Re: [galaxy-dev] Problem fetching updates to toolshed tool
PS: when I make the section empty again in the original tool_conf.xml it doesn't show up anymore in that section. :-( Actually the complete section is again invisible. Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 6 februari 2012 8:45 Aan: 'Greg Von Kuster'; Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool Hi Greg, Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an EMPTY section in the tool_conf.xml menu where I want the toolshed tools to go to at the moment. To keep it maintainable for now at testing. But It does not show up in the bullet list of sections to install to (as these sections also do not show up in the menu itself until they cotain a valid tool xml). Other custom sections are there. Part of the tool_conf.xml /section label text=External tools id=externaltools / section name=ToolShed auto tools id=toolshedtools /section I added an empty tool file= / line in the section and still not there. Adding a valid tool lets it show up in the bullit list as it now also shows up in the left panel.. (as expected). Another test on the EMPTY section when I tried adding the tool providing THE SAME section name as custom in the field as a new tool panel section... it just adds it to the end of the section lists in the left. But it does work. It also remains working when I enable my own section menu again by adding another tool to the xml first. The section with the same name shows up on two places in the section list when adding tools from toolshed (as expected). Probably due to the different section id. There might be a possible problem when the id turns out the same as an already used one? I manually altered the shed_tool_conf.xml to match my section name and id and everything is ok. Maybe something to look into? Just a minor issue I think. Keep up the good work! Alex Van: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu]mailto:[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: vrijdag 3 februari 2012 22:16 Aan: Ira Cooke CC: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems. To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well. Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up. On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote: Hello Ira, Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance. It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy. Thanks! Greg Von Kuster On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote: Hi, We've been running into an issue when attempting to create a new toolshed tool. We have the toolshed and the main galaxy web app setup and running, but updating our tool to the latest version always fails. When clicking Get updates on our installed tool we find that the initial request is sent fine to the community application, but the reply is missing a slash after the galaxy url. This causes the request to fail. Our solution to this problem was to modify lib/galaxy/webapps/community/controllers/repository.py on line 795
[galaxy-dev] Postgresql To Galaxy
Hi , i have created postgreSQL database where i have created all functions and views which performs annotations and some other functions , how can i show my postgresql database table to galaxyas output . i have connected my database from universe_wsgi.ini to my linux host where i am running galaxy and my database is on windows host, i need the python script which take values from table and show them back to galaxy. THANKS ___ 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/
Re: [galaxy-dev] Problem fetching updates to toolshed tool
Hello Alex, Empty sections are not displayed in the Galaxy tool panel by design. However, can you clarify the behavior when installing a tool shed repository? Are you saying that empty sections cannot be selected for containing the tool shed repository tools because they are not displayed in the radio button selection list during installation time? If this is the case, then I'll take a look at this. Thanks! Greg On Feb 6, 2012, at 3:29 AM, Bossers, Alex wrote: PS: when I make the section empty again in the original tool_conf.xml it doesn’t show up anymore in that section. :-( Actually the complete section is again invisible. Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 6 februari 2012 8:45 Aan: 'Greg Von Kuster'; Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool Hi Greg, Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an EMPTY section in the tool_conf.xml menu where I want the toolshed tools to go to at the moment. To keep it maintainable for now at testing. But It does not show up in the bullet list of sections to install to (as these sections also do not show up in the menu itself until they cotain a valid tool xml). Other custom sections are there. Part of the tool_conf.xml /section label text=External tools id=externaltools / section name=ToolShed auto tools id=toolshedtools /section I added an empty tool file=”” / line in the section and still not there. Adding a valid tool lets it show up in the bullit list as it now also shows up in the left panel.. (as expected). Another test on the EMPTY section when I tried adding the tool providing THE SAME section name as custom in the field as a new tool panel section... it just adds it to the end of the section lists in the left. But it does work. It also remains working when I enable my own section menu again by adding another tool to the xml first. The section with the same name shows up on two places in the section list when adding tools from toolshed (as expected). Probably due to the different section id. There might be a possible problem when the id turns out the same as an already used one? I manually altered the shed_tool_conf.xml to match my section name and id and everything is ok. Maybe something to look into? Just a minor issue I think. Keep up the good work! Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: vrijdag 3 februari 2012 22:16 Aan: Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems. To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well. Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up. On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote: Hello Ira, Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance. It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy. Thanks! Greg Von Kuster On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote: Hi, We've been running into an issue when attempting to create a
[galaxy-dev] xml tool wrapper conditional
Dear all, I'm working on a tool wrapper which for a sequence scoring tool. It's supposed to score sequences either using a library installed to galaxy (tool-data/models.loc) or datasets from the user history. I tried to implement this behavior using the conditional / when value mechanism, simplified code follows below. Using locally installed models (from models.loc) fails with NotFound: cannot find 'models', although in the details view of the failed tool run model database points to the right file. Using the model file from the history works. Defining _only_ locally installed models from models.loc also works (removing the conditional stuff and leaving only the part inside when value='local' /when). The commandline might look a bit strange but is correct. Can anybody spot what is going wrong here? Regards, Holger -- command calcModels --scoreFasta -- --fa $fasta_in --bgFa $fasta_background --models $models $output_table /command inputs param format=fasta name=fasta_in type=data label=Input Fasta File / param format=fasta name=fasta_background type=data label=Background Fasta File / conditional name=ModelSource param name=models type=select label=model source help=History or installed models? value=local option value=localLocally installed models/option option value=historyModels from your history/option /param when value=local param name=models type=select label=model database options from_file=models.loc column name=name index=1/ column name=value index=2/ /options /param /when when value=history param name=models type=data format=tabular label=model database / /when /conditional /inputs -- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511 ___ 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/
[galaxy-dev] Tool syntax to embed external web page doesn't quite work as desired anymore
Hi everyone, It used to be in the previous or so galaxy-dist that if you wanted to have a tool which displayed a web page from another web app in the center Galaxy frame you simply did: tool name=View External Web Page id=view_external_page version=1.0.0 descriptionfrom External App/description inputs action=http://my/url/path; check_values=false method=get / /tool But this doesn't work anymore, instead you get a form with an Execute button which you then have to click on in order to go to the external web page you wanted to embed. How do I get the old desired behavior? regards, Leandro ___ 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/
[galaxy-dev] Writing a database interative tool
Hi Galaxy Developers
I aim to write a tool that will interact with Postgres database; here is what I
wrote to test database connectivity. This script resides in
/galaxy-dist/tools/test_tool/ and gets invoked from the front end. However
script generate following error: No module named psycopg2.
Here is my code:
#!/usr/bin/env python
import os.path
import os
from galaxy import eggs
from galaxy.model import *
from sqlalchemy import *
engine = create_engine('postgresql://postgres:@192.168.0.6:5432/galaxy')
connection = engine.connect()
result_set = connection.execute( select id from galaxy_user )
for row in result_set:
print row[ 'id' ]
connection.close()
Traceback (most recent call last):
File /galaxy-dist/tools/overlapanalysis/db_test.py, line 10, in ?
engine = create_engine('postgresql://postgres:@192.168.0.6:5432/galaxy')
File
/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/__init__.py,
line 223, in create_engine
return strategy.create(*args, **kwargs)
File
/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/strategies.py,
line 62, in create
dbapi = dialect_cls.dbapi(**dbapi_args)
File
/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/databases/postgres.py,
line 368, in dbapi
import psycopg2 as psycopg
ImportError: No module named psycopg2
Thanks for any help.
Regards
MK
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Re: [galaxy-dev] Postgresql To Galaxy
On Feb 6, 2012, at 6:37 AM, Rehan Saleem wrote: Hi , i have created postgreSQL database where i have created all functions and views which performs annotations and some other functions , how can i show my postgresql database table to galaxyas output . i have connected my database from universe_wsgi.ini to my linux host where i am running galaxy and my database is on windows host, i need the python script which take values from table and show them back to galaxy. THANKS Hi Rehan, I am a little unsure what you're trying to do. Do you want to display contents of this database in some sort of display within Galaxy, use them as tool inputs, or outputs? I would not suggest using this custom database as Galaxy's database (set in database_connection) if it contains separate data from the Galaxy application. Galaxy should live in its own database away from any other tables you use for other purposes. --nate ___ 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/ ___ 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/
Re: [galaxy-dev] Problem fetching updates to toolshed tool
This problem should be fixed in change set 6672:e38a9eb21336, which is now available in our central repo. Thanks for reporting this, and let me know if you discover other issues. Greg On Feb 6, 2012, at 7:54 AM, Bossers, Alex wrote: Greg, Exactly as you say. You cannot insert the repository tool when it’s an empty section. Sorry for being unclear. Alex Van: Greg Von Kuster [mailto:g...@bx.psu.edu] Verzonden: maandag 6 februari 2012 12:57 Aan: Bossers, Alex CC: Ira Cooke; galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool Hello Alex, Empty sections are not displayed in the Galaxy tool panel by design. However, can you clarify the behavior when installing a tool shed repository? Are you saying that empty sections cannot be selected for containing the tool shed repository tools because they are not displayed in the radio button selection list during installation time? If this is the case, then I'll take a look at this. Thanks! Greg On Feb 6, 2012, at 3:29 AM, Bossers, Alex wrote: PS: when I make the section empty again in the original tool_conf.xml it doesn’t show up anymore in that section. :-( Actually the complete section is again invisible. Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 6 februari 2012 8:45 Aan: 'Greg Von Kuster'; Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool Hi Greg, Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an EMPTY section in the tool_conf.xml menu where I want the toolshed tools to go to at the moment. To keep it maintainable for now at testing. But It does not show up in the bullet list of sections to install to (as these sections also do not show up in the menu itself until they cotain a valid tool xml). Other custom sections are there. Part of the tool_conf.xml /section label text=External tools id=externaltools / section name=ToolShed auto tools id=toolshedtools /section I added an empty tool file=”” / line in the section and still not there. Adding a valid tool lets it show up in the bullit list as it now also shows up in the left panel.. (as expected). Another test on the EMPTY section when I tried adding the tool providing THE SAME section name as custom in the field as a new tool panel section... it just adds it to the end of the section lists in the left. But it does work. It also remains working when I enable my own section menu again by adding another tool to the xml first. The section with the same name shows up on two places in the section list when adding tools from toolshed (as expected). Probably due to the different section id. There might be a possible problem when the id turns out the same as an already used one? I manually altered the shed_tool_conf.xml to match my section name and id and everything is ok. Maybe something to look into? Just a minor issue I think. Keep up the good work! Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: vrijdag 3 februari 2012 22:16 Aan: Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems. To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well. Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up. On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote: Hello Ira, Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that
Re: [galaxy-dev] Writing a database interative tool
On Feb 4, 2012, at 7:53 AM, Matloob Khushi wrote:
Hi Galaxy Developers
I aim to write a tool that will interact with Postgres database; here is what
I wrote to test database connectivity. This script resides in
/galaxy-dist/tools/test_tool/ and gets invoked from the front end. However
script generate following error: No module named psycopg2.
Here is my code:
#!/usr/bin/env python
import os.path
import os
from galaxy import eggs
Right here, add:
eggs.require('psycopg2')
--nate
from galaxy.model import *
from sqlalchemy import *
engine = create_engine('postgresql://postgres:@192.168.0.6:5432/galaxy')
connection = engine.connect()
result_set = connection.execute( select id from galaxy_user )
for row in result_set:
print row[ 'id' ]
connection.close()
Traceback (most recent call last):
File /galaxy-dist/tools/overlapanalysis/db_test.py, line 10, in ?
engine = create_engine('postgresql://postgres:@192.168.0.6:5432/galaxy')
File
/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/__init__.py,
line 223, in create_engine
return strategy.create(*args, **kwargs)
File
/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/strategies.py,
line 62, in create
dbapi = dialect_cls.dbapi(**dbapi_args)
File
/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/databases/postgres.py,
line 368, in dbapi
import psycopg2 as psycopg
ImportError: No module named psycopg2
Thanks for any help.
Regards
MK
___
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/
___
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/
Re: [galaxy-dev] Problems with custom data types and sniffers in shed tools
Hello Ira, I believe proprietary datatype sniffers included in tool shed repositories are loading as expected - at least I cannot reproduce the behavior you are seeing. The datatypes_conf.xml file included in the latest revision of the gmap repository on the main Galaxy tool shed looks like this: ?xml version=1.0? datatypes datatype_files datatype_file name=gmap.py/ /datatype_files registration datatype extension=gmapdb type=galaxy.datatypes.gmap:GmapDB display_in_upload=False/ datatype extension=gmapsnpindex type=galaxy.datatypes.gmap:GmapSnpIndex display_in_upload=False/ datatype extension=iit type=galaxy.datatypes.gmap:IntervalIndexTree display_in_upload=True/ datatype extension=splicesites.iit type=galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree display_in_upload=True/ datatype extension=introns.iit type=galaxy.datatypes.gmap:IntronsIntervalIndexTree display_in_upload=True/ datatype extension=snps.iit type=galaxy.datatypes.gmap:SNPsIntervalIndexTree display_in_upload=True/ datatype extension=gmap_annotation type=galaxy.datatypes.gmap:IntervalAnnotation display_in_upload=False/ datatype extension=gmap_splicesites type=galaxy.datatypes.gmap:SpliceSiteAnnotation display_in_upload=True/ datatype extension=gmap_introns type=galaxy.datatypes.gmap:IntronAnnotation display_in_upload=True/ datatype extension=gmap_snps type=galaxy.datatypes.gmap:SNPAnnotation display_in_upload=True/ /registration sniffers sniffer type=galaxy.datatypes.gmap:IntervalAnnotation/ sniffer type=galaxy.datatypes.gmap:SpliceSiteAnnotation/ sniffer type=galaxy.datatypes.gmap:IntronAnnotation/ sniffer type=galaxy.datatypes.gmap:SNPAnnotation/ /sniffers /datatypes Here is the snippet of my paster log when I install the gmap tool shed repository - notice that the tools, datatypes and sniffers are all loaded. I'm installing it from a local tool shed, but I downloaded the latest version from the main Galaxy tool shed and uploaded it with no changes to my local tool shed for testing. galaxy.web.controllers.admin_toolshed DEBUG 2012-02-06 10:50:33,686 Loading new tool panel section: gmap galaxy.util.shed_util DEBUG 2012-02-06 10:50:33,687 Installing repository 'gmap' galaxy.util.shed_util DEBUG 2012-02-06 10:50:33,687 Cloning http://t...@gvk.bx.psu.edu:9009/repos/test/gmap destination directory: gmap requesting all changes adding changesets adding manifests adding file changes added 1 changesets with 10 changes to 10 files updating to branch default 10 files updated, 0 files merged, 0 files removed, 0 files unresolved galaxy.util.shed_util DEBUG 2012-02-06 10:50:34,062 Updating cloned repository to revision dbcccd1e4dfd 0 files updated, 0 files merged, 0 files removed, 0 files unresolved docutils WARNING 2012-02-06 10:50:34,388 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. galaxy.util.shed_util DEBUG 2012-02-06 10:50:34,437 Adding new row (or updating an existing row) for repository 'gmap' in the tool_shed_repository table. docutils WARNING 2012-02-06 10:50:34,533 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. docutils WARNING 2012-02-06 10:50:34,657 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. galaxy.tools DEBUG 2012-02-06 10:50:34,718 Reloading section: gmap galaxy.tools DEBUG 2012-02-06 10:50:34,769 Loaded tool id: gvk.bx.psu.edu:9009/repos/test/gmap/gmap/2.0.1, version: 2.0.1. galaxy.tools DEBUG 2012-02-06 10:50:34,813 Loaded tool id: gvk.bx.psu.edu:9009/repos/test/gmap/gmap_build/2.0.0, version: 2.0.0. docutils WARNING 2012-02-06 10:50:34,846 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. galaxy.tools DEBUG 2012-02-06 10:50:34,877 Loaded tool id: gvk.bx.psu.edu:9009/repos/test/gmap/gsnap/2.0.1, version: 2.0.1. galaxy.tools DEBUG 2012-02-06 10:50:34,911 Loaded tool id: gvk.bx.psu.edu:9009/repos/test/gmap/gmap_iit_store/2.0.0, version: 2.0.0. galaxy.tools DEBUG 2012-02-06 10:50:34,962 Loaded tool id: gvk.bx.psu.edu:9009/repos/test/gmap/gmap_snpindex/2.0.0, version: 2.0.0. galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,147 Loading datatypes from /Users/gvk/workspaces_2008/shed_tools/gvk.bx.psu.edu/repos/test/gmap/dbcccd1e4dfd/gmap/gmap-93911bac43da/tool-data/datatypes_conf.xml galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,159 Loaded sniffer for datatype: galaxy.datatypes.gmap:IntervalAnnotation galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,160 Loaded sniffer for datatype: galaxy.datatypes.gmap:SpliceSiteAnnotation galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,161 Loaded sniffer for datatype: galaxy.datatypes.gmap:IntronAnnotation galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,161 Loaded sniffer for datatype: galaxy.datatypes.gmap:SNPAnnotation If I stop and
Re: [galaxy-dev] Postgresql To Galaxy
On Feb 6, 2012, at 10:56 AM, Rehan Saleem wrote: Hi Nate, well i don’t want to use galaxy default database , i want to set my own tools for example, i have created a function totaloverlapcount and its work perfectly fine in my separate postgresql database called ova , now i want to add a tool in galaxy with a name Total Overlap Count , as we know whenever we want to add a tool we configure it in tool_config file. Now if a user click on Total Overlap Count then my postgresql function totaloverlapcount should be called , and that function will perform query on my own created database(ova) and then return the result into galaxy interface Hi Rehan, Please use 'reply all' to keep replies on the mailing list. Since your tool already works with a separate postgres database outside of Galaxy, you should be able to add the tool to Galaxy without modification. I presume the tool has some means of knowing what host, user and port to connect to, and the setup of this information is the same as it would be when running it on the command line (via a config file, environment, hardcoded in the tool...?). --nate From: Nate Coraor n...@bx.psu.edu To: Rehan Saleem pk_re...@yahoo.com Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Sent: Monday, February 6, 2012 8:07 PM Subject: Re: [galaxy-dev] Postgresql To Galaxy On Feb 6, 2012, at 6:37 AM, Rehan Saleem wrote: Hi , i have created postgreSQL database where i have created all functions and views which performs annotations and some other functions , how can i show my postgresql database table to galaxyas output . i have connected my database from universe_wsgi.ini to my linux host where i am running galaxy and my database is on windows host, i need the python script which take values from table and show them back to galaxy. THANKS Hi Rehan, I am a little unsure what you're trying to do. Do you want to display contents of this database in some sort of display within Galaxy, use them as tool inputs, or outputs? I would not suggest using this custom database as Galaxy's database (set in database_connection) if it contains separate data from the Galaxy application. Galaxy should live in its own database away from any other tables you use for other purposes. --nate ___ 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/ ___ 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/
Re: [galaxy-dev] xml tool wrapper conditional
I'm only guessing here, but maybe the issue is that the parameter names are all the same (namely model). Did you try with only unique names? Especially this one: param name=models type=select label=model source help=History or installed models? value=local should get it's own name. Sarah On 02/06/2012 03:38 PM, Holger Klein wrote: Dear all, I'm working on a tool wrapper which for a sequence scoring tool. It's supposed to score sequences either using a library installed to galaxy (tool-data/models.loc) or datasets from the user history. I tried to implement this behavior using theconditional /when value mechanism, simplified code follows below. Using locally installed models (from models.loc) fails with NotFound: cannot find 'models', although in the details view of the failed tool run model database points to the right file. Using the model file from the history works. Defining _only_ locally installed models from models.loc also works (removing theconditional stuff and leaving only the part insidewhen value='local' /when). The commandline might look a bit strange but is correct. Can anybody spot what is going wrong here? Regards, Holger -- command calcModels --scoreFasta -- --fa $fasta_in --bgFa $fasta_background --models $models $output_table /command inputs param format=fasta name=fasta_in type=data label=Input Fasta File / param format=fasta name=fasta_background type=data label=Background Fasta File / conditional name=ModelSource param name=models type=select label=model source help=History or installed models? value=local option value=localLocally installed models/option option value=historyModels from your history/option /param when value=local param name=models type=select label=model database options from_file=models.loc column name=name index=1/ column name=value index=2/ /options /param /when when value=history param name=models type=data format=tabular label=model database / /when /conditional /inputs ___ 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/
Re: [galaxy-dev] More helpful cluster job names
On Feb 3, 2012, at 7:30 AM, Peter Cock wrote: On Fri, Feb 3, 2012 at 11:55 AM, Ryan Golhar ngsbioinformat...@gmail.com wrote: 'qstat -f | grep jobname' will give you the full jobname without truncation. Sadly not on our version of SGE - which appears to be SGE 6.2u5 - you get a bit more information but the job name is still truncated as before. Personally, I think the qstat reporting gives too little information. I agree. Try qstat -j job_id I've written a perl script to parse the output of qstat -f to give a bit more information. So truncation of jobnames for qstat shouldn't be an issue. Maybe you're right that it is possible to interrogate SGE for the full name, but I still think Galaxy's job names could be more informative. This was implemented for the PBS runner, I've carried over the format from that to the DRMAA runner in e4d1dd3bdd0d. The format is: gjob_id_tool_id_user_email --nate Regards, Peter ___ 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/ ___ 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/
Re: [galaxy-dev] More helpful cluster job names
On Feb 6, 2012, at 1:05 PM, Nate Coraor wrote: On Feb 3, 2012, at 7:30 AM, Peter Cock wrote: On Fri, Feb 3, 2012 at 11:55 AM, Ryan Golhar ngsbioinformat...@gmail.com wrote: 'qstat -f | grep jobname' will give you the full jobname without truncation. Sadly not on our version of SGE - which appears to be SGE 6.2u5 - you get a bit more information but the job name is still truncated as before. Personally, I think the qstat reporting gives too little information. I agree. Try qstat -j job_id I've written a perl script to parse the output of qstat -f to give a bit more information. So truncation of jobnames for qstat shouldn't be an issue. Maybe you're right that it is possible to interrogate SGE for the full name, but I still think Galaxy's job names could be more informative. This was implemented for the PBS runner, I've carried over the format from that to the DRMAA runner in e4d1dd3bdd0d. The format is: gjob_id_tool_id_user_email Correction, you'll need 74b6319b38b4 since the only valid characters in a DRMAA job name are alphanumeric or underscores. --nate Regards, Peter ___ 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/ ___ 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/ ___ 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/
[galaxy-dev] manage_db.sh error
Hi Galaxy Team, I am running a small local instance of Galaxy and I've run into a database error following an upgrade to the Jan27th galaxy-dist release. The last line when I run run.sh tells me to upgrade my database: Exception: Your database has version '85' but this code expects version '90'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. But when I run the manage_db.sh I run into the following errors: $ sh manage_db.sh Traceback (most recent call last): File ./scripts/manage_db.py, line 12, in module from migrate.versioning.shell import main File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/shell.py, line 7, in module from migrate.versioning.base import * File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/base/__init__.py, line 5, in module from const import databases,operations File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/base/const.py, line 7, in module from sqlalchemy.util import OrderedDict ImportError: No module named sqlalchemy.util The first thing that pops out is that I the sqlalchemy egg is part of py2.7 while I am using python2.6. Any suggestions on how to troubleshoot this? thanks, zach cp ___ 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/
[galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch
Hi All, I'm looking to batch process 40 large data sets with the same galaxy workflow. This obviously can be done in a brute-force manual manner. However, is there a better way to schedule/invoke these jobs in batch 1) from the UI with a plugin 2) command-line 3) web-service Thanks in advance for any pointers. Dave ___ 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/
Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch
Hi Dave,Yes, galaxy's standard run-workflow dialog has a feature where you can select multiple datasets as input for a single "Input Dataset" step. To do this, click the icon referenced by the tooltip in the screenshot below to select multiple files. All parameters remain static between executions except for the single input dataset that gets modified for each run, and that only one input dataset can be set to multiple files in this fashion.-DannonOn Feb 6, 2012, at 4:18 PM, Dave Lin wrote:Hi All,I'm looking to batch process 40 large data sets with the same galaxy workflow.This obviously can be done in a brute-force manual manner. However, is there a better way to schedule/invoke these jobs in batch 1) from the UI with a plugin2) command-line3) web-serviceThanks in advance for any pointers.Dave ___Please keep all replies on the list by using "reply all"in your mail client. To manage your subscriptions to thisand other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/___ 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/
Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch
Thank you Dannon. That is helpful. What if I need to specify multiple inputs per run (i.e. .csfasta + .qual file)? -Dave On Mon, Feb 6, 2012 at 1:27 PM, Dannon Baker dannonba...@me.com wrote: Hi Dave, Yes, galaxy's standard run-workflow dialog has a feature where you can select multiple datasets as input for a single Input Dataset step. To do this, click the icon referenced by the tooltip in the screenshot below to select multiple files. All parameters remain static between executions except for the single input dataset that gets modified for each run, and that only one input dataset can be set to multiple files in this fashion. -Dannon On Feb 6, 2012, at 4:18 PM, Dave Lin wrote: Hi All, I'm looking to batch process 40 large data sets with the same galaxy workflow. This obviously can be done in a brute-force manual manner. However, is there a better way to schedule/invoke these jobs in batch 1) from the UI with a plugin 2) command-line 3) web-service Thanks in advance for any pointers. Dave ___ 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/ PastedGraphic-2.png___ 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/
Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch
This method only works for single inputs at the moment, though eventually it'd be nice to allow pairing. Another option for you would be to use the workflows API, with which you can definitely specify multiple inputs. See workflow_execute.py in the scripts/api folder of your galaxy installation for one method of doing this. -Dannon On Feb 6, 2012, at 4:53 PM, Dave Lin wrote: Thank you Dannon. That is helpful. What if I need to specify multiple inputs per run (i.e. .csfasta + .qual file)? -Dave On Mon, Feb 6, 2012 at 1:27 PM, Dannon Baker dannonba...@me.com wrote: Hi Dave, Yes, galaxy's standard run-workflow dialog has a feature where you can select multiple datasets as input for a single Input Dataset step. To do this, click the icon referenced by the tooltip in the screenshot below to select multiple files. All parameters remain static between executions except for the single input dataset that gets modified for each run, and that only one input dataset can be set to multiple files in this fashion. -Dannon PastedGraphic-2.png On Feb 6, 2012, at 4:18 PM, Dave Lin wrote: Hi All, I'm looking to batch process 40 large data sets with the same galaxy workflow. This obviously can be done in a brute-force manual manner. However, is there a better way to schedule/invoke these jobs in batch 1) from the UI with a plugin 2) command-line 3) web-service Thanks in advance for any pointers. Dave ___ 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/ ___ 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/
Re: [galaxy-dev] Problem with latest database upgrade
Hi Greg,I tried the downgrade/upgrade path and got the exact same message I sent before.I am using a postgres database that is running on local host.I did indeed install some toolshed repositories before I tried to upgrade.I also tried to downgrade to 89 and then upgrade, with the exact same message.ThonOn Feb 06, 2012, at 10:51 AM, Greg Von Kuster g...@bx.psu.edu wrote:Hello Thon,Attempting to run the migration script twice to the same version always poses problems. Can you downgrade successfully as follows?sh manage_db.sh downgrade 90If so, downgrade, then upgrade again and send the paster log from the clean upgrade if you see a problem. Also:What database are you using? Have you installed any tool shed repositories into your local Galaxy instance?Thanks,GregOn Feb 6, 2012, at 1:32 PM, Thon Deboer wrote:Hi,I updated to the latest galaxy-central version but got this error when trying to upgrade...Any ideas? It seems the table had already been created (this was the second time I run upgrade) but the JSON error was one that showed up the first time...)ThanksThonsh manage_db.sh upgrade90 - 91...Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table.0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,847 Creating tool_version table failed: (ProgrammingError) relation "tool_version" already exists'\nCREATE TABLE tool_version (\n\tid SERIAL NOT NULL, \n\tcreate_time TIMESTAMP WITHOUT TIME ZONE, \n\tupdate_time TIMESTAMP WITHOUT TIME ZONE, \n\ttool_id VARCHAR(255), \n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' {}0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,847 Creating tool_version table failed: (ProgrammingError) relation "tool_version" already exists'\nCREATE TABLE tool_version (\n\tid SERIAL NOT NULL, \n\tcreate_time TIMESTAMP WITHOUT TIME ZONE, \n\tupdate_time TIMESTAMP WITHOUT TIME ZONE, \n\ttool_id VARCHAR(255), \n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' {}0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,863 Creating tool_version_association table failed: (ProgrammingError) relation "tool_version_association" already exists'\nCREATE TABLE tool_version_association (\n\tid SERIAL NOT NULL, \n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version (id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' {}0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,863 Creating tool_version_association table failed: (ProgrammingError) relation "tool_version_association" already exists'\nCREATE TABLE tool_version_association (\n\tid SERIAL NOT NULL, \n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version (id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' {}Traceback (most recent call last): File "./scripts/manage_db.py", line 63, in module main( repository=repo, url="" ) File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 349, in _migrate schema.runchange(ver, change, changeset.step) File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange change.run(self.engine, step) File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 101, in run func() File "lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py", line 78, in upgrade repository_metadata = from_json_string( str( row[1] ) ) File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/__init__.py", line 384, in loads File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py", line 402, in decode File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py", line 420, in raw_decodesimplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)Regards,Thon de Boer, Ph.D.Bioinformatics Guru+1-650-799-6839thondeb...@me.comLinkedIn Profile___Please keep all replies on the list by using "reply all"in your mail client. To manage your subscriptions to thisand other Galaxy lists, please use the interface at:
Re: [galaxy-dev] Problem with latest database upgrade
I manually dropped the tool_version and tool_association table in the database and I am left with the JSON error as shown below:90 - 91...Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table.Traceback (most recent call last): File "./scripts/manage_db.py", line 63, in module main( repository=repo, url="" ) File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 349, in _migrate schema.runchange(ver, change, changeset.step) File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange change.run(self.engine, step) File "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 101, in run func() File "lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py", line 78, in upgrade repository_metadata = from_json_string( str( row[1] ) ) File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/__init__.py", line 384, in loads File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py", line 402, in decode File "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py", line 420, in raw_decodesimplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)On Feb 06, 2012, at 02:08 PM, Anthonius deBoer thondeb...@me.com wrote:Hi Greg,I tried the downgrade/upgrade path and got the exact same message I sent before.I am using a postgres database that is running on local host.I did indeed install some toolshed repositories before I tried to upgrade.I also tried to downgrade to 89 and then upgrade, with the exact same message.ThonOn Feb 06, 2012, at 10:51 AM, Greg Von Kuster g...@bx.psu.edu wrote:Hello Thon,Attempting to run the migration script twice to the same version always poses problems. Can you downgrade successfully as follows?sh manage_db.sh downgrade 90If so, downgrade, then upgrade again and send the paster log from the clean upgrade if you see a problem. Also:What database are you using? Have you installed any tool shed repositories into your local Galaxy instance?Thanks,GregOn Feb 6, 2012, at 1:32 PM, Thon Deboer wrote:Hi,I updated to the latest galaxy-central version but got this error when trying to upgrade...Any ideas? It seems the table had already been created (this was the second time I run upgrade) but the JSON error was one that showed up the first time...)ThanksThonsh manage_db.sh upgrade90 - 91...Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table.0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,847 Creating tool_version table failed: (ProgrammingError) relation "tool_version" already exists'\nCREATE TABLE tool_version (\n\tid SERIAL NOT NULL, \n\tcreate_time TIMESTAMP WITHOUT TIME ZONE, \n\tupdate_time TIMESTAMP WITHOUT TIME ZONE, \n\ttool_id VARCHAR(255), \n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' {}0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,847 Creating tool_version table failed: (ProgrammingError) relation "tool_version" already exists'\nCREATE TABLE tool_version (\n\tid SERIAL NOT NULL, \n\tcreate_time TIMESTAMP WITHOUT TIME ZONE, \n\tupdate_time TIMESTAMP WITHOUT TIME ZONE, \n\ttool_id VARCHAR(255), \n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' {}0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,863 Creating tool_version_association table failed: (ProgrammingError) relation "tool_version_association" already exists'\nCREATE TABLE tool_version_association (\n\tid SERIAL NOT NULL, \n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version (id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' {}0091_add_tool_version_tables DEBUG 2012-02-06 10:23:39,863 Creating tool_version_association table failed: (ProgrammingError) relation "tool_version_association" already exists'\nCREATE TABLE tool_version_association (\n\tid SERIAL NOT NULL, \n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version (id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n'
Re: [galaxy-dev] Problem with latest database upgrade
Can you replace lines 75 - 86 of the file ~/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py with the following for loop and send me your paster log? Thanks! for row in result: tool_shed_repository_id = row[0] try: repository_metadata = from_json_string( str( row[1] ) ) # Create a new row in the tool table for each tool included in repository. We will NOT # handle tool_version_associaions because we do not have the information we need to do so. tools = repository_metadata.get( 'tools', [] ) for tool_dict in tools: cmd = INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s) % \ ( nextval( 'tool_version' ), localtimestamp(), localtimestamp(), tool_dict[ 'guid' ], tool_shed_repository_id ) db_session.execute( cmd ) count += 1 except Exception, e: print Repository metadata: , str( row[1] ) print Exception setting tool versions for tools in tool_shed_repository with id: , str( tool_shed_repository_id ) print str( e ) The lines of code you are replacing look like this: for row in result: if row[1]: tool_shed_repository_id = row[0] repository_metadata = from_json_string( str( row[1] ) ) # Create a new row in the tool table for each tool included in repository. We will NOT # handle tool_version_associaions because we do not have the information we need to do so. tools = repository_metadata.get( 'tools', [] ) for tool_dict in tools: cmd = INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s) % \ ( nextval( 'tool_version' ), localtimestamp(), localtimestamp(), tool_dict[ 'guid' ], tool_shed_repository_id ) db_session.execute( cmd ) count += 1 On Feb 6, 2012, at 5:23 PM, Anthonius deBoer wrote: I manually dropped the tool_version and tool_association table in the database and I am left with the JSON error as shown below: 90 - 91... Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table. Traceback (most recent call last): File ./scripts/manage_db.py, line 63, in module main( repository=repo, url=db_url ) File /home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py, line 150, in main ret = command_func(**kwargs) File /home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py, line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File /home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py, line 349, in _migrate schema.runchange(ver, change, changeset.step) File /home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py, line 184, in runchange change.run(self.engine, step) File /home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py, line 101, in run func() File lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py, line 78, in upgrade repository_metadata = from_json_string( str( row[1] ) ) File /home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/__init__.py, line 384, in loads File /home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py, line 402, in decode File /home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py, line 420, in raw_decode simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0) On Feb 06, 2012, at 02:08 PM, Anthonius deBoer thondeb...@me.com wrote: Hi Greg, I tried the downgrade/upgrade path and got the exact same message I sent before. I am using a postgres database that is running on local host. I did indeed install some toolshed repositories before I tried to upgrade. I also tried to downgrade to 89 and then upgrade, with the exact same message. Thon On Feb 06, 2012, at 10:51 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Thon, Attempting to run the migration script twice to the same version always poses problems. Can you downgrade successfully as follows? sh manage_db.sh downgrade 90 If so, downgrade, then upgrade again and send the paster log from the clean upgrade if you see a problem. Also: What database are you using? Have you installed any tool shed repositories into your local Galaxy instance? Thanks, Greg On Feb 6, 2012, at 1:32 PM, Thon Deboer wrote: Hi, I updated to the latest galaxy-central version but got this error when
[galaxy-dev] Galaxy Main Server Tool Repository
Dear all, New bee here. Wonder if this is the right place to post following questions: We are interested in setting up a server like galaxy main server. Wonder which Linux Platform is the main server running on. Also is there a method for batch installing tools that now are available on the main galaxy server? If not, wonder if can point me to the documentation of the main galaxy server installation. Please excuse me if this is not the right list! Thanks a lot! Charlie -- Li Charlie Xia PhD Candidate Computational Biology and Bioinformatics Program at University of Southern California 1050 Childs Way, RRI 416C Los Angeles, CA 90089-2910, USA OP: 213-740-5168 ___ 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/
Re: [galaxy-dev] Galaxy Main Server Tool Repository
Hi Charlie, Our main galaxy server is actually running CentOS 5.10. The galaxy cloud instances are built on Ubuntu 10.04 LTS. That said, as far as I know, any *nix with python 2.5 or above should work fine. The following two links have lots of information regarding setting up your own server: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Automated setup of many tools is available currently via mi-deployment, see https://bitbucket.org/afgane/mi-deployment for more information on that. In coming months, automated deployment of many tool binaries will be available directly from within Galaxy via the Tool Shed. And lastly, this is definitely the right list for this type of question. Thanks for your interest in Galaxy! Dannon On Feb 6, 2012, at 4:53 PM, Li Charlie Xia wrote: Dear all, New bee here. Wonder if this is the right place to post following questions: We are interested in setting up a server like galaxy main server. Wonder which Linux Platform is the main server running on. Also is there a method for batch installing tools that now are available on the main galaxy server? If not, wonder if can point me to the documentation of the main galaxy server installation. Please excuse me if this is not the right list! Thanks a lot! Charlie -- Li Charlie Xia PhD Candidate Computational Biology and Bioinformatics Program at University of Southern California 1050 Childs Way, RRI 416C Los Angeles, CA 90089-2910, USA OP: 213-740-5168 ___ 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/ ___ 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/
Re: [galaxy-dev] running functional tests on a galaxy server
Hi Chris and Nate, I'm also interested in being able to run functional tests against either our production server or a test server with an identical setup to make sure that not only the tools are working but their interaction with various compute resources are also working etc. If we get this going we would like to run this automatically and regularly so that administrators and users will be able to see whether particular tools are working or not. Regards. Steve McMahon Solutions architect senior systems administrator ASC Cluster Services Information Management Technology (IMT) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcma...@csiro.aumailto:steve.mcma...@csiro.au | www.csiro.auhttp://www.csiro.au/ PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600 ___ 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/
Re: [galaxy-dev] Problem fetching updates to toolshed tool
Greg, I just removed the dummy entry from our normal tool_conf.xml and the previously installed tool from the tool shed now nicely shows up in the menu. Also when installing new tools from the toolshed the radio list nicely shows the empty section in the panel to install too section. Haven't tested it with an empty section AND an empty shed_tool_conf thoughwill try to later...when I figured out how to completely remove a tool from the system. Thanks for the quick fix! Alex Van: Greg Von Kuster [mailto:g...@bx.psu.edu] Verzonden: maandag 6 februari 2012 16:21 Aan: Bossers, Alex CC: Ira Cooke; galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool This problem should be fixed in change set 6672:e38a9eb21336, which is now available in our central repo. Thanks for reporting this, and let me know if you discover other issues. Greg On Feb 6, 2012, at 7:54 AM, Bossers, Alex wrote: Greg, Exactly as you say. You cannot insert the repository tool when it's an empty section. Sorry for being unclear. Alex Van: Greg Von Kuster [mailto:g...@bx.psu.edu]mailto:[mailto:g...@bx.psu.edu] Verzonden: maandag 6 februari 2012 12:57 Aan: Bossers, Alex CC: Ira Cooke; galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool Hello Alex, Empty sections are not displayed in the Galaxy tool panel by design. However, can you clarify the behavior when installing a tool shed repository? Are you saying that empty sections cannot be selected for containing the tool shed repository tools because they are not displayed in the radio button selection list during installation time? If this is the case, then I'll take a look at this. Thanks! Greg On Feb 6, 2012, at 3:29 AM, Bossers, Alex wrote: PS: when I make the section empty again in the original tool_conf.xml it doesn't show up anymore in that section. :-( Actually the complete section is again invisible. Van: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu]mailto:[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 6 februari 2012 8:45 Aan: 'Greg Von Kuster'; Ira Cooke CC: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool Hi Greg, Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an EMPTY section in the tool_conf.xml menu where I want the toolshed tools to go to at the moment. To keep it maintainable for now at testing. But It does not show up in the bullet list of sections to install to (as these sections also do not show up in the menu itself until they cotain a valid tool xml). Other custom sections are there. Part of the tool_conf.xml /section label text=External tools id=externaltools / section name=ToolShed auto tools id=toolshedtools /section I added an empty tool file= / line in the section and still not there. Adding a valid tool lets it show up in the bullit list as it now also shows up in the left panel.. (as expected). Another test on the EMPTY section when I tried adding the tool providing THE SAME section name as custom in the field as a new tool panel section... it just adds it to the end of the section lists in the left. But it does work. It also remains working when I enable my own section menu again by adding another tool to the xml first. The section with the same name shows up on two places in the section list when adding tools from toolshed (as expected). Probably due to the different section id. There might be a possible problem when the id turns out the same as an already used one? I manually altered the shed_tool_conf.xml to match my section name and id and everything is ok. Maybe something to look into? Just a minor issue I think. Keep up the good work! Alex Van: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu]mailto:[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: vrijdag 3 februari 2012 22:16 Aan: Ira Cooke CC: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems. To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository
