Re: [galaxy-dev] enable emboss tools

[Björn Grüning]

Hi Paul,

the EMBOSS Tools are located in the http://toolshed.g2.bx.psu.edu/. You
need to install them from there.

http://wiki.g2.bx.psu.edu/Tool%
20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance

Hope that helps!
Bjoern

> Hi,
> 
> I'm trying to enable all the emboss tools on a local galaxy install.
> I found this tidbit (below) which I thought might help, but when I
> look at the tool_conf.xml, I don't see a list of emboss tools to
> uncomment.
> What should I try next?
> 
> 
> Kelly Vincent kpvincent at bx.psu.edu
> Fri Jan 14 11:26:37 EST 2011
> Previous message: [galaxy-dev] Restricted user builds
> Next message: [galaxy-dev] API connection error
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
> Rob,
> 
> When you start the Galaxy server, it looks in tool_conf.xml for which
> tools to load. Note that functional tests use tool_conf.xml.sample,
> and we leave the EMBOSS tools commented out in that file, so your
> tool_conf.xml file will still have them commented out if you haven't
> changed that. Uncomment the relevant lines and the EMBOSS tools should
> show up. After making changes to tool_conf.xml, you'll have to restart
> the server.
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
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Re: [galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

[Derrick Lin]

Thanks Jeremy,

I am sure it's trivial for us to do a manual clean up

Cheers,
D

On Fri, Sep 14, 2012 at 1:05 PM, Jeremy Goecks wrote:

> Cleaning up the datasets manually is the best suggestion for now. We're
> planning to enhance the clean up scripts to automatically delete history
> export files soon.
>
> Best,
> J.
>
> On Sep 13, 2012, at 10:37 PM, Derrick Lin wrote:
>
> > hi guys,
> >
> > I have been trying to clean up some old histories and datasets on our
> local galaxy. I have spotted one very old dataset file with big size didn't
> get removed no matter what.
> >
> > I went to check the reports webapp, that dataset isn't on the largest
> unpurged data files list (despite it has bigger size).
> >
> > Then I moved on to checking the database, no history or library
> associates with that dataset. Finally, I found its trace in
> job_to_input_dataset, so I could identified the job id and found that it's
> the file created by history Export to File.
> >
> > I also find relevant entry in job_export_history_archive. Since such
> datasets are not associated with any history, library, the documented
> dataset cleanup method does not work on them.
> >
> > Any suggestion?
> >
> > Regards,
> > Derrick
> > ___
> > 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/
>
>
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Re: [galaxy-dev] [galaxy-user] No output produced.....

[Jeremy Goecks]

The problem is likely your use of the from_work_dir attribute. 

I can see by the logging code that you're using an old(er) version of Galaxy, 
and it's likely that this attribute isn't functioning correctly in your 
instance. We've recently improved the implementation of from_work_dir, and 
you'll need to update your Galaxy instance to get these improvements.

Let us know if you still have problems after updating.

Finally, please direct tool and installation questions to the galaxy-dev 
mailing list rather than the galaxy-user mailing list. The galaxy-user mailing 
list is for tool usage and analysis questions.

Best,
J.

On Sep 13, 2012, at 9:06 PM,  wrote:

> Hi,
> I have my own image registration tool that I’ve created on my own local 
> instance of galaxy.
>  
> The method takes in two images (*.nii.gz) formats and registers them 
> together, and produces one registered *.nii.gz file and a *.trsf matrix file.
>  
> The first issue encountered was the method was expecting *.nii.gz files as 
> inputs but was receiving *.dat files. I navigated around this problem as 
> shown by the files below:
>  
> - <
>   <  two images
>   <   interpreter="bash">$__root_dir__/tools/registration/reg-wrapper.sh $moving 
> $fixed $outputTRSF $outputImage
> - <  
>   < />
>   <
>   <
>   < label="Image output file" help="Output Image File must have .nii.gz 
> extension" />
>
> - <  
>   <
>   < />
>
>   <  This tool uses Affine Registration to register two images.
>   
>  
> #!/bin/bash
> MOVING=`mktemp --suffix .nii.gz`
> FIXED=`mktemp --suffix .nii.gz`
> cat $1 > $MOVING
> cat $2 > $FIXED
> /usr/local/MILXView.12.08.1/BashScripts/RegisterAliBabaAffine -m $MOVING -f 
> $FIXED -t $3 -o $4
> RC=$?
> if [[ $RC == 0 ]]; then
>   OUTPUTTRSF=`mktemp --suffix .trsf`
>   OUTPUTIMG=`mktemp --suffix .nii.gz`
>   cat  $OUTPUTTRSF > $3
>   cat  $OUTPUTIMG > $4
>   rm $OUTPUTTRSF
>   rm $OUTPUTIMG
> fi
>  
> rm $MOVING
> rm $FIXED
>  
> exit $RC
>  
> This allows them to pass the *.nii.gz files that the registration method is 
> expecting.
>  
> Everything works fine and I can see output generated in the job_working_dir 
> and the history turns green...
>  
> galaxy@bmladmin-OptiPlex-745:~$ ls -lrt 
> ~/galaxy-dist/database/job_working_directory/000/27/
> total 2940
> -rw--- 1 galaxy nogroup   0 Sep 13 10:15 tmpRfHsOP_stderr
> -rw-r--r-- 1 galaxy nogroup 241 Sep 13 10:35 output.trsf
> -rw--- 1 galaxy nogroup  80 Sep 13 10:35 tmplmK0V2_stdout
> -rw-r--r-- 1 galaxy nogroup 2998272 Sep 13 10:38 output.nii.gz
>  
> However, the problem occurs when the files are copied from 
> ~/galaxy-dist/database/job_working_directory/000/27/ to 
> ~/galaxy-dist/database/files/000/. When this happens the files become size = 
> 0.
>  
> Any ideas?
>  
> -rw-r--r-- 1 galaxy nogroup   0 Sep 13 09:36 
> /home/galaxy/galaxy-dist/database/files/000/dataset_40.dat
> -rw-r--r-- 1 galaxy nogroup   0 Sep 13 09:36 
> /home/galaxy/galaxy-dist/database/files/000/dataset_41.dat
> -rw-r--r-- 1 galaxy nogroup   0 Sep 13 10:38 
> /home/galaxy/galaxy-dist/database/files/000/dataset_43.dat
> -rw-r--r-- 1 galaxy nogroup   0 Sep 13 10:38 
> /home/galaxy/galaxy-dist/database/files/000/dataset_42.dat
>  
>  
> The output in galaxy.log indicates it is successful:
>  
> /home/galaxy/galaxy-dist/tools/registration/reg-wrapper.sh 
> /home/galaxy/galaxy-dist/database/files/000/dataset_23.dat 
> /home/galaxy/galaxy-dist/database/files/000/dataset_20.dat output.trsf 
> output.nii.gz galaxy.jobs DEBUG 2012-09-13 10:38:10,334 The tool did not 
> define exit code or stdio handling; checking stderr for success galaxy.jobs 
> DEBUG 2012-09-13 10:38:10,361 finish(): Moved 
> /home/galaxy/galaxy-dist/database/job_working_directory/000/27/output.trsf to 
> /home/galaxy/galaxy-dist/database/files/000/dataset_42.dat as directed by 
> from_work_dir galaxy.jobs DEBUG 2012-09-13 10:38:10,380 finish(): Moved 
> /home/galaxy/galaxy-dist/database/job_working_directory/000/27/output.nii.gz 
> to /home/galaxy/galaxy-dist/database/files/000/dataset_43.dat as directed by 
> from_work_dir galaxy.jobs DEBUG 2012-09-13 10:38:10,609 job 27 ended
>  
> Is the issue copying *.nii.gz files and *.trsf file into *.dat files? Anyway 
> around this?
>  
> I’ve also modified ~/galaxy-dist/lib/galaxy/jobs/__init__.py (line 363) to 
> change shutil.move
>  
> To shutil.copy2 (same results)
>  
> Also put in a different output path to copy to. But essentially we have files 
> with size in ~/galaxy-dist/database/job_working_directory/000/id/, but they 
> files are size  0 after the move into ~/galaxy-dist/database/files/000
>  
>  
> Thanks
>  
> Neil
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Re: [galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

[Jeremy Goecks]

Cleaning up the datasets manually is the best suggestion for now. We're 
planning to enhance the clean up scripts to automatically delete history export 
files soon.

Best,
J. 

On Sep 13, 2012, at 10:37 PM, Derrick Lin wrote:

> hi guys,
> 
> I have been trying to clean up some old histories and datasets on our local 
> galaxy. I have spotted one very old dataset file with big size didn't get 
> removed no matter what.
> 
> I went to check the reports webapp, that dataset isn't on the largest 
> unpurged data files list (despite it has bigger size).
> 
> Then I moved on to checking the database, no history or library associates 
> with that dataset. Finally, I found its trace in job_to_input_dataset, so I 
> could identified the job id and found that it's the file created by history 
> Export to File.
> 
> I also find relevant entry in job_export_history_archive. Since such datasets 
> are not associated with any history, library, the documented dataset cleanup 
> method does not work on them.
> 
> Any suggestion?
> 
> Regards,
> Derrick
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/


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[galaxy-dev] reinstall

[Paul Tanger]

So I successfully added the emboss tools to galaxy, but I failed to
create a tool panel section for them.
So I thought I would uninstall them and install them again, this time
creating a tool panel section.
I'm following the instructions here (
http://wiki.g2.bx.psu.edu/Tool%20Shed#Deactivating_and_uninstalling_tool_shed_repositories_installed_into_a_local_Galaxy_instance
), but I'm getting this error when trying to reinstall the tool
repository:

AttributeError: 'NoneType' object has no attribute 'endswith'

Any ideas what I should do to get this reinstalled?

Thanks!
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[galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

[Derrick Lin]

hi guys,

I have been trying to clean up some old histories and datasets on our local
galaxy. I have spotted one very old dataset file with big size didn't get
removed no matter what.

I went to check the reports webapp, that dataset isn't on the largest
unpurged data files list (despite it has bigger size).

Then I moved on to checking the database, no history or library associates
with that dataset. Finally, I found its trace in job_to_input_dataset, so I
could identified the job id and found that it's the file created by history
Export to File.

I also find relevant entry in job_export_history_archive. Since such
datasets are not associated with any history, library, the documented
dataset cleanup method does not work on them.

Any suggestion?

Regards,
Derrick
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Re: [galaxy-dev] enable emboss tools

[Paul Tanger]

Ok I just gave up and did a fresh install and it seems to work.  Thanks for
your help.

On Thu, Sep 13, 2012 at 7:17 PM, Greg Von Kuster  wrote:

> Hi Paul,
>
> You should be able to get things working using the same sql command in the
> email below.  This process will be a new UI feature in the next Galaxy
> release.
>
> Greg Von Kuster
>
> On Sep 13, 2012, at 6:15 PM, Paul Tanger wrote:
>
> > Thanks for your help with this.  So I updated to the latest version,
> > but didn't read the instructions about creating a tools directory and
> > so I have repositories stuck in limbo, like described here:
> >
> -
> > Re: [galaxy-dev] Can't get automatic toolshed installation to work
> > Greg Von Kuster
> > Fri, 03 Aug 2012 17:58:58 -0700
> >
> > To get the repositories out of the limbo state, you'll have to get into
> your
> > database and run the following sql command.  Doing this will allow you to
> > install those repositories that were in limbo.  After they are
> installed, you
> > can uninstall them if you want to.  The case on the Strings is necessary.
> >
> > update tool_shed_repository set status = 'New' where status = 'Cloning';
> >
> > It was great to talk with you at the conference as well!
> >
> > Greg
> > http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg06437.html
> >
> -
> >
> > I'm just using the sqlite that came with the galaxy-dist, so I don't
> > know how to enter that sql command?
> >
> > On Thu, Sep 13, 2012 at 3:58 PM, Greg Von Kuster 
> wrote:
> >> Hi Paul,
> >>
> >> You have to be running the latest Galaxy dist release from
> >> https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance.
> >> Your repository tip should be e6444e7a1685.
> >>
> >> Greg Von Kuster
> >>
> >> On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote:
> >>
> >> Hmm, ok this tool shed is all new to me.  I followed the instructions
> >> until when I click on the "preview and install", I get this error:
> >>
> >> Not Found
> >>
> >> The resource could not be found.
> >> No action for /admin_toolshed/prepare_for_install
> >>
> >> On Thu, Sep 13, 2012 at 2:51 PM, Greg Von Kuster 
> wrote:
> >>
> >> Hi Paul,
> >>
> >>
> >> It seems that you probably did not use the Emboss tools in your local
> Galaxy
> >> instance before (maybe you have a new instance).  If this is the case,
> you
> >> can install the emboss_datatypes repository and the emboss_5 repository
> from
> >> the main Galaxy tool shed using the Admin UI features on your local
> galaxy
> >> instance.  See the following sections of the tool shed wiki for details.
> >>
> >>
> >>
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
> >>
> >>
> >>
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_data_types_into_a_local_Galaxy_instance
> >>
> >>
> >> Greg Von Kuster
> >>
> >>
> >>
> >> On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
> >>
> >>
> >> Hi,
> >>
> >>
> >> I'm trying to enable all the emboss tools on a local galaxy install.
> >>
> >> I found this tidbit (below) which I thought might help, but when I
> >>
> >> look at the tool_conf.xml, I don't see a list of emboss tools to
> >>
> >> uncomment.
> >>
> >> What should I try next?
> >>
> >>
> >>
> >> Kelly Vincent kpvincent at bx.psu.edu
> >>
> >> Fri Jan 14 11:26:37 EST 2011
> >>
> >> Previous message: [galaxy-dev] Restricted user builds
> >>
> >> Next message: [galaxy-dev] API connection error
> >>
> >> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
> >>
> >> Rob,
> >>
> >>
> >> When you start the Galaxy server, it looks in tool_conf.xml for which
> >>
> >> tools to load. Note that functional tests use tool_conf.xml.sample,
> >>
> >> and we leave the EMBOSS tools commented out in that file, so your
> >>
> >> tool_conf.xml file will still have them commented out if you haven't
> >>
> >> changed that. Uncomment the relevant lines and the EMBOSS tools should
> >>
> >> show up. After making changes to tool_conf.xml, you'll have to restart
> >>
> >> the server.
> >>
> >> ___
> >>
> >> 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/
>
>
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Re: [galaxy-dev] enable emboss tools

[Greg Von Kuster]

Hi Paul,

You should be able to get things working using the same sql command in the 
email below.  This process will be a new UI feature in the next Galaxy release.

Greg Von Kuster

On Sep 13, 2012, at 6:15 PM, Paul Tanger wrote:

> Thanks for your help with this.  So I updated to the latest version,
> but didn't read the instructions about creating a tools directory and
> so I have repositories stuck in limbo, like described here:
> -
> Re: [galaxy-dev] Can't get automatic toolshed installation to work
> Greg Von Kuster
> Fri, 03 Aug 2012 17:58:58 -0700
> 
> To get the repositories out of the limbo state, you'll have to get into your
> database and run the following sql command.  Doing this will allow you to
> install those repositories that were in limbo.  After they are installed, you
> can uninstall them if you want to.  The case on the Strings is necessary.
> 
> update tool_shed_repository set status = 'New' where status = 'Cloning';
> 
> It was great to talk with you at the conference as well!
> 
> Greg
> http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg06437.html
> -
> 
> I'm just using the sqlite that came with the galaxy-dist, so I don't
> know how to enter that sql command?
> 
> On Thu, Sep 13, 2012 at 3:58 PM, Greg Von Kuster  wrote:
>> Hi Paul,
>> 
>> You have to be running the latest Galaxy dist release from
>> https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance.
>> Your repository tip should be e6444e7a1685.
>> 
>> Greg Von Kuster
>> 
>> On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote:
>> 
>> Hmm, ok this tool shed is all new to me.  I followed the instructions
>> until when I click on the "preview and install", I get this error:
>> 
>> Not Found
>> 
>> The resource could not be found.
>> No action for /admin_toolshed/prepare_for_install
>> 
>> On Thu, Sep 13, 2012 at 2:51 PM, Greg Von Kuster  wrote:
>> 
>> Hi Paul,
>> 
>> 
>> It seems that you probably did not use the Emboss tools in your local Galaxy
>> instance before (maybe you have a new instance).  If this is the case, you
>> can install the emboss_datatypes repository and the emboss_5 repository from
>> the main Galaxy tool shed using the Admin UI features on your local galaxy
>> instance.  See the following sections of the tool shed wiki for details.
>> 
>> 
>> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
>> 
>> 
>> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_data_types_into_a_local_Galaxy_instance
>> 
>> 
>> Greg Von Kuster
>> 
>> 
>> 
>> On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
>> 
>> 
>> Hi,
>> 
>> 
>> I'm trying to enable all the emboss tools on a local galaxy install.
>> 
>> I found this tidbit (below) which I thought might help, but when I
>> 
>> look at the tool_conf.xml, I don't see a list of emboss tools to
>> 
>> uncomment.
>> 
>> What should I try next?
>> 
>> 
>> 
>> Kelly Vincent kpvincent at bx.psu.edu
>> 
>> Fri Jan 14 11:26:37 EST 2011
>> 
>> Previous message: [galaxy-dev] Restricted user builds
>> 
>> Next message: [galaxy-dev] API connection error
>> 
>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>> 
>> Rob,
>> 
>> 
>> When you start the Galaxy server, it looks in tool_conf.xml for which
>> 
>> tools to load. Note that functional tests use tool_conf.xml.sample,
>> 
>> and we leave the EMBOSS tools commented out in that file, so your
>> 
>> tool_conf.xml file will still have them commented out if you haven't
>> 
>> changed that. Uncomment the relevant lines and the EMBOSS tools should
>> 
>> show up. After making changes to tool_conf.xml, you'll have to restart
>> 
>> the server.
>> 
>> ___
>> 
>> 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/
>> 
>> 
>> 
>> 
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/


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[galaxy-dev] markupsafe module confliction problem

[Fenglou Mao]

Galaxy imported a library which already existed in the python system
folder. See the error message below.

Is that because RedHat 6 used a "python-marksafe", but Galaxy installation
program did not recognize it? Or Galaxy require a higher version of
markupsafe module?

/home/x/work/galaxy-dist/
lib/galaxy/__init__.py:79: UserWarning: Module
markupsafe was already imported from
/usr/lib64/python2.6/site-packages/markupsafe/__init__.pyc, but
/home/x/work/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg
is being added to sys.path
  self.check_version_conflict()

The system package is python-markupsafe-0.9.2-4.el6.x86_64
Galaxy has a newer version, it is
MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg

Any idea how to resolve this problem?
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Re: [galaxy-dev] enable emboss tools

[Paul Tanger]

Thanks for your help with this.  So I updated to the latest version,
but didn't read the instructions about creating a tools directory and
so I have repositories stuck in limbo, like described here:
-
Re: [galaxy-dev] Can't get automatic toolshed installation to   work
Greg Von Kuster
Fri, 03 Aug 2012 17:58:58 -0700

To get the repositories out of the limbo state, you'll have to get into your
database and run the following sql command.  Doing this will allow you to
install those repositories that were in limbo.  After they are installed, you
can uninstall them if you want to.  The case on the Strings is necessary.

update tool_shed_repository set status = 'New' where status = 'Cloning';

It was great to talk with you at the conference as well!

Greg
http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg06437.html
-

I'm just using the sqlite that came with the galaxy-dist, so I don't
know how to enter that sql command?

On Thu, Sep 13, 2012 at 3:58 PM, Greg Von Kuster  wrote:
> Hi Paul,
>
> You have to be running the latest Galaxy dist release from
> https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance.
> Your repository tip should be e6444e7a1685.
>
> Greg Von Kuster
>
> On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote:
>
> Hmm, ok this tool shed is all new to me.  I followed the instructions
> until when I click on the "preview and install", I get this error:
>
> Not Found
>
> The resource could not be found.
> No action for /admin_toolshed/prepare_for_install
>
> On Thu, Sep 13, 2012 at 2:51 PM, Greg Von Kuster  wrote:
>
> Hi Paul,
>
>
> It seems that you probably did not use the Emboss tools in your local Galaxy
> instance before (maybe you have a new instance).  If this is the case, you
> can install the emboss_datatypes repository and the emboss_5 repository from
> the main Galaxy tool shed using the Admin UI features on your local galaxy
> instance.  See the following sections of the tool shed wiki for details.
>
>
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
>
>
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_data_types_into_a_local_Galaxy_instance
>
>
> Greg Von Kuster
>
>
>
> On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
>
>
> Hi,
>
>
> I'm trying to enable all the emboss tools on a local galaxy install.
>
> I found this tidbit (below) which I thought might help, but when I
>
> look at the tool_conf.xml, I don't see a list of emboss tools to
>
> uncomment.
>
> What should I try next?
>
>
>
> Kelly Vincent kpvincent at bx.psu.edu
>
> Fri Jan 14 11:26:37 EST 2011
>
> Previous message: [galaxy-dev] Restricted user builds
>
> Next message: [galaxy-dev] API connection error
>
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
> Rob,
>
>
> When you start the Galaxy server, it looks in tool_conf.xml for which
>
> tools to load. Note that functional tests use tool_conf.xml.sample,
>
> and we leave the EMBOSS tools commented out in that file, so your
>
> tool_conf.xml file will still have them commented out if you haven't
>
> changed that. Uncomment the relevant lines and the EMBOSS tools should
>
> show up. After making changes to tool_conf.xml, you'll have to restart
>
> the server.
>
> ___
>
> 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/
>
>
>
>
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Re: [galaxy-dev] enable emboss tools

[Greg Von Kuster]

Hi Paul,

You have to be running the latest Galaxy dist release from 
https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance.  Your 
repository tip should be e6444e7a1685.

Greg Von Kuster

On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote:

> Hmm, ok this tool shed is all new to me.  I followed the instructions
> until when I click on the "preview and install", I get this error:
> 
> Not Found
> 
> The resource could not be found.
> No action for /admin_toolshed/prepare_for_install
> 
> On Thu, Sep 13, 2012 at 2:51 PM, Greg Von Kuster  wrote:
>> Hi Paul,
>> 
>> It seems that you probably did not use the Emboss tools in your local Galaxy 
>> instance before (maybe you have a new instance).  If this is the case, you 
>> can install the emboss_datatypes repository and the emboss_5 repository from 
>> the main Galaxy tool shed using the Admin UI features on your local galaxy 
>> instance.  See the following sections of the tool shed wiki for details.
>> 
>> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
>> 
>> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_data_types_into_a_local_Galaxy_instance
>> 
>> Greg Von Kuster
>> 
>> 
>> On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
>> 
>>> Hi,
>>> 
>>> I'm trying to enable all the emboss tools on a local galaxy install.
>>> I found this tidbit (below) which I thought might help, but when I
>>> look at the tool_conf.xml, I don't see a list of emboss tools to
>>> uncomment.
>>> What should I try next?
>>> 
>>> 
>>> Kelly Vincent kpvincent at bx.psu.edu
>>> Fri Jan 14 11:26:37 EST 2011
>>> Previous message: [galaxy-dev] Restricted user builds
>>> Next message: [galaxy-dev] API connection error
>>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>>> Rob,
>>> 
>>> When you start the Galaxy server, it looks in tool_conf.xml for which
>>> tools to load. Note that functional tests use tool_conf.xml.sample,
>>> and we leave the EMBOSS tools commented out in that file, so your
>>> tool_conf.xml file will still have them commented out if you haven't
>>> changed that. Uncomment the relevant lines and the EMBOSS tools should
>>> show up. After making changes to tool_conf.xml, you'll have to restart
>>> the server.
>>> ___
>>> 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/
>> 
> 

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Re: [galaxy-dev] enable emboss tools

[Paul Tanger]

Hmm, ok this tool shed is all new to me.  I followed the instructions
until when I click on the "preview and install", I get this error:

Not Found

The resource could not be found.
No action for /admin_toolshed/prepare_for_install

On Thu, Sep 13, 2012 at 2:51 PM, Greg Von Kuster  wrote:
> Hi Paul,
>
> It seems that you probably did not use the Emboss tools in your local Galaxy 
> instance before (maybe you have a new instance).  If this is the case, you 
> can install the emboss_datatypes repository and the emboss_5 repository from 
> the main Galaxy tool shed using the Admin UI features on your local galaxy 
> instance.  See the following sections of the tool shed wiki for details.
>
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
>
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_data_types_into_a_local_Galaxy_instance
>
> Greg Von Kuster
>
>
> On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
>
>> Hi,
>>
>> I'm trying to enable all the emboss tools on a local galaxy install.
>> I found this tidbit (below) which I thought might help, but when I
>> look at the tool_conf.xml, I don't see a list of emboss tools to
>> uncomment.
>> What should I try next?
>>
>>
>> Kelly Vincent kpvincent at bx.psu.edu
>> Fri Jan 14 11:26:37 EST 2011
>> Previous message: [galaxy-dev] Restricted user builds
>> Next message: [galaxy-dev] API connection error
>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>> Rob,
>>
>> When you start the Galaxy server, it looks in tool_conf.xml for which
>> tools to load. Note that functional tests use tool_conf.xml.sample,
>> and we leave the EMBOSS tools commented out in that file, so your
>> tool_conf.xml file will still have them commented out if you haven't
>> changed that. Uncomment the relevant lines and the EMBOSS tools should
>> show up. After making changes to tool_conf.xml, you'll have to restart
>> the server.
>> ___
>> 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/
>

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Re: [galaxy-dev] Small enhancment to the tarball parsing.

[Greg Von Kuster]

Hello Bjorn,

I've committed your patch in change set revision 7669:5088185a5bca, which is 
currently running on the test Galaxy tools shed.  The fix will be moved to the 
main Galaxy tool shed at the time of the next Galaxy release, currently 
scheduled for the end of next week.

Regarding the main tool shed tracking Galaxy dist, that means that the main 
tool shed gets updated only when the Galaxy dist repository gets updated - this 
is now going to occur about every two weeks.  Running the code from the Galaxy 
central repository may not fully work if going against the main Galaxy tool 
shed, but the test Galaxy tool shed tracks the Galaxy central code, so things 
should work there.

Until recently, both the main tool shed and the test tool shed tracked Galaxy 
central, but the community requested that the main tool shed tracks the stable 
Galaxy dist repository instead of the development Galaxy central repository.

Regarding contributed fixes, please keep them coming, as they are very much 
appreciated!  I may have misunderstood one of your previous messages if I 
responded in a way that was confusing.  If so, I apologize.

Thanks so much for all of your help and contributions!

Greg Von Kuster


On Sep 10, 2012, at 2:45 PM, Björn Grüning wrote:

> Hi Greg,
> 
> what did you think about the attached patch?
> In my setup i have 'deployment folder' where i symlink all different
> wrapper under a new logical structure for toolshed deployment. That
> directory gets tarred. Unfortunately a few files ending up as hard-link
> in the tarball. At least TarInfo returns true.
> 
> TarInfo.islnk()
> Return True if it is a hard link.
> 
> If im not wrong it does not hurt to also allow hard-links. Also it would
> be nice to know which file is the offender, if a tarball gets rejected.
> 
> One question to the galaxy-dist. The toolshed is now tracking
> galaxy-dist? What does that mean? That all development is happening in
> galaxy-dist and not in central? That would mean that it is not possible
> to run central with both galaxy and the toolshed? Im a little bit
> confused. When i will find a bug in galaxy or the toolshed in
> galaxy-central the bug should not be fixed and posted?
> 
> Thanks,
> Bjoern
> 
> 
> 
> -- 
> Björn Grüning
> Albert-Ludwigs-Universität Freiburg
> Institute of Pharmaceutical Sciences
> Pharmaceutical Bioinformatics
> Hermann-Herder-Strasse 9
> D-79104 Freiburg i. Br.
> 
> Tel.:  +49 761 203-4872
> Fax.:  +49 761 203-97769
> E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> Web: http://www.pharmaceutical-bioinformatics.org/
> 


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Re: [galaxy-dev] Size of the genome indexes repos in Galaxy Main

[Derrick Lin]

Thanks Nate,

D

On Thu, Sep 13, 2012 at 10:43 PM, Nate Coraor  wrote:

> On Sep 12, 2012, at 8:28 PM, Derrick Lin wrote:
>
> > Hi guys,
> >
> > Just a quick question about the total size of the genome indexes just
> made available via rsync server?
>
>
> Hi Derrick,
>
> The full size is around 3 TB.
>
> --nate
>
> >
> > Cheers,
> > Derrick
> > ___
> > Please keep all replies on the list by using "reply all"
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> > and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
>
>
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Re: [galaxy-dev] enable emboss tools

[Greg Von Kuster]

Hi Paul,

It seems that you probably did not use the Emboss tools in your local Galaxy 
instance before (maybe you have a new instance).  If this is the case, you can 
install the emboss_datatypes repository and the emboss_5 repository from the 
main Galaxy tool shed using the Admin UI features on your local galaxy 
instance.  See the following sections of the tool shed wiki for details.

http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance

http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_data_types_into_a_local_Galaxy_instance

Greg Von Kuster


On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:

> Hi,
> 
> I'm trying to enable all the emboss tools on a local galaxy install.
> I found this tidbit (below) which I thought might help, but when I
> look at the tool_conf.xml, I don't see a list of emboss tools to
> uncomment.
> What should I try next?
> 
> 
> Kelly Vincent kpvincent at bx.psu.edu
> Fri Jan 14 11:26:37 EST 2011
> Previous message: [galaxy-dev] Restricted user builds
> Next message: [galaxy-dev] API connection error
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
> Rob,
> 
> When you start the Galaxy server, it looks in tool_conf.xml for which
> tools to load. Note that functional tests use tool_conf.xml.sample,
> and we leave the EMBOSS tools commented out in that file, so your
> tool_conf.xml file will still have them commented out if you haven't
> changed that. Uncomment the relevant lines and the EMBOSS tools should
> show up. After making changes to tool_conf.xml, you'll have to restart
> the server.
> ___
> 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/


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[galaxy-dev] Picard Reorder tool's reference genome box

[Shantanu Pavgi]

Our local Galaxy instance doesn't have an auto-fill option working with 
Picard-Reorder-SAM/BAM tool's 'select a reference genome' box. We do have a 
'tool-data/picard_index.loc' file with genome build-ids for picard tools. Do we 
need to configure anything else to get reference genome field working? Any 
pointers will be really helpful.

Galaxy revision: ec29ce8e27a1
Picard tools version: 1.56

--
Thanks,
Shantanu
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Re: [galaxy-dev] toolshed upload problem

[Greg Von Kuster]

Hi David,

I committed a fix for this issue in changeset 7662:c4ced3262d0d, which is 
currently available only in the Galaxy central repository.  The fix will be 
available in the next Galaxy release scheduled for the end of next week.

Thanks for reporting this problem, and sorry for the inconvenience.

Greg Von Kuster

On Sep 12, 2012, at 6:16 PM, David Hoover wrote:

> I've created a repository in the test toolshed and tried uploading gzipped 
> tarballs with all files required.  I have several tool config files (.xml) 
> wrapping a single python script with some tool-data dependencies.
> 
> If I upload a single tool config file with the dependencies, everything is 
> ok.  However, if I try uploading more than one config file at a time, it 
> complains with the error message for all but one of the config files:
> 
> *.xml - This file requires an entry for "'gatk2_picard_indexes'" in the 
> tool_data_table_conf.xml file. Upload a file named 
> tool_data_table_conf.xml.sample to the repository that includes the required 
> entry to correct this error.
> 
> The tool_data_table_conf.xml.sample file already exists within the tarball.  
> Nothing changes if I upload the file separately.
> 
> Any ideas?
> 
> David Hoover
> Helix Systems Staff
> ___
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[galaxy-dev] enable emboss tools

[Paul Tanger]

Hi,

I'm trying to enable all the emboss tools on a local galaxy install.
I found this tidbit (below) which I thought might help, but when I
look at the tool_conf.xml, I don't see a list of emboss tools to
uncomment.
What should I try next?


Kelly Vincent kpvincent at bx.psu.edu
Fri Jan 14 11:26:37 EST 2011
Previous message: [galaxy-dev] Restricted user builds
Next message: [galaxy-dev] API connection error
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Rob,

When you start the Galaxy server, it looks in tool_conf.xml for which
tools to load. Note that functional tests use tool_conf.xml.sample,
and we leave the EMBOSS tools commented out in that file, so your
tool_conf.xml file will still have them commented out if you haven't
changed that. Uncomment the relevant lines and the EMBOSS tools should
show up. After making changes to tool_conf.xml, you'll have to restart
the server.
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Re: [galaxy-dev] tool_data_table.xml and *.loc not installed with repository

[Greg Von Kuster]

Hello Birgit,

I've committed a fix for this issue in change set revision 7668:802413bc137b, 
which is currently running on the test tool shed and is currently available 
only in the Galaxy central repository.  This fix will be include in the ext 
Galaxy distribution scheduled for the end of next week.  You'll have to pull 
from the Galaxy central repo if you want to use the fix before the next release.

Sorry for the inconvenience on this,

Greg Von Kuster


On Sep 10, 2012, at 4:30 PM, Birgit Crain wrote:

> I downloaded the latest galaxy-dist this morning and I used the test toolshed 
> to test my repository first before I upload it to the main toolshed.
> Thanks
> 
> Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete 
> Genomics, Inc.
> (650) 428-6023 office | (408) 605-3938 mobile
> bcr...@completegenomics.com
> 
> 
> From: Greg Von Kuster 
> Date: Monday, September 10, 2012 1:06 PM
> To: Birgit Crain 
> Cc: "galaxy-dev@lists.bx.psu.edu" 
> Subject: Re: [galaxy-dev] tool_data_table.xml and *.loc not installed with 
> repository
> 
> Hello Birgit,
> 
> It looks like you are attempting to install from the test Galaxy tool shed, 
> which tracks fairly closely to the Galaxy central repository on bitbucket.  
> What changeset revision of Galaxy are you running?  It will always speed up 
> our handling of issues like this if you include this information in your 
> initial emails in the future.
> 
> The main Galaxy tool shed now track the Galaxy dist repository on bitbucket.
> 
> Thanks,
> 
> Greg Von Kuster
> 
> On Sep 10, 2012, at 3:44 PM, Birgit Crain wrote:
> 
>> Hi 
>> 
>> I got a problem with the tool_data_table.xml and tool-data/*.loc files when 
>> testing the download of my repository.
>> 
>> My repository contains a *.loc.sample file and a 
>> tool_data_table_conf.xml.sample (they were unchanged from my last upload to 
>> the repository).
>> When installing the repository I get the following messages:
>> 
>> 172.22.128.28 - - [10/Sep/2012:11:46:16 -0700] "GET 
>> /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2F
>>  HTTP/1.1" 302 - "http://lx-galaxy-1:8080/admin_toolshed/browse_tool_sheds"; 
>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 
>> Firefox/15.0.1"
>> 172.22.128.28 - - [10/Sep/2012:11:46:39 -0700] "GET 
>> /admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&repository_ids=96d1ef4698eaa22d&changeset_revisions=982e19c29ec0
>>  HTTP/1.1" 200 - 
>> "http://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=96d1ef4698eaa22d&changeset_revision=982e19c29ec0&webapp=galaxy";
>>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 
>> Firefox/15.0.1"
>> Adding new row (or updating an existing row) for repository 
>> 'testing_cgatools' in the tool_shed_repository table.
>> galaxy.web.controllers.admin_toolshed DEBUG 2012-09-10 11:47:27,751 
>> Appending to tool panel section: CG tools
>> 172.22.128.28 - - [10/Sep/2012:11:47:27 -0700] "POST 
>> /admin_toolshed/prepare_for_install?encoded_repo_info_dicts=606805d7b3160cf8502df2b105df5510f61a250c%3A7b2274657374696e675f636761746f6f6c73223a205b22746869732069732061207465737420222c2022687474703a2f2f74657374746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f62637261696e2d636f6d706c65746567656e6f6d6963732f74657374696e675f636761746f6f6c73222c2022393832653139633239656330222c20223233222c202262637261696e2d636f6d706c65746567656e6f6d696373222c206e756c6c5d7d&includes_tools=True&tool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2F&includes_tool_dependencies=False
>>  HTTP/1.1" 302 - 
>> "http://lx-galaxy-1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&repository_ids=96d1ef4698eaa22d&changeset_revisions=982e19c29ec0";
>>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 
>> Firefox/15.0.1"
>> 172.22.128.28 - - [10/Sep/2012:11:47:27 -0700] "GET 
>> /admin_toolshed/initiate_repository_installation?shed_repository_ids=f2db41e1fa331b3e&reinstalling=False&encoded_kwd=80e690a1cf32f1294e27873f210c5344dc427413%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

Re: [galaxy-dev] Automatic installation of third party dependancies

[Lance Parsons]

Actually, I think that is exactly the issue.  I DO have 3:f7a5b54a8d4f 
installed. I've run into a related issue before, but didn't fully 
understand it.


I believe what happened was:
1) I pushed revision 3:f7a5b54a8d4f to the tool shed which contained the 
first revision of version 0.2 of the htseq-count tool.
2) I installed the htseq-count tool from the tool shed, getting revision 
3:f7a5b54a8d4f
3) I pushed an update to version 0.2 of the htseq-count tool. The only 
changes were to tool-dependencies so I thought it would be safe to leave 
the version number alone (perhaps this is problem?)

4) I attempted to get updates and ran into the issue I described.

I also ran into this (I believe it was with freebayes, but not sure) 
when I removed (uninstalled) a particular revision of a tool. Then the 
tool was updated. I went to install and and it said that I already had a 
previous revision installed and should install that. However, I couldn't 
since the tool shed won't allow installation of old revisions of the 
same version of a tool.


Let me know if there is anything I can do to help sort this out.

Lance

Greg Von Kuster wrote:

Hi Lance,

What is the changeset revision that you installed?  It looks like you 
could only have installed one of the following 3 revisions:


1:14e18dc9ed13 

2:f5d08224af89 

4:14bec14f4290 



Since you could not have installed 3:f7a5b54a8d4f 
, 
I'm not quite sure how you could be trying to update to 4.  Did you 
install 4 and are trying to get updates?


I've tried several things but am not able to reproduce this behavior, 
so it's difficult to determine what may be causing the problem


Greg Von Kuster

On Sep 12, 2012, at 3:08 PM, Lance Parsons wrote:

I've updated my development system now, and when I try to get updates 
for that particular tool (htseq_count) I run into the following 
error.  Any ideas on how I can/should fix this?  Thanks.


URL: 
http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=htseq_count&owner=lparsons&changeset_revision=f7a5b54a8d4f&latest_changeset_revision=14bec14f4290&latest_ctx_rev=4 

File 
'/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', 
line 364 in respond

app_iter = self.application(environ, detect_start_response)
File 
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', 
line 98 in __call__

environ, self.app)
File 
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', 
line 539 in intercept_output

app_iter = application(environ, replacement_start_response)
File 
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', 
line 80 in __call__

return self.application(environ, start_response)
File 
'/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py', 
line 91 in __call__

return self.app( environ, start_response )
File 
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', 
line 632 in __call__

return self.application(environ, start_response)
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py', 
line 160 in __call__

body = method( trans, **kwargs )
File 
'/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py', 
line 184 in decorator

return func( self, trans, *args, **kwargs )
File 
'/data/galaxy-dev/galaxy-dev/lib/galaxy/web/controllers/admin_toolshed.py', 
line 1469 in update_to_changeset_revision

update_repository( repo, latest_ctx_rev )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util.py', line 
1655 in update_repository

rev=ctx_rev )
File 
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py', 
line 5661 in update

rev = scmutil.revsingle(repo, rev, rev).rev()
File 
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', 
line 515 in revsingle

l = revrange(repo, [revspec])
File 
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', 
line 588 in revrange

for r in m(repo, range(len(repo))):
File 
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', 
line 1414 in mfunc

return getset(repo, subset, tree)
File 
'/data/galaxy-dev/galaxy-dev/eggs/mercurial

Re: [galaxy-dev] problem in Fastq tool

[Daniel Blankenberg]

Hi Felix,

Thanks for reporting this error, it has been fixed in revision 
7663:cc064ff4249b. Please let us know if you encounter additional issues.


Thanks for using Galaxy,

Dan


On Sep 10, 2012, at 12:23 PM, Felix Homa wrote:

> Hello,
>  
> We noticed a problem with the tool Filter Fastq. It seemed to mishandle the 
> paired-end checkbox. Here is the XML which seems to not work:
>  
>truevalue="paired_end" falsevalue="single_end" checked="False"/>
>  
> Concretely, $paired_end.value return True or False as value and not 
> "paired_end" or "single_end", so in the python code execution,
>  
> #if $paired_end.value == 'single_end':
>  qual_scores_split = [ qual_scores ]
> #else:
>  qual_scores_split = [ qual_scores[ 0:int( len( qual_scores ) / 2 ) ], 
> qual_scores[ int( len( qual_scores ) / 2 ): ]]
>  
> Always go in the else, always splitting reads even when they are single_end.
>  
> It induces wrong results in our read filtering.
>  
> I hope the explanation is clear enough
>  
> Best regards,
>  
> Felix
>  
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[galaxy-dev] Galaxy VM

[kauerbach]

Hello, 



Can anyone tell me if there is a  Galaxy VM available for download that 
definitely contains the NCBI-BLAST tools?  



I have seen several download links for Galaxy VMs that include some tools, but 
it is not clear what tools precisely  they contain, and if BLAST is one of 
them. 



Thank you. 




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Re: [galaxy-dev] Automatic installation of third party dependancies

[Greg Von Kuster]

Hi Lance,

I installed your htseq repository and all 3 tool dependencies installed fine on 
my mac, so the xml definition works!

Greg Von Kuster

On Sep 11, 2012, at 5:50 PM, Lance Parsons wrote:

> Thanks Greg. I used you're updated version and added numpy as a separate 
> dependency.  It seems to work in my development system. I haven't updated my 
> qa or production versions yet, so I can't check there.  Perhaps you could 
> test it and let me know if there are issues, etc.
> 
> Glad I can be of help.
> 
> Lance
> 
> Greg Von Kuster wrote:
>> 
>> Hello Lance,
>> 
>> See my inline comments.
>> 
>> 
>> On Sep 4, 2012, at 3:15 PM, Lance Parsons wrote:
>> 
>>> I've put together a tool wrapper for the htseq-count script that is part of 
>>> the HTSeq python package and uploaded that to the tool shed.  However, I 
>>> have discovered that the tool dependancies do not install properly.  There 
>>> are a couple of issues that I've run into.
>>> 
>>> 1) The biggest issue is the inability to set both the PYTHONPATH and PATH 
>>> environment variables as part of installation.  If I put two separate 
>>>  tags, then the second overwrites the first 
>>> in the env.sh file. If instead, I put two  tags 
>>> within the action, only one (the second) gets executed during installation.
>> 
>> The above issues have been corrected in changeset 7621:108cda898646, which 
>> is currently available only in the Galaxy central repository.  There is a 
>> new Galaxy distribution scheduled to go out today, but unfortunately this 
>> changeset will not be included.  From here on, Galaxy releases are 
>> tentatively scheduled for every 2 weeks, so if you don't want to pull from 
>> the Galaxy central repository, the fix should be available in the next 
>> release 2 weeks from now.
>> 
>> I've slightly altered your tool_dependencies.xml file (mostly because I've 
>> implemented support for a new "make_directory" tag.  It is attached below - 
>> you should updated your tool_dependencies.xml file in your htseq_count 
>> repository with this updated version.
>> 
>> 
>>> 2) Another issue is the inability to install Numpy as a dependancy to 
>>> HTSeq.  I can get Numpy to install, but it won't be in the PYTHONPATH when 
>>> HTSeq is installed (or executed).
>> 
>> Were you attempting to install numpy as another package defined in your 
>> tool-dependencies.xml file?   If so, the fixes in the above changeset should 
>> allow you to do that now since you can install it before htseq and set 
>> PYTHONPATH to point to numpy  as part of the installation.
>> 
>> Let me know if you need additional help or bump into further problems.   The 
>> tool dependency installation components are fairly immature, so adding 
>> enhancements for new tools like yours is very valuable.
>> 
>> Thanks for your help on this,
>> 
>> Greg Von Kuster
>> 
>> 
>>> Any thoughts on how to address these issues would be appreciated.
>>> 
>>> -- 
>>> Lance Parsons - Scientific Programmer
>>> 134 Carl C. Icahn Laboratory
>>> Lewis-Sigler Institute for Integrative Genomics
>>> Princeton University
>>> 
>>> ___
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>>> and other Galaxy lists, please use the interface at:
>>> 
>>> http://lists.bx.psu.edu/
>> 
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 

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Re: [galaxy-dev] environment variables and paths for toolshed tools

[Greg Von Kuster]

Hello David,

I've just committed change set 7656:6aadac8026cb to the Galaxy central 
repository that provides the ability to do what you need here.  It would be 
great if you could try things out and let me know if you run into any problems. 
 

I've been working with nikhil-joshi's deseq_and_sam2counts repository in the 
main Galaxy tool shed because his tools require this new feature as well.  This 
example should provide you with the information you'll need to tweak your tool 
shed repository so that your tool dependencies are located where they get 
installed rather than attempting to move them to ${GALAXY_DATA_INDEX_DIR} or 
some other location.

Here is the tool_dependency.xml file entry for locating a directory referred to 
by an environment variable name R_SCRIPT_PATH.





$REPOSITORY_INSTALL_DIR




The  tag, is still supported inside  tag sets, but 
when defined at the xml root level, it will locate dependencies included in the 
installed tool shed repository.  Of course, the above tool_dependencies.xml 
file could of course also include entries for tool dependencies that are 
packages, For example:





$REPOSITORY_INSTALL_DIR




http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz
./configure 
--prefix=$INSTALL_DIR
make

$INSTALL_DIR/bin




You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build 
R.




These tool dependency definitions are handled as described in the following 
section of the tool shed wiki:

http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories

So in order for the dependencies to be handled when the repository is 
installed, they must be defined in at least one of the  tag sets 
in at least 1 tool config in the repository.  So, the  tag set in 
the deseq.xml tool config file will look something like this (there are more 
requirement tags defined here than in the tool_dependencies.xml fiel above, but 
you should get the idea).



R_SCRIPT_PATH
R
Bioconductor
DESeq
aroma.light
lattice



The  tag set in the deseq.xml tool config is also slightly altered.  
Here is the way it looks before using this new approach:


 stderr_wrapper.py Rscript ${GALAXY_DATA_INDEX_DIR}/deseq.R $counts 
$column_types $comparison $top_table $diagnostic_html 
"$diagnostic_html.files_path" "$counts.name"


To use this new feature, the command string now uses the R_SCRIPT_PATH 
environment variable ( notice the required backslash to escape the $ )



stderr_wrapper.py Rscript \$R_SCRIPT_PATH/deseq.R $counts $column_types 
$comparison $top_table $diagnostic_html "$diagnostic_html.files_path" 
"$counts.name"


When installed from the tool shed, a tool dependency object named R_SCRIPT_PATH 
will be created and associated with the installed repository.  The dependency 
will have a pointer to the env.sh file that is created to set the value of the 
R_SCRIPT_PATH environment variable.

Let me know if you bump into any issues in getting this working for your tools.

Thanks!

Greg Von Kuster


On Sep 12, 2012, at 1:00 PM, David Hoover wrote:

> Are there any environment variables that are honored by toolshed installed 
> tools?  I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or 
> $GALAXY_HOME, then uploaded it the test toolshed, then installed it 
> automatically.  Neither of these resolved to what I expected.  I don't want 
> to hard-code the path in the xml tool file, but rather have a default 
> location for other executables and jar files.  How should this best be done?
> 
> David Hoover
> Helix Systems Staff
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[galaxy-dev] FTP problem

[Rémy Dernat]

Hi,

I follow this tutorial to configure FTP with galaxy :
wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP

However, even if I can [ log into / upload file to / donwload file to
] my ftp server with my Galaxy account, I can not retrieve these data
on my Galaxy Web server.
It says : "Your FTP upload directory contains no files."
The directory with my email account is created and the file exists.

I have to say that my proftpd account is a special account : ftpgalaxy
(like the howto).

This is not the user used by the galaxy daemon process. If I change
the user to the galaxy daemon user (which is 'galaxy'), I can not
login anymore into my ftp server.

The only way to login on my ftp server is tu put my UID/GID used by
'ftpgalaxy' account in my SELECT query.

Those two servers are not on the same computer. But those 2 accounts
exists with the same UID/GID on both computers.


Any help would be appreciated.

Regards,
Remy
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Re: [galaxy-dev] Size of the genome indexes repos in Galaxy Main

[Nate Coraor]

On Sep 12, 2012, at 8:28 PM, Derrick Lin wrote:

> Hi guys,
> 
> Just a quick question about the total size of the genome indexes just made 
> available via rsync server?


Hi Derrick,

The full size is around 3 TB.

--nate

> 
> Cheers,
> Derrick
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