And for support/help, the galaxy-dev(a)bx.psu.edu mailing list is good. We can help where you have trouble. Many biologist and small labs go this route. http://wiki.galaxyproject.org/MailingLists Another option is a SlipStream appliance. All options are here: http://wiki.galaxyproject.org/BigPicture/Choices Please review and let us know if you need more help, Jen Galaxy team On 12/6/13 7:31 AM, Arno, Matthew wrote: > Dear Jennifer - thanks for the email support - I will give it a try. > > Also, I was wondering whether it's possible to buy a little more access to Galaxy? I don't have any kind of cluster/server set up I can use or set up galaxy on. I have no idea how to use a cloud 'instance' - I am just a biologist who is just about able to use your browser GUI, and just about able to understand things. > > So basically I need to know how much would it cost for a bit more storage and a bit more processing power? Something in between the public server and your other suggestions. > > Thanks, > Matt > > ---------------------- > Matthew Arno, Ph.D. > Genomics Centre Manager > Franklin-Wilkins Building (Waterloo Campus) King's College London T > +44 (0) 207 848 4286 www.kcl.ac.uk/genomics > > The contents of this email are strictly confidential. It may not be transmitted in part or in whole to any other individual or groups of individuals. > This email is intended solely for the use of the individual(s) to whom they are addressed and should not be released to any third party without the consent of the sender. > > > > -----Original Message----- > From: Jennifer Jackson [mailto:jen@bx.psu.edu] > Sent: 28 November 2013 23:59 > To: galaxy-bugs(a)bx.psu.edu; Arno, Matthew > Subject: Re: [galaxy-bugs] Galaxy tool error report from > matthew.arno(a)kcl.ac.uk > > Hello Matt, > > You are following an RNA-seq example? Here is one from our team in case you haven't seen it: > https://usegalaxy.org/u/jeremy/p/interactive-rna-seq-with-trackster > http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-se > q > > But let's get it prepped correctly first - > > It looks like the upload was incomplete or the file is truncated locally (before upload, perhaps as you were moving it around on your own system). If you use the tool "Text Manipulation -> Select last lines from a dataset" at default on dataset #4, then look at the output, you will be viewing the end of the file. > > I ran FastQC on just the first few sequences, and your data has quality score encoding as "Sanger / Illumina 1.9". This translates to the datatype ".fastqsanger" in Galaxy. You can just assign this, then run FastQC to proceed with trimming, etc. > > Full details are here: > http://wiki.galaxyproject.org/Support#Dataset_special_cases > > It looks as if browser upload was used? For files near/over 2G, FTP is > required: > http://wiki.galaxyproject.org/Support#Loading_data > > Best! > > Jen > Galaxy team > > On 11/28/13 6:54 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 "usegalaxy.org" >> --------------------------------------------------------------------- >> - >> ------- This is in reference to dataset id 7146374 from history id >> 1694389 >> --------------------------------------------------------------------- >> - >> ------- You should be able to view the history containing the related >> history item >> >> 18: FASTQ Groomer on data 4 >> >> by logging in as a Galaxy admin user to the Galaxy instance >> referenced above and pointing your browser to the following link. >> >> usegalaxy.org/history/view?id=af8aac32a6b50fb7 >> --------------------------------------------------------------------- >> - >> ------- The user 'matthew.arno(a)kcl.ac.uk' provided the following >> information: >> >> hi - I am trying to read in some FastQ files from an Ion Proton run: is there a specific workflow/pipeline for this? They are RNAseq/transcriptomic samples, so I want to be able to run the tophat workflow. I have tried the FastQ groomer which has failed like this and even fastQC report fails, so I am guessing it has something to do with the format from ion proton... >> >> Cheers, >> matt >> --------------------------------------------------------------------- >> - >> ------- >> job id: 6151484 >> tool id: fastq_groomer >> job pid or drm id: 189480 >> --------------------------------------------------------------------- >> - >> ------- >> job command line: >> None >> --------------------------------------------------------------------- >> - >> ------- >> job stderr: >> Traceback (most recent call last): >> File "/galaxy/main/server/tools/fastq/fastq_groomer.py", line 42, in <module> >> if __name__ == "__main__": main() >> File "/galaxy/main/server/tools/fastq/fastq_groomer.py", line 22, in main >> for read_count, fastq_read in enumerate( reader( open( input_filename ), format = input_type, apply_galaxy_conventions = True ) ): >> File "/galaxy/main/server/lib/galaxy_utils/sequence/fastq.py", line 466, in __iter__ >> yield self.next() >> File "/galaxy/main/server/lib/galaxy_utils/sequence/fastq.py", line 504, in next >> raise e >> Exception: Invalid FASTQ file: could not find quality score of sequence identifier @UIPGM:01360:12780. >> >> --------------------------------------------------------------------- >> - >> ------- >> job stdout: >> There was an error reading your input file. Your input file is likely malformed. >> It is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below. >> However, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism. >> >> The reported error is: 'Invalid FASTQ file: could not find quality score of sequence identifier @UIPGM:01360:12780.'. >> The last valid FASTQ read had an identifier of '@UIPGM:01349:12777'. >> The error in your file occurs between lines '39516093' and '39516095', which corresponds to byte-offsets '2257518563' and '2257518593', and contains the text (30 of 30 bytes shown): >> >> @UIPGM:01360:12780 >> ATCTGATACG >> >> >> --------------------------------------------------------------------- >> - >> ------- >> job info: >> None >> --------------------------------------------------------------------- >> - >> ------- >> job traceback: >> None >> --------------------------------------------------------------------- >> - >> ------- >> (This is an automated message). > -- > Jennifer Hillman-Jackson > http://galaxyproject.org > > -- Jennifer Hillman-Jackson http://galaxyproject.org

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IDR-plot
by Federico Zambelli 06 Dec '13

06 Dec '13

Hi, recently I installed the idr_package from the Galaxy tool-shed but the tool IDR-plot does not work for my Galaxy instance. This is the error message: GPL Ghostscript 8.70: **** Could not open temporary file ./database/tmp/gs_DtCtic **** Unable to open the initial device, quitting. mv: cannot stat `./idrPlot-plot.pdf': No such file or directory It seems it doesn't find an expected temporary file. Does anybody have suggestions? Many thanks -- ============================================ Federico Zambelli, Ph.D. Bioinformatics, Evolution and Comparative Genomics Lab Dept. of Biosciences University of Milano - Italy What can be asserted without proof can be dismissed without proof. ============================================

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Re: [galaxy-dev] Problem installing tool_ Galaxy local
by Greg Von Kuster 06 Dec '13

06 Dec '13

Hello Valeria, Unfortunately the s_mart repository seems to be in a broken state on the main Galaxy Tool Shed. I assume you are installing the repository from the main Tool Shed: http://toolshed.g2.bx.psu.edu/view/yufei-luo/s_mart Some of the tools (maybe all, I haven't looked at all of them) define functional tests, but the repository does not contain any of the test data files, so the Tool Shed's install and test framework cannot validate the tools in this repository. You'll notice that the repository's "Automated tool test results" container displays this: Automated tool test results Tool test results Automated test environment Tools missing tests or test data The error I get installing s_mart from the main Tool Shed is the following. I believe this error may be osx specific. Are you trying to install into an osx environment? If not, can you send the snippet of your Galaxy paster log so we can see the error you are encountering? Error cloning repository: case-folding collision between SMART/Java/Python/compareOverlapping.py and SMART/Java/Python/CompareOverlapping.py Fixing the above problem requires the repository owner, so you'll have to contact them and let them know of the problem. You can contact the owner via the Repository Actions popup menu for the repository. If you contact them, perhaps you can also let them know they should add functional test data for the tests defined in the repository's tools. Thanks, Greg Von Kuster On Dec 5, 2013, at 8:50 PM, Valeria Parreira Pinto <vparreir(a)uoguelph.ca> wrote: > > Hi Greg, > Sorry if I lost you sending you the wrong screen. I have done all those steps, I saw that screen, than I clicked smart button, it went to another screen (which asks the name of the new tool and where to place) (which I sent part of it, showing the smart icon) for installation. Next step, I could see the status as cloning (yellow) and then error (red ). > I have done at least 3 times...always shows status:error > VP > > > > > _____________________________________________ > Valeria Parreira, Ph.D > Adjunct Faculty > Department of Pathobiology > OVC, University of Guelph, > Guelph, Ontario, N1G 2W1, Canada > Tel: +1 (519) 824-4120 - Ext. 54717(lab) and 54679 (office) > vparreir(a)uoguelph.ca > > > ----- Original Message ----- > From: Greg Von Kuster <greg(a)bx.psu.edu> > To: Valeria Parreira Pinto <vparreir(a)uoguelph.ca> > Cc: galaxy-dev(a)bx.psu.edu Dev <galaxy-dev(a)bx.psu.edu> > Sent: Thu, 05 Dec 2013 19:32:22 -0500 (EST) > Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local > > Hi Valeria, > > On Dec 5, 2013, at 4:59 PM, Valeria Parreira Pinto <vparreir(a)uoguelph.ca> wrote: > > > Hi Greg, > > I have done that...take a look. However this time I saw something different see below > > > > > > Installed tool shed repositories > > Update tool shed status > > > > Advanced Search > > > > You can now attempt to install the repository named s_mart again. > > > > Name ↓ Description Owner Revision Installation Status Tool shed > > > > s_mart > > S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data. > > yufei-luo > > b6481845eb0d > > New > > toolshed.g2.bx.psu.edu > > Updates are available in the Tool Shed for this revision > > A newer installable revision is available for this repository > > This is the latest installable revision of this repository > > This repository is deprecated in the Tool Shed > > This repository contains exported workflows > > Unable to get information from the Tool Shed > > > > The above page showing that the s_mart repository is in the New state implies that it is ready for installation, You can install it by clicking the right part of the s_mart button which will pop up a menu from which you can choose to install the repository. After the repository goes through the installation process, it should be displayed in the Installed state. If there were errors, it wil be in an Error state. If it si in an Installed state with no errors, then you should be able to see any contained tools in your Galaxy tool panel. > > > > > > and then this time I could see S-MART in the list: > > > > > > NGS: Mapping > > NGS: Indel Analysis > > NGS: RNA Analysis > > NGS: SAM Tools > > NGS: GATK Tools (beta) > > NGS: Peak Calling > > NGS: Simulation > > Phenotype Association > > VCF Tools > > S-MART > > Choose an existing section in your tool panel to contain the installed tools (optional). > > > > Clicking Install without selecting a tool panel section will load the installed tools into the tool panel outside of any sections. > > > > It did not work and I can not see S-MART in my tool box. > > Thank you for your attention. > > VP > > ___________________________________________ > > > > > > From: "Greg Von Kuster" <greg(a)bx.psu.edu> > > To: "Valeria Parreira Pinto" <vparreir(a)uoguelph.ca> > > Cc: "galaxy-dev(a)bx.psu.edu Dev" <galaxy-dev(a)bx.psu.edu> > > Sent: Thursday, December 5, 2013 4:33:34 PM > > Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local > > > > Click on the "Admin" option from the top menu bar, then click on the "Mange installed tool shed repositories. The find the "s_mart" repository from that page and clck on it. The from the "Repository Actions" menu, select "Reset to install" or "Repair repository" if it is available. > > > > On Dec 5, 2013, at 4:08 PM, Valeria Parreira Pinto <vparreir(a)uoguelph.ca> wrote: > > > > Hi Greg, > > > > I have done at least twice just to double check From Repository actions - reset to install > > This is what a I see: > > > > > > Monitor installing tool shed repositories > > Name Description Owner Revision Status > > s_mart S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data. yufei-luo b6481845eb0d > > Error > > > > > > The page Monitor installing tool shed repositories.... status error... > > VP > > > > > > > > From: "Greg Von Kuster" <greg(a)bx.psu.edu> > > To: "Valeria Parreira Pinto" <vparreir(a)uoguelph.ca> > > Cc: "galaxy-dev(a)bx.psu.edu Dev" <galaxy-dev(a)bx.psu.edu> > > Sent: Thursday, December 5, 2013 3:45:04 PM > > Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local > > > > What happens if you choose "Reset to install" from the "Repository Actions" menu? You should be presented with a page that shows the repository as uninstalled, at which time you can attempt to install it again. > > > > > > On Dec 5, 2013, at 3:11 PM, Valeria Parreira Pinto <vparreir(a)uoguelph.ca> wrote: > > > > Hi Greg, > > > > It did not work...This is what I see: > > > > > > This repository is not installed correctly (see the Repository installation error below). Choose Reset to install from the Repository Actions menu, correct problems if necessary and try installing the repository again. > > > > However, there no information regarding ti the error below. > > What is your suggestion? > > VP > > > > > > > > > > From: "Greg Von Kuster" <greg(a)bx.psu.edu> > > To: "Valeria Parreira Pinto" <vparreir(a)uoguelph.ca> > > Cc: "galaxy-dev(a)bx.psu.edu Dev" <galaxy-dev(a)bx.psu.edu> > > Sent: Thursday, December 5, 2013 1:19:59 PM > > Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local > > > > Hi Valeria, > > > > Please always replay-all to keep email threads on the original list. > > > > Your setting for tool_dependency_dir should not be as you've stated: > > > > tool_dependency_dir = tool_dependencies > > > > It should be an actual path on your local file system, something like: > > > > tool_dependency_dir = ../tool_dependencies > > > > If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory. > > > > I cannot guarantee that this change will solve your problem, but it will be a step in the right direction. After making this change, let us know if you still see problems. > > > > Greg Von Kuster > > > > > > On Dec 5, 2013, at 12:13 PM, Valeria Parreira Pinto <vparreir(a)uoguelph.ca> wrote: > > > > Hi Greg, > > > > Unfortunately, it is not working...sorry bug you again. > > I know nothing about programming...this is what I have done: ( I have tried to follow http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies) > > > > In universe_wsgi.ini modified > > #tool_dependency_dir = None > > tool_dependency_dir = tool_dependencies > > > > In shell > > > > Valerias-MacBook-Pro:galaxy-dist vrparreira$ cd tool_dependencies > > Valerias-MacBook-Pro:tool_dependencies vrparreira$ mkdir smart > > Valerias-MacBook-Pro:tool_dependencies vrparreira$ cd > > Valerias-MacBook-Pro:~ vrparreira$ cd galaxy-dist > > Valerias-MacBook-Pro:galaxy-dist vrparreira$ sh run.sh --reload > > > > > > This is what I see on the shell (I am not sure that is necessary): > > > > 127.0.0.1 - - [05/Dec/2013:11:52:59 -0400] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=613e73b56070623c&changeset_revisions=b6481845eb0d HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories?status=done&me…." "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > tool_shed.util.tool_util DEBUG 2013-12-05 11:53:16,026 Loading new tool panel section: S-MART > > tool_shed.util.shed_util_common DEBUG 2013-12-05 11:53:16,026 Adding new row (or updating an existing row) for repository 's_mart' in the tool_shed_repository table, status set to 'New'. > > tool_shed.util.tool_util DEBUG 2013-12-05 11:53:16,039 Appending to tool panel section: S-MART > > 127.0.0.1 - - [05/Dec/2013:11:53:15 -0400] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?tool_shed_url=http…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:19 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:22 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:25 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:28 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:31 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:34 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:37 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:40 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:43 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:46 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:49 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:52 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:55 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:53:58 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > tool_shed.util.shed_util_common DEBUG 2013-12-05 11:54:00,240 Error cloning repository: case-folding collision between SMART/Java/Python/compareOverlapping.py and SMART/Java/Python/CompareOverlapping.py > > tool_shed.galaxy_install.repository_util DEBUG 2013-12-05 11:54:00,624 Removed repository installation directory: /Users/vrparreira/shed_tools/toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/b6481845eb0d > > 127.0.0.1 - - [05/Dec/2013:11:53:16 -0400] "POST /admin_toolshed/manage_repositories HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:54:00 -0400] "GET /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:54:01 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:54:04 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:54:07 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:54:08 -0400] "GET /admin_toolshed/manage_repository?id=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:54:17 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:54:23 -0400] "GET /admin/review_tool_migration_stages HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:54:35 -0400] "GET /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:54:44 -0400] "GET /admin/reload_tool HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:54:51 -0400] "GET /forms/browse_form_definitions HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 127.0.0.1 - - [05/Dec/2013:11:54:54 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > > > > > If you could help me it would be great. Thanks in advance, > > Valeria > > _____________________________________________ > > > > > > From: "Greg Von Kuster" <greg(a)bx.psu.edu> > > To: "Valeria Parreira Pinto" <vparreir(a)uoguelph.ca> > > Cc: galaxy-dev(a)bx.psu.edu > > Sent: Wednesday, December 4, 2013 3:54:26 PM > > Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local > > > > Hello Valeria, > > > > The setting for tool_dependency_dir must be an actual path on your local file system, something like: > > > > tool_dependency_dir = ../tool_dependencies > > > > Make sure that you set the location to a place that is safe for installing files. > > > > Greg Von Kuster > > > > On Dec 4, 2013, at 3:09 PM, Valeria Parreira Pinto <vparreir(a)uoguelph.ca> wrote: > > > > Hi > > > > I am having problems to install a tool from tool shed named S_MART (attached paper) on my local Galaxy. > > The reason to install S_MART is to use DETR'PROK (attached paper) in Galaxy. > > The first time, I got a warning before installing S-MART saying: > > " set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing" > > > > In the universe_wsgi_ini: > > > > Path to the directory in which managed tool dependencies are placed. To use > > # the dependency system, see the documentation at: > > # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies > > #tool_dependency_dir = None > > tool_dependency_dir = tool_dependency_dir > > > > I have follow the instructions of the Matthias Zytnicki (paper's author). I did not work, still with error, however now it does not mention where or what to do!! > > > > Could you please let me know what would be the problem? and How to fix it? > > Thanks in advance, > > Valeria > > > > > > > > > > <DETR_PROK.pdf><SMART.pdf>___________________________________________________________ > > 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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