Re: [galaxy-dev] Setting the output label based on input parameters?

[Nikhil Joshi]

It looks like the Cheetah syntax only is parsed within the 
tags so I figured out a way to do it... but it seems hackish.  I
basically changed the string values of truevalue and falsevalue within the
parameter to be an English sentence that would become the label for the
output.  I.e., in the input section:



and in the output section:



This seems wrong to do, but it does work.  If anyone has a better method,
please let me know!

- Nik.

On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi  wrote:

> It's actually a boolean checkbox. so I basically want the label to
> change based upon whether or not the checkbox is checked.  Is there any way
> to do that?  Again, I've tried using the Cheetah syntax to do the #if #end
> inside the  tags but that didn't work.
>
> - Nik.
>
>
> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB wrote:
>
>>
>> I meant to say label="${input}" or label="${input.value}.
>>
>> If it's a select field then you can change the option values to the text
>> you want to add to your output label.
>>
>> Shaun
>>
>>
>>
>>
>>
>>
>> Quoting Kanwei Li  on Wed, 24 Aug 2011 20:34:57 -0400:
>>
>>  Hi Nikhil,
>>>
>>> The tool templates are Cheetah templates, so you can do things like:
>>>
>>> 
>>> %if param == True:
>>>   
>>> %else
>>>  
>>> %endif
>>> 
>>>
>>> Thanks,
>>>
>>> K
>>>
>>> On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi 
>>> wrote:
>>>
>>>  Hi all,

 Is there a way to set the label of the output based on the input
 parameters?  Perhaps by using the  tag?  Basically, I want the
 output label to be different if the user sets a particular parameter to
 be
 true.

 - Nik.

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>>>
>>
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>>
>
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[galaxy-dev] API keys and id encryption (silly questions)

[Louise-Amélie Schmitt]

Hello everyone,

These questions are a bit silly but I'm really ignorant when it comes to 
security. Sorry about that.


Why use API keys instead of  user names? Is it to to prevent anyone from 
figuring out who is behind an URL? Or did I miss the point?


Also, why encrypt the dataset/library/folder ids when a simple display 
is enough to get them?


Thanks
L-A
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Re: [galaxy-dev] Setting the output label based on input parameters?

[Ross]

>> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB 
>> wrote:
>>>
>>> I meant to say label="${input}" or label="${input.value}.
>>>

Nikhil, did you try as Shaun and others have suggested? Any available
string parameter can be used in a label as far as I can tell.

This is a common idiom - ask for a string ('title') to describe the
job/output for posterity, then in an output:



There's even a built in ${on_string} if you just want the file name
plus some history ids?


On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi  wrote:
> It looks like the Cheetah syntax only is parsed within the 
> tags so I figured out a way to do it... but it seems hackish.  I
> basically changed the string values of truevalue and falsevalue within the
> parameter to be an English sentence that would become the label for the
> output.  I.e., in the input section:
>
>  falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/>
>
> and in the output section:
>
> 
>
> This seems wrong to do, but it does work.  If anyone has a better method,
> please let me know!
>
> - Nik.
>
> On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi  wrote:
>>
>> It's actually a boolean checkbox. so I basically want the label to
>> change based upon whether or not the checkbox is checked.  Is there any way
>> to do that?  Again, I've tried using the Cheetah syntax to do the #if #end
>> inside the  tags but that didn't work.
>>
>> - Nik.
>>
>> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB 
>> wrote:
>>>
>>> I meant to say label="${input}" or label="${input.value}.
>>>
>>> If it's a select field then you can change the option values to the text
>>> you want to add to your output label.
>>>
>>> Shaun
>>>
>>>
>>>
>>>
>>>
>>> Quoting Kanwei Li  on Wed, 24 Aug 2011 20:34:57 -0400:
>>>
 Hi Nikhil,

 The tool templates are Cheetah templates, so you can do things like:

 
 %if param == True:
   
 %else
  
 %endif
 

 Thanks,

 K

 On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi 
 wrote:

> Hi all,
>
> Is there a way to set the label of the output based on the input
> parameters?  Perhaps by using the  tag?  Basically, I want the
> output label to be different if the user sets a particular parameter to
> be
> true.
>
>

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Re: [galaxy-dev] next galaxy-dist update

[Glen Beane]

Bump!

We want to upgrade to get some of the newer features (since we skipped the last 
dist update), but we don't want to upgrade now and then have a new dist release 
in a few days.  Can any developer comment on the timeline for the next Galaxy 
dist release?


On Aug 23, 2011, at 8:32 AM, Glen Beane wrote:

> We are in need of a galaxy upgrade (we missed the last galaxy-dist update at 
> the end of June). However, we don't want to update to a 2 month old release 
> only to have a new release come out shortly after.  Could someone on the 
> development team give me an estimate of when the next galaxy-dist update will 
> happen?
> 
> 
> --
> Glen L. Beane
> Senior Software Engineer
> The Jackson Laboratory
> (207) 288-6153
> 
> 
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--
Glen L. Beane
Senior Software Engineer
The Jackson Laboratory
(207) 288-6153


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Re: [galaxy-dev] migrate the database schema from 80 to 81

[Nate Coraor]

Jack Zhu wrote:
> Hi all,
> 
> I have problems with updating my local instance of Galaxy.
> Specifically I can not migrate the database schema from 80 to 81:

Hi Jack,

Thanks for reporting this issue.  It has been fixed in changeset
5951:62d51750d7df.

--nate

> 
> --
> $$ sh manage_db.sh upgrade
> 
> 80 -> 81...
> 
> Migration script to add a 'tool_version' column to the hda/ldda tables.
> 
> Traceback (most recent call last):
>   File "./scripts/manage_db.py", line 63, in 
> main( repository=repo, url=db_url )
>   File 
> "/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py",
> line 150, in main
> ret = command_func(**kwargs)
>   File 
> "/home/zhujack/bin/galaxy/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/zhujack/bin/galaxy/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/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
> line 184, in runchange
> change.run(self.engine, step)
>   File 
> "/home/zhujack/bin/galaxy/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/0081_add_tool_version_to_hda_ldda.py",
> line 17, in upgrade
> metadata.reflect()
>   File 
> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py",
> line 1733, in reflect
> Table(name, self, **reflect_opts)
>   File 
> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py",
> line 108, in __call__
> return type.__call__(self, name, metadata, *args, **kwargs)
>   File 
> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py",
> line 236, in __init__
> _bind_or_error(metadata).reflecttable(self, 
> include_columns=include_columns)
>   File 
> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 1265, in reflecttable
> self.dialect.reflecttable(conn, table, include_columns)
>   File 
> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py",
> line 1673, in reflecttable
> only=include_columns)
>   File 
> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py",
> line 2139, in reflect
> self._add_column(table, line, charset, only)
>   File 
> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py",
> line 2227, in _add_column
> type_instance = col_type(*type_args, **type_kw)
>   File 
> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py",
> line 569, in __init__
> super(MSBigInteger, self).__init__(display_width, **kw)
> TypeError: super(type, obj): obj must be an instance or subtype of type
> --
> 
> Your help will be greatly appreciated.
> 
> Jack
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[galaxy-dev] contribute tools to galaxy?

[Dongjun Chung]

Hi All,

I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the
great work.

I have a question regarding contribution of software to galaxy. We developed
a ChIP-seq peak calling algorithm and software (R package) and hope to
contribute it to galaxy. I have read the wiki and prior mailing list about
the contribution system but it is still somewhat confusing to me.

1. It seems that I can contribute our software to "tool shed" if I prepare
appropriate code & definition files. Then, users can download and use it
with their locally installed galaxy. However, these files committed to tool
shed will not appear in galaxy main or test servers. Am I correct?

2. What is clear relationship between main/test servers & tool shed? Can we
contribute our software to main or test servers as well? Or only galaxy core
developers can add new tools to galaxy main or test servers? If so, which
software is considered to be added to servers? Are they chosen from tools
contributed to tool shed?

3. If our software is a R package, then users need to download and install
it first in their R system before they use our software within their galaxy
system even in the case they have appropriate definition files. Am I right?
Or is there any better solution for this?

Thanks!

Best,
Dongjun
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[galaxy-dev] contribute tools to galaxy?

[Dongjun Chung]

Hi All,

I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the
great work.

I have a question regarding contribution of software to galaxy. We developed
a ChIP-seq peak calling algorithm and software (R package) and hope to
contribute it to galaxy. I have read the wiki and prior mailing list about
the contribution system but it is still somewhat confusing to me.

1. It seems that I can contribute our software to "tool shed" if I prepare
appropriate code & definition files. Then, users can download and use it
with their locally installed galaxy. However, these files committed to tool
shed will not appear in galaxy main or test servers. Am I correct?

2. What is clear relationship between main/test servers & tool shed? Can we
contribute our software to main or test servers as well? Or only galaxy core
developers can add new tools to galaxy main or test servers? If so, which
software is considered to be added to servers? Are they chosen from tools
contributed to tool shed?

3. If our software is a R package, then users need to download and install
it first in their R system before they use our software within their galaxy
system even in the case they have appropriate definition files. Am I right?
Or is there any better solution for this?

Thanks!

Best,
Dongjun
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Re: [galaxy-dev] API keys and id encryption (silly questions)

[Nate Coraor]

Louise-Amélie Schmitt wrote:
> Hello everyone,
> 
> These questions are a bit silly but I'm really ignorant when it
> comes to security. Sorry about that.
> 
> Why use API keys instead of  user names? Is it to to prevent anyone
> from figuring out who is behind an URL? Or did I miss the point?

Hi L-A,

To provide a username password, we'd either need to implement HTTP
Authentication in Galaxy for these resources, or encode it in the URL.
If in the URL, the password have to be non-plaintext which would require
encoding on the user's end.  The key model seemed to be simplest since
it doesn't require you to handle HTTP Authentication in your client-side
code.

> Also, why encrypt the dataset/library/folder ids when a simple
> display is enough to get them?

Anywhere that the IDs are visible are remnants of old code and should
eventually be removed.

--nate

> 
> Thanks
> L-A
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Re: [galaxy-dev] next galaxy-dist update

[Nate Coraor]

It's looking like tomorrow or Wednesday at this point.  We're working on
the new feature documentation and news brief right now.

--nate

Glen Beane wrote:
> Bump!
> 
> We want to upgrade to get some of the newer features (since we skipped the 
> last dist update), but we don't want to upgrade now and then have a new dist 
> release in a few days.  Can any developer comment on the timeline for the 
> next Galaxy dist release?
> 
> 
> On Aug 23, 2011, at 8:32 AM, Glen Beane wrote:
> 
> > We are in need of a galaxy upgrade (we missed the last galaxy-dist update 
> > at the end of June). However, we don't want to update to a 2 month old 
> > release only to have a new release come out shortly after.  Could someone 
> > on the development team give me an estimate of when the next galaxy-dist 
> > update will happen?
> > 
> > 
> > --
> > Glen L. Beane
> > Senior Software Engineer
> > The Jackson Laboratory
> > (207) 288-6153
> > 
> > 
> > ___
> > 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/
> 
> --
> Glen L. Beane
> Senior Software Engineer
> The Jackson Laboratory
> (207) 288-6153
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] install with EPD python?

[Nate Coraor]

Paul Tanger wrote:
> Yes it works with the default python install.  Any way I can get it working
> with EPD python?

I've never worked with EPD and since it's not free it's unlikely we can
do much debugging on it here.  It would appear that they bundle a
version of pkg_resources which changes the DistributionNotFound class,
but it's hard to know exactly what's going on here.

One thing that might shed a bit of light on it would be to print
sys.path and pkg_resources at the top of:

galaxy-dist/lib/galaxy/eggs/__init__.py 

After the import of pkg_resources and see which version it's using.

--nate

> 
> On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor  wrote:
> 
> > Paul Tanger wrote:
> > > Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought)
> > python
> > > 2.6 (EPD version 6.1-1)?  I get this error which I suspect is related to
> > the
> > > fact that I have EPD python, not the generic python that was
> > preinstalled?
> > >  Any ideas?
> > >
> > > Thanks!
> > >
> > > Some eggs are out of date, attempting to fetch...
> > > Traceback (most recent call last):
> > >   File "./scripts/fetch_eggs.py", line 30, in 
> > > c.resolve() # Only fetch eggs required by the config
> > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
> > > 345, in resolve
> > > egg.resolve()
> > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
> > > 184, in resolve
> > > if e.args[0].project_name != self.distribution.project_name:
> > > AttributeError: 'str' object has no attribute 'project_name'
> > > Fetch failed.
> >
> > Hi Paul,
> >
> > Can you give it a try with the system Python and see if you get the same
> > result?  All you need to do is put:
> >
> >/System/Library/Frameworks/Python.framework/Versions/2.6/bin
> >
> > At the head of your $PATH.
> >
> > Thanks,
> > --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/
> >
> >
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Re: [galaxy-dev] Galaxy Test disk quota

[Nate Coraor]

Crystal Goh wrote:
> 
> Dear Nate,
>  
> Thanks.
>  
> I used multiple account as I have several csfasta and qual files and each 
> file is large in size.
>  
> My account is gohweip...@hotmail.com.
> Can I get increement for disk quota for this account so that I can used only 
> 1 account that can proceess 6 each csfasta and qual files?

Sure.

--nate

>  
> Thanks Nate and thanks galaxy.
>  
> Best regards,
> Crystal
>  
> 
> > Date: Fri, 26 Aug 2011 14:52:51 -0400
> > From: n...@bx.psu.edu
> > To: crysta...@live.com.my
> > CC: galaxy-...@bx.psu.edu
> > Subject: Re: [galaxy-dev] Galaxy Test disk quota
> > 
> > Crystal Goh wrote:
> > > 
> > > Hi, I am Crystal.
> > > 
> > > As Tophat for SOLiD only available in Galaxy Test (not available in 
> > > Galaxy Main), I uploaded my csfasta and qual files to Galaxy Test. As the 
> > > file size very big, the disk space used up is 13.5Gb and I cannot use any 
> > > tool. This means after uploading raw data, I cannot manipulate any data 
> > > as the size of raw data itself already exceeds 10Gb.
> > > 
> > > May I know any alternative that I can use? 
> > > 
> > > Thank you very much!
> > 
> > Hi Crystal,
> > 
> > Which account are you using on Galaxy Test? I noticed that you have
> > multiple. I can increase your quota for this.
> > 
> > --nate
> > 
> > > 
> > > Best regards,
> > > Crystal 
> > 
> > > ___
> > > 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/
> > 
> ea  
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Re: [galaxy-dev] install with EPD python?

[Paul Tanger]

It is free for academic use.  I'll try what you suggested below - thanks!

On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor  wrote:

> Paul Tanger wrote:
> > Yes it works with the default python install.  Any way I can get it
> working
> > with EPD python?
>
> I've never worked with EPD and since it's not free it's unlikely we can
> do much debugging on it here.  It would appear that they bundle a
> version of pkg_resources which changes the DistributionNotFound class,
> but it's hard to know exactly what's going on here.
>
> One thing that might shed a bit of light on it would be to print
> sys.path and pkg_resources at the top of:
>
>galaxy-dist/lib/galaxy/eggs/__init__.py
>
> After the import of pkg_resources and see which version it's using.
>
> --nate
>
> >
> > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor  wrote:
> >
> > > Paul Tanger wrote:
> > > > Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought)
> > > python
> > > > 2.6 (EPD version 6.1-1)?  I get this error which I suspect is related
> to
> > > the
> > > > fact that I have EPD python, not the generic python that was
> > > preinstalled?
> > > >  Any ideas?
> > > >
> > > > Thanks!
> > > >
> > > > Some eggs are out of date, attempting to fetch...
> > > > Traceback (most recent call last):
> > > >   File "./scripts/fetch_eggs.py", line 30, in 
> > > > c.resolve() # Only fetch eggs required by the config
> > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> line
> > > > 345, in resolve
> > > > egg.resolve()
> > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> line
> > > > 184, in resolve
> > > > if e.args[0].project_name != self.distribution.project_name:
> > > > AttributeError: 'str' object has no attribute 'project_name'
> > > > Fetch failed.
> > >
> > > Hi Paul,
> > >
> > > Can you give it a try with the system Python and see if you get the
> same
> > > result?  All you need to do is put:
> > >
> > >/System/Library/Frameworks/Python.framework/Versions/2.6/bin
> > >
> > > At the head of your $PATH.
> > >
> > > Thanks,
> > > --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/
> > >
> > >
>
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Re: [galaxy-dev] install with EPD python?

[Paul Tanger]

sys path is:

['/Users/paultanger/galaxy-dist/scripts',
'/Users/paultanger/python/scripts',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
'/Users/paultanger/galaxy-dist/lib']

pkg_resources is:




On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger wrote:

> It is free for academic use.  I'll try what you suggested below - thanks!
>
>
> On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor  wrote:
>
>> Paul Tanger wrote:
>> > Yes it works with the default python install.  Any way I can get it
>> working
>> > with EPD python?
>>
>> I've never worked with EPD and since it's not free it's unlikely we can
>> do much debugging on it here.  It would appear that they bundle a
>> version of pkg_resources which changes the DistributionNotFound class,
>> but it's hard to know exactly what's going on here.
>>
>> One thing that might shed a bit of light on it would be to print
>> sys.path and pkg_resources at the top of:
>>
>>galaxy-dist/lib/galaxy/eggs/__init__.py
>>
>> After the import of pkg_resources and see which version it's using.
>>
>> --nate
>>
>> >
>> > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor  wrote:
>> >
>> > > Paul Tanger wrote:
>> > > > Has anyone gotten galaxy installed on a mac 10.5 with EPD
>> (enthought)
>> > > python
>> > > > 2.6 (EPD version 6.1-1)?  I get this error which I suspect is
>> related to
>> > > the
>> > > > fact that I have EPD python, not the generic python that was
>> > > preinstalled?
>> > > >  Any ideas?
>> > > >
>> > > > Thanks!
>> > > >
>> > > > Some eggs are out of date, attempting to fetch...
>> > > > Traceback (most recent call last):
>> > > >   File "./scripts/fetch_eggs.py", line 30, in 
>> > > > c.resolve() # Only fetch eggs required by the config
>> > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
>> line
>> > > > 345, in resolve
>> > > > egg.resolve()
>> > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
>> line
>> > > > 184, in resolve
>> > > > if e.args[0].project_name != self.distribution.project_name:
>> > > > AttributeError: 'str' object has no attribute 'project_name'
>> > > > Fetch failed.
>> > >
>> > > Hi Paul,
>> > >
>> > > Can you give it a try with the system Python and see if you get the
>> same
>> > > result?  All you need to do is put:
>> > >
>> > >/System/Library/Frameworks/Python.framework/Versions/2.6/bin
>> > >
>> > > At the head of your $PATH.
>> > >
>> > > Thanks,
>> > > --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/
>> > >
>> > >
>>
>
>
>
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Re: [galaxy-dev] [API] Error message forwarding

[Nate Coraor]

Louise-Amélie Schmitt wrote:
> Hi,
> 
> I ran into a little something that is a bit annoying for debug when
> trying to upload files through the API with
> library_upload_from_import_dir.py. When the specified folder is
> wrong, python tries to process the error tuple like a dict, so the
> original error is hard to find.
> 
> I modified a little the code to avoid that. It might not work in all
> cases but at least it solved my problem.
> 
> Here is the original code:
> 
> lib/galaxy/web/api/contents.py l.145->end
> 
> else:
> rval = []
> for k, v in output.items():
> if type( v ) ==
> trans.app.model.LibraryDatasetDatasetAssociation:
> v = v.library_dataset
> encoded_id = trans.security.encode_id( create_type +
> '.' + str( v.id ) )
> rval.append( dict( id = encoded_id,
>name = v.name,
>url = url_for( 'content',
> library_id=library_id, id=encoded_id ) ) )
> return rval
> 
> Here is how I modified it:
> 
> else:
> rval = []
> try:
> for k, v in output.items():
> if type( v ) ==
> trans.app.model.LibraryDatasetDatasetAssociation:
> v = v.library_dataset
> encoded_id = trans.security.encode_id(
> create_type + '.' + str( v.id ) )
> rval.append( dict( id = encoded_id,
> name = v.name,
> url = url_for( 'content',
> library_id=library_id, id=encoded_id ) ) )
> return rval
> except:
> log.debug( 'HTTP Error %s: %s' % ( output[0], output[1] ) )
> return None
> 
> Since it saves me some time & energy I just wanted to share it, so I
> hope it can help.
> Best
> L-A

Hi L-A,

Thanks for finding this.  It's been fixed in 5952:832538ba7258.

--nate

> ___
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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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Re: [galaxy-dev] API keys and id encryption (silly questions)

[Louise-Amélie Schmitt]

Le 29/08/2011 15:52, Nate Coraor a écrit :

Louise-Amélie Schmitt wrote:

Hello everyone,

These questions are a bit silly but I'm really ignorant when it
comes to security. Sorry about that.

Why use API keys instead of  user names? Is it to to prevent anyone
from figuring out who is behind an URL? Or did I miss the point?

Hi L-A,

To provide a username password, we'd either need to implement HTTP
Authentication in Galaxy for these resources, or encode it in the URL.
If in the URL, the password have to be non-plaintext which would require
encoding on the user's end.  The key model seemed to be simplest since
it doesn't require you to handle HTTP Authentication in your client-side
code.



Ok, I actually missed the point, thanks! :D


Also, why encrypt the dataset/library/folder ids when a simple
display is enough to get them?

Anywhere that the IDs are visible are remnants of old code and should
eventually be removed.


Sorry I meant the encrypted ids. Why encrypt them? is it to prevent any 
direct use of the database?


Thanks,
L-A


--nate


Thanks
L-A
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[galaxy-dev] mycoplasma genomes - suggestion

[Lukasz Kielpinski]

Hello everybody,

I would like to suggest including mycoplasma genomes (preferably all
genomes in one file) as reference genomes. It would enable fast
checking if cells used for deep-seq experiments were not contaminated.

Best,
Lukasz
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Re: [galaxy-dev] install with EPD python?

[Nate Coraor]

Paul Tanger wrote:
> sys path is:
> 
> ['/Users/paultanger/galaxy-dist/scripts',
> '/Users/paultanger/python/scripts',
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
> '/Users/paultanger/galaxy-dist/lib']

Hi Paul,

If you replace:

lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", 
"lib" ) )
sys.path.append( lib )

With:

lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", 
"lib" ) )
sys.path.insert( 0, lib )

In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an
effect?

--nate

> 
> pkg_resources is:
>  '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
> 
> 
> 
> On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger wrote:
> 
> > It is free for academic use.  I'll try what you suggested below - thanks!
> >
> >
> > On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor  wrote:
> >
> >> Paul Tanger wrote:
> >> > Yes it works with the default python install.  Any way I can get it
> >> working
> >> > with EPD python?
> >>
> >> I've never worked with EPD and since it's not free it's unlikely we can
> >> do much debugging on it here.  It would appear that they bundle a
> >> version of pkg_resources which changes the DistributionNotFound class,
> >> but it's hard to know exactly what's going on here.
> >>
> >> One thing that might shed a bit of light on it would be to print
> >> sys.path and pkg_resources at the top of:
> >>
> >>galaxy-dist/lib/galaxy/eggs/__init__.py
> >>
> >> After the import of pkg_resources and see which version it's using.
> >>
> >> --nate
> >>
> >> >
> >> > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor  wrote:
> >> >
> >> > > Paul Tanger wrote:
> >> > > > Has anyone gotten galaxy installed on a mac 10.5 with EPD
> >> (enthought)
> >> > > python
> >> > > > 2.6 (EPD version 6.1-1)?  I get this error which I suspect is
> >> related to
> >> > > the
> >> > > > fact that I have EPD python, not the generic python that was
> >> > > preinstalled?
> >> > > >  Any ideas?
> >> > > >
> >> > > > Thanks!
> >> > > >
> >> > > > Some eggs are out of date, attempting to fetch...
> >> > > > Traceback (most recent call last):
> >> > > >   File "./scripts/fetch_eggs.py", line 30, in 
> >> > > > c.resolve() # Only fetch eggs required by the config
> >> > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> >> line
> >> > > > 345, in resolve
> >> > > > egg.resolve()
> >> > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> >> line
> >> > > > 184, in resolve
> >> > > > if e.args[0].project_name != self.distribution.project_name:
> >> > > > AttributeError: 'str' object has no attribute 'project_name'
> >> > > > Fetch failed.
> >> > >
> >> > > Hi Paul,
> >> > >
> >> > > Can you give it a try with the system Python and see if you get the
> >> same
> >> > > result?  All you need to do is put:
> >> > >
> >> > >/System/Library/Frameworks/Python.framework/Versions/2.6/bin
> >> > >
> >> > > At the head of your $PATH.
> >> > >
> >> > > Thanks,
> >> > > --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/
> >> > >
> >> > >
> >>
> >
> >
> >
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Re: [galaxy-dev] install with EPD python?

[Paul Tanger]

Getting somewhere, but it looks like it can't find numpy 1.6?
error returned is:

 pkg_resources is: 
Some eggs are out of date, attempting to fetch...

 pkg_resources is: 
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg
Traceback (most recent call last):
  File "./scripts/fetch_eggs.py", line 32, in 
c.resolve() # Only fetch eggs required by the config
  File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
347, in resolve
egg.resolve()
  File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
197, in resolve
return self.version_conflict( e.args[0], e.args[1] )
  File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
228, in version_conflict
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env,
egg.fetch )
  File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in
resolve
raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: numpy==1.6.0
Fetch failed.

On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor  wrote:

> Paul Tanger wrote:
> > sys path is:
> >
> > ['/Users/paultanger/galaxy-dist/scripts',
> > '/Users/paultanger/python/scripts',
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
> >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
> >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
> >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
> >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
> >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
> >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
> >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
> > '/Users/paultanger/galaxy-dist/lib']
>
> Hi Paul,
>
> If you replace:
>
>lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..",
> "lib" ) )
>sys.path.append( lib )
>
> With:
>
>lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..",
> "lib" ) )
>sys.path.insert( 0, lib )
>
> In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an
> effect?
>
> --nate
>
> >
> > pkg_resources is:
> >  >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
> >
> >
> >
> > On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger  >wrote:
> >
> > > It is free for academic use.  I'll try what you suggested below -
> thanks!
> > >
> > >
> > > On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor  wrote:
> > >
> > >> Paul Tanger wrote:
> > >> > Yes it works with the default python install.  Any way I can get it
> > >> working
> > >> > with EPD python?
> > >>
> > >> I've never worked with EPD and since it's not free it's unlikely we
> can
> > >> do much debugging on it here.  It would appear that they bundle a
> > >> version of pkg_resources which changes the DistributionNotFound class,
> > >> but it's hard to know exactly what's going on here.
> > >>
> > >> One thing that might shed a bit of light on it would be to print
> > >> sys.path and pkg_resources at the top of:
> > >>
> > >>galaxy-dist/lib/galaxy/eggs/__init__.py
> > >>
> > >> After the import of pkg_resources and see which version it's using.
> > >>
> > >> --nate
> > >>
> > >> >
> > >> > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor 
> wrote:
> > >> >
> > >> > > Paul Tanger wrote:
> > >> > > > Has anyone gotten galaxy installed on a mac 10.5 with EPD
> > >> (enthought)
> > >> > > python
> > >> > > > 2.6 (EPD version 6.1-1)?  I get this error which I suspect is
> > >> related to
> > >> > > the
> > >> > > > fact that I have EPD python, not the generic python that was
> > >> > > preinstalled?
> > >> > > >  Any ideas?
> > >> > > >
> > >> > > > Thanks!
> > >> > > >
> > >> > > > Some eggs are out of date, attempting to fetch...
> > >> > > > Traceback (most recent call last):
> > >> > > >   File "./scripts/fetch_eggs.py", line 30, in 
> > >> > > > c.resolve() # Only fetch eggs required by the config
> > >> > > >   File
> "/Use

Re: [galaxy-dev] install with EPD python?

[Nate Coraor]

Paul Tanger wrote:
> Getting somewhere, but it looks like it can't find numpy 1.6?
> error returned is:
> 
>  pkg_resources is:  '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'>
> Some eggs are out of date, attempting to fetch...
> 
>  pkg_resources is:  '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>
> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg
> Traceback (most recent call last):
>   File "./scripts/fetch_eggs.py", line 32, in 
> c.resolve() # Only fetch eggs required by the config
>   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
> 347, in resolve
> egg.resolve()
>   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
> 197, in resolve
> return self.version_conflict( e.args[0], e.args[1] )
>   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
> 228, in version_conflict
> r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env,
> egg.fetch )
>   File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in
> resolve
> raise DistributionNotFound(req)  # XXX put more info here
> pkg_resources.DistributionNotFound: numpy==1.6.0
> Fetch failed.

It could be a conflict with the existing version, try:

python -ES ./scripts/fetch_eggs.py

--nate

> 
> On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor  wrote:
> 
> > Paul Tanger wrote:
> > > sys path is:
> > >
> > > ['/Users/paultanger/galaxy-dist/scripts',
> > > '/Users/paultanger/python/scripts',
> > > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
> > > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
> > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
> > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
> > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
> > > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
> > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
> > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
> > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
> > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
> > > '/Users/paultanger/galaxy-dist/lib']
> >
> > Hi Paul,
> >
> > If you replace:
> >
> >lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..",
> > "lib" ) )
> >sys.path.append( lib )
> >
> > With:
> >
> >lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..",
> > "lib" ) )
> >sys.path.insert( 0, lib )
> >
> > In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an
> > effect?
> >
> > --nate
> >
> > >
> > > pkg_resources is:
> > >  > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
> > >
> > >
> > >
> > > On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger  > >wrote:
> > >
> > > > It is free for academic use.  I'll try what you suggested below -
> > thanks!
> > > >
> > > >
> > > > On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor  wrote:
> > > >
> > > >> Paul Tanger wrote:
> > > >> > Yes it works with the default python install.  Any way I can get it
> > > >> working
> > > >> > with EPD python?
> > > >>
> > > >> I've never worked with EPD and since it's not free it's unlikely we
> > can
> > > >> do much debugging on it here.  It would appear that they bundle a
> > > >> version of pkg_resources which changes the DistributionNotFound class,
> > > >> but it's hard to know exactly what's going on here.
> > > >>
> > > >> One thing that might shed a bit of light on it would be to print
> > > >> sys.path and pkg_resources at the top of:
> > > >>
> > > >>galaxy-dist/lib/galaxy/eggs/__init__.py
> > > >>
> > > >> After the import of pkg_resources and see which version it's using.
> > > >>
> > > >> --nate
> > > >>
> > > >> >
> > > >> > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor 
> > wrote:
> > > >> >
> > > >> > > Paul Tanger wrote:
> > > >> > > > Has anyone gotten galaxy installed on a mac 10.5 with EPD
> > > >> (enthought)
> > > >> > > python
> > > >> > > > 2.6 (EPD version 6.1-1)?  I get this error wh

Re: [galaxy-dev] API keys and id encryption (silly questions)

[Nate Coraor]

Louise-Amélie Schmitt wrote:
> Le 29/08/2011 15:52, Nate Coraor a écrit :
> >Louise-Amélie Schmitt wrote:
> >>Hello everyone,
> >>
> >>These questions are a bit silly but I'm really ignorant when it
> >>comes to security. Sorry about that.
> >>
> >>Why use API keys instead of  user names? Is it to to prevent anyone
> >>from figuring out who is behind an URL? Or did I miss the point?
> >Hi L-A,
> >
> >To provide a username password, we'd either need to implement HTTP
> >Authentication in Galaxy for these resources, or encode it in the URL.
> >If in the URL, the password have to be non-plaintext which would require
> >encoding on the user's end.  The key model seemed to be simplest since
> >it doesn't require you to handle HTTP Authentication in your client-side
> >code.
> >
> 
> Ok, I actually missed the point, thanks! :D
> 
> >>Also, why encrypt the dataset/library/folder ids when a simple
> >>display is enough to get them?
> >Anywhere that the IDs are visible are remnants of old code and should
> >eventually be removed.
> 
> Sorry I meant the encrypted ids. Why encrypt them? is it to prevent
> any direct use of the database?

There are a couple of reasons - the first is that since by default, data
is public, we wanted to make it non-trivial to just run sequentially
through IDs to view related data.

The other is that some people may prefer that it not be obvious how many
datasets/jobs/libraries/etc. there are on their server.

--nate

> 
> Thanks,
> L-A
> 
> >--nate
> >
> >>Thanks
> >>L-A
> >>___
> >>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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and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] install with EPD python?

[Paul Tanger]

That worked, for everything but pysam.  I also tried to install it directly:

pysam 0.4.2 couldn't be downloaded automatically.  You can try
building it by hand with:
  python scripts/scramble.py -e pysam

Some eggs are out of date, attempting to fetch...

 pkg_resources is: 
pysam 0.4.2 couldn't be downloaded automatically.  You can try
building it by hand with:
  python scripts/scramble.py -e pysam
Fetch failed.

On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor  wrote:

> Paul Tanger wrote:
> > Getting somewhere, but it looks like it can't find numpy 1.6?
> > error returned is:
> >
> >  pkg_resources is:  > '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'>
> > Some eggs are out of date, attempting to fetch...
> >
> >  pkg_resources is:  > '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>
> > Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> > Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
> > Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg
> > Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg
> > Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg
> > Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg
> > Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg
> > Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg
> > Fetched
> http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg
> > Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg
> > Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg
> > Traceback (most recent call last):
> >   File "./scripts/fetch_eggs.py", line 32, in 
> > c.resolve() # Only fetch eggs required by the config
> >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
> > 347, in resolve
> > egg.resolve()
> >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
> > 197, in resolve
> > return self.version_conflict( e.args[0], e.args[1] )
> >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
> > 228, in version_conflict
> > r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ),
> env,
> > egg.fetch )
> >   File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in
> > resolve
> > raise DistributionNotFound(req)  # XXX put more info here
> > pkg_resources.DistributionNotFound: numpy==1.6.0
> > Fetch failed.
>
> It could be a conflict with the existing version, try:
>
>python -ES ./scripts/fetch_eggs.py
>
> --nate
>
> >
> > On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor  wrote:
> >
> > > Paul Tanger wrote:
> > > > sys path is:
> > > >
> > > > ['/Users/paultanger/galaxy-dist/scripts',
> > > > '/Users/paultanger/python/scripts',
> > > > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
> > > > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
> > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
> > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
> > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
> > > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
> > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
> > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
> > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
> > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
> > > > '/Users/paultanger/galaxy-dist/lib']
> > >
> > > Hi Paul,
> > >
> > > If you replace:
> > >
> > >lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ),
> "..",
> > > "lib" ) )
> > >sys.path.append( lib )
> > >
> > > With:
> > >
> > >lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ),
> "..",
> > > "lib" ) )
> > >sys.path.insert( 0, lib )
> > >
> > > In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an
> > > effect?
> > >
> > > --nate
> > >
> > > >
> > > > pkg_resources is:
> > > >  > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
> > > >
> > > >
> > > >
> > > > On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger <
> paul.tan...@colostate.edu
> > > >wrote:
> > > >
> > > > > It is free for academic use.  I'll try what you suggested below -
> > > thanks!
> > > > >
> > > > >
> > > > > On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor 
> wrote:
> > > > >
> > > > >> Paul Tanger wrote:
> > > > >> > Yes it works with the default python install.  Any way I can get
> it
> > > > >> working
> > > > >> > with EPD python?
> > > > >>
> > > > >> I've never worked with EPD and since it's not free it's unlikely
> we
> > > can
> > > > >> do much debugging on it here.  It would appear that they 

Re: [galaxy-dev] Galaxy Test disk quota

[Crystal Goh]

Dear Nate,
 
Thank you very much.
 
Best regards,
Crystal
 

> Date: Mon, 29 Aug 2011 10:04:21 -0400
> From: n...@bx.psu.edu
> To: crysta...@live.com.my
> CC: galaxy-...@bx.psu.edu
> Subject: Re: [galaxy-dev] Galaxy Test disk quota
> 
> Crystal Goh wrote:
> > 
> > Dear Nate,
> > 
> > Thanks.
> > 
> > I used multiple account as I have several csfasta and qual files and each 
> > file is large in size.
> > 
> > My account is gohweip...@hotmail.com.
> > Can I get increement for disk quota for this account so that I can used 
> > only 1 account that can proceess 6 each csfasta and qual files?
> 
> Sure.
> 
> --nate
> 
> > 
> > Thanks Nate and thanks galaxy.
> > 
> > Best regards,
> > Crystal
> > 
> > 
> > > Date: Fri, 26 Aug 2011 14:52:51 -0400
> > > From: n...@bx.psu.edu
> > > To: crysta...@live.com.my
> > > CC: galaxy-...@bx.psu.edu
> > > Subject: Re: [galaxy-dev] Galaxy Test disk quota
> > > 
> > > Crystal Goh wrote:
> > > > 
> > > > Hi, I am Crystal.
> > > > 
> > > > As Tophat for SOLiD only available in Galaxy Test (not available in 
> > > > Galaxy Main), I uploaded my csfasta and qual files to Galaxy Test. As 
> > > > the file size very big, the disk space used up is 13.5Gb and I cannot 
> > > > use any tool. This means after uploading raw data, I cannot manipulate 
> > > > any data as the size of raw data itself already exceeds 10Gb.
> > > > 
> > > > May I know any alternative that I can use? 
> > > > 
> > > > Thank you very much!
> > > 
> > > Hi Crystal,
> > > 
> > > Which account are you using on Galaxy Test? I noticed that you have
> > > multiple. I can increase your quota for this.
> > > 
> > > --nate
> > > 
> > > > 
> > > > Best regards,
> > > > Crystal 
> > > 
> > > > ___
> > > > 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/
> > > 
> > ea 
  ___
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:

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Re: [galaxy-dev] install with EPD python?

[Nate Coraor]

Paul Tanger wrote:
> That worked, for everything but pysam.  I also tried to install it directly:
> 
> pysam 0.4.2 couldn't be downloaded automatically.  You can try
> building it by hand with:
>   python scripts/scramble.py -e pysam
> 
> Some eggs are out of date, attempting to fetch...
> 
>  pkg_resources is:  '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>
> pysam 0.4.2 couldn't be downloaded automatically.  You can try
> building it by hand with:
>   python scripts/scramble.py -e pysam
> Fetch failed.

What platform do you get from:

python ./scripts/get_platforms.py

?  Note that this needs to have the path changed from append to insert
as in the previous scripts.

Thanks,
--nate

> 
> On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor  wrote:
> 
> > Paul Tanger wrote:
> > > Getting somewhere, but it looks like it can't find numpy 1.6?
> > > error returned is:
> > >
> > >  pkg_resources is:  > > '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'>
> > > Some eggs are out of date, attempting to fetch...
> > >
> > >  pkg_resources is:  > > '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>
> > > Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> > > Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
> > > Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg
> > > Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg
> > > Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg
> > > Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg
> > > Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg
> > > Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg
> > > Fetched
> > http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg
> > > Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg
> > > Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg
> > > Traceback (most recent call last):
> > >   File "./scripts/fetch_eggs.py", line 32, in 
> > > c.resolve() # Only fetch eggs required by the config
> > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
> > > 347, in resolve
> > > egg.resolve()
> > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
> > > 197, in resolve
> > > return self.version_conflict( e.args[0], e.args[1] )
> > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line
> > > 228, in version_conflict
> > > r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ),
> > env,
> > > egg.fetch )
> > >   File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in
> > > resolve
> > > raise DistributionNotFound(req)  # XXX put more info here
> > > pkg_resources.DistributionNotFound: numpy==1.6.0
> > > Fetch failed.
> >
> > It could be a conflict with the existing version, try:
> >
> >python -ES ./scripts/fetch_eggs.py
> >
> > --nate
> >
> > >
> > > On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor  wrote:
> > >
> > > > Paul Tanger wrote:
> > > > > sys path is:
> > > > >
> > > > > ['/Users/paultanger/galaxy-dist/scripts',
> > > > > '/Users/paultanger/python/scripts',
> > > > > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
> > > > > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
> > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
> > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
> > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
> > > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
> > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
> > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
> > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
> > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
> > > > > '/Users/paultanger/galaxy-dist/lib']
> > > >
> > > > Hi Paul,
> > > >
> > > > If you replace:
> > > >
> > > >lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ),
> > "..",
> > > > "lib" ) )
> > > >sys.path.append( lib )
> > > >
> > > > With:
> > > >
> > > >lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ),
> > "..",
> > > > "lib" ) )
> > > >sys.path.insert( 0, lib )
> > > >
> > > > In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an
> > > > effect?
> > > >
> > > > --nate
> > > >
> > > > >
> > > > > pkg_resources is:
> > > > >  > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
> > > > >
> > > > >
> > > > >
> > > > > On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger <
> > paul.tan...@colostate.edu
> > > > >wrote:

Re: [galaxy-dev] install with EPD python?

[Paul Tanger]

I don't know if I did this correctly, but the output from
python get_platforms.py
is:
macosx-10.5-i386-ucs2

On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor  wrote:

> Paul Tanger wrote:
> > That worked, for everything but pysam.  I also tried to install it
> directly:
> >
> > pysam 0.4.2 couldn't be downloaded automatically.  You can try
> > building it by hand with:
> >   python scripts/scramble.py -e pysam
> >
> > Some eggs are out of date, attempting to fetch...
> >
> >  pkg_resources is:  > '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>
> > pysam 0.4.2 couldn't be downloaded automatically.  You can try
> > building it by hand with:
> >   python scripts/scramble.py -e pysam
> > Fetch failed.
>
> What platform do you get from:
>
>python ./scripts/get_platforms.py
>
> ?  Note that this needs to have the path changed from append to insert
> as in the previous scripts.
>
> Thanks,
> --nate
>
> >
> > On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor  wrote:
> >
> > > Paul Tanger wrote:
> > > > Getting somewhere, but it looks like it can't find numpy 1.6?
> > > > error returned is:
> > > >
> > > >  pkg_resources is:  > > > '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'>
> > > > Some eggs are out of date, attempting to fetch...
> > > >
> > > >  pkg_resources is:  > > > '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>
> > > > Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> > > > Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
> > > > Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg
> > > > Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg
> > > > Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg
> > > > Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg
> > > > Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg
> > > > Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg
> > > > Fetched
> > > http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg
> > > > Fetched
> http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg
> > > > Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg
> > > > Traceback (most recent call last):
> > > >   File "./scripts/fetch_eggs.py", line 32, in 
> > > > c.resolve() # Only fetch eggs required by the config
> > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> line
> > > > 347, in resolve
> > > > egg.resolve()
> > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> line
> > > > 197, in resolve
> > > > return self.version_conflict( e.args[0], e.args[1] )
> > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> line
> > > > 228, in version_conflict
> > > > r = pkg_resources.working_set.resolve( ( dist.as_requirement(),
> ),
> > > env,
> > > > egg.fetch )
> > > >   File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line
> 565, in
> > > > resolve
> > > > raise DistributionNotFound(req)  # XXX put more info here
> > > > pkg_resources.DistributionNotFound: numpy==1.6.0
> > > > Fetch failed.
> > >
> > > It could be a conflict with the existing version, try:
> > >
> > >python -ES ./scripts/fetch_eggs.py
> > >
> > > --nate
> > >
> > > >
> > > > On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor 
> wrote:
> > > >
> > > > > Paul Tanger wrote:
> > > > > > sys path is:
> > > > > >
> > > > > > ['/Users/paultanger/galaxy-dist/scripts',
> > > > > > '/Users/paultanger/python/scripts',
> > > > > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
> > > > > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
> > > > > >
> > > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
> > > > > >
> > > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
> > > > > >
> > > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
> > > > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
> > > > > >
> > > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
> > > > > >
> > > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
> > > > > >
> > > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
> > > > > >
> > > > >
> > >
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
> > > > > > '/Users/paultanger/galaxy-dist/lib']
> > > > >
> > > > > Hi Paul,
> > > > >
> > > > > If you replace:
> > > > >
> > > > >lib = os.path.abspath( os.path.join( os.path.dirname( __file__
> ),
> > > "..",
> > > > > "lib" ) )
> > > > >sys.path.append( lib )
> > > > >
> > > > > With:
> > > > >
> > > > >lib = os.path.abspath( os.path.join( os.path.dirname( __file__
> ),
> > > "..",
> > > > > "lib" ) )
> > > > >sys.path.in

Re: [galaxy-dev] install with EPD python?

[Nate Coraor]

Paul Tanger wrote:
> I don't know if I did this correctly, but the output from
> python get_platforms.py
> is:
> macosx-10.5-i386-ucs2

Okay, it looks like EPD python is only compiled for one platform.  To
use this, you'll need to scramble your own versions of the eggs which
use C code.  Could you try scrambling pysam as instructed below and see
what the results are?  You will have to do this for each egg that can't
be downloaded.

--nate

> 
> On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor  wrote:
> 
> > Paul Tanger wrote:
> > > That worked, for everything but pysam.  I also tried to install it
> > directly:
> > >
> > > pysam 0.4.2 couldn't be downloaded automatically.  You can try
> > > building it by hand with:
> > >   python scripts/scramble.py -e pysam
> > >
> > > Some eggs are out of date, attempting to fetch...
> > >
> > >  pkg_resources is:  > > '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>
> > > pysam 0.4.2 couldn't be downloaded automatically.  You can try
> > > building it by hand with:
> > >   python scripts/scramble.py -e pysam
> > > Fetch failed.
> >
> > What platform do you get from:
> >
> >python ./scripts/get_platforms.py
> >
> > ?  Note that this needs to have the path changed from append to insert
> > as in the previous scripts.
> >
> > Thanks,
> > --nate
> >
> > >
> > > On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor  wrote:
> > >
> > > > Paul Tanger wrote:
> > > > > Getting somewhere, but it looks like it can't find numpy 1.6?
> > > > > error returned is:
> > > > >
> > > > >  pkg_resources is:  > > > > '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'>
> > > > > Some eggs are out of date, attempting to fetch...
> > > > >
> > > > >  pkg_resources is:  > > > > '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>
> > > > > Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> > > > > Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg
> > > > > Fetched
> > > > http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg
> > > > > Fetched
> > http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg
> > > > > Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg
> > > > > Traceback (most recent call last):
> > > > >   File "./scripts/fetch_eggs.py", line 32, in 
> > > > > c.resolve() # Only fetch eggs required by the config
> > > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> > line
> > > > > 347, in resolve
> > > > > egg.resolve()
> > > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> > line
> > > > > 197, in resolve
> > > > > return self.version_conflict( e.args[0], e.args[1] )
> > > > >   File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> > line
> > > > > 228, in version_conflict
> > > > > r = pkg_resources.working_set.resolve( ( dist.as_requirement(),
> > ),
> > > > env,
> > > > > egg.fetch )
> > > > >   File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line
> > 565, in
> > > > > resolve
> > > > > raise DistributionNotFound(req)  # XXX put more info here
> > > > > pkg_resources.DistributionNotFound: numpy==1.6.0
> > > > > Fetch failed.
> > > >
> > > > It could be a conflict with the existing version, try:
> > > >
> > > >python -ES ./scripts/fetch_eggs.py
> > > >
> > > > --nate
> > > >
> > > > >
> > > > > On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor 
> > wrote:
> > > > >
> > > > > > Paul Tanger wrote:
> > > > > > > sys path is:
> > > > > > >
> > > > > > > ['/Users/paultanger/galaxy-dist/scripts',
> > > > > > > '/Users/paultanger/python/scripts',
> > > > > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
> > > > > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
> > > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
> > > > > > >
> > > > > >
> > > >
> > '/Library/Frameworks/Python.framework/Versions/6.1/l

Re: [galaxy-dev] Display BAM with IGV

[Nate Coraor]

Iry Witham wrote:
> Hi Nate,
> 
> I have been able to get this to work on a Mac and Windows XP within
> limited guide lines.  The following are what I had to do to make it work:
> 
> My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome
> ver.13.0.782.215 and Safari 5.1 (6534.50).  In addition I have installed Max
> OS 10.6.8 Supplemental Update 1.0.  My PC is running Windows XP SP3 with
> Java 1.6.0_26, Firefox 3.6.20 and IE8.  Windows updates are at current
> levels.  I have not tested this on Windows 7.
> 
> I am currently able to run the IGV-web tool from Galaxy via Firefox, Crome
> and Safari on the Mac and IE8 only on Windows.  When I use either Firefox or
> Crome on Windows I get the following error.
> 
> 
> ERROR [2011-08-24 09:22:40,169]  [TrackLoader.java:211]
> [SwingWorker-pool-20352093-thread-1]  java.lang.RuntimeException:
> java.lang.RuntimeException: Error loading file:
> http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
> 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
> 
> ERROR [2011-08-24 09:22:40,169]  [TrackManager.java:245]
> [SwingWorker-pool-20352093-thread-1]  Error loading tracks
> 
> org.broad.igv.exceptions.DataLoadException: An error occurred while
> loading:
> http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
> 0aa/data/galaxy_afa21414c9c9e7eb.bamjava.lang.RuntimeException: Error
> loading file: 
> http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
> 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
> 
> at org.broad.igv.track.TrackLoader.load(TrackLoader.java:212)
> 
> at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
> 
> at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
> 
> at 
> org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.java
> :2775)
> 
> at com.jidesoft.utils.SwingWorker$1.call(Unknown Source)
> 
> at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
> 
> at java.util.concurrent.FutureTask.run(Unknown Source)
> 
> at com.jidesoft.utils.SwingWorker.run(Unknown Source)
> 
> at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown
> Source)
> 
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
> 
> at java.lang.Thread.run(Unknown Source)
> 
> This error appears to be different from the original, at least in
> details though the results are the same.  I am also going to post this with
> IGV support.

Hi Iry,

If you get anything back from the IGV folks please post a followup.
Since IGV runs in the local JVM, that it works with one browser and not
another on the same system doesn't make a lot of sense.

--nate

> 
> Thanks,
> Iry
> 
> 
> On 8/15/11 2:46 PM, "Nate Coraor"  wrote:
> 
> > Iry Witham wrote:
> >> Hi Nate,
> >> 
> >> I have checked the nginx.conf file and they comply to the 
> >> documentation:
> >> 
> >>  #  added to allow nginx to handle file downloads
> >> location /_x_accel_redirect/ {
> >> internal;
> >> alias /;
> >> 
> >> I have also confirmed that the universe_wsgi.ini file contains the
> >> following:
> >> 
> >> And the following to the [app:main] section of universe_wsgi.ini:
> >> nginx_x_accel_redirect_base = /_x_accel_redirect
> >> 
> >> Iry
> > 
> > This will need some in-depth debugging, then.
> > 
> > If you access Galaxy directly via the port of its built-in web server
> > (by default, 8080), and request to display a dataset, does it set the
> > X-Accel-Redirect header in the response?
> > 
> > If you access the same dataset via the nginx address but rename the
> > underlying disk file, do you get an error message from nginx or from
> > Galaxy?
> > 
> > --nate
> > 
> >> 
> >> On 8/15/11 10:46 AM, "Nate Coraor"  wrote:
> >> 
> >>> Iry Witham wrote:
>  Hi Everyone,
>  
>  I have been tasked with getting the IGV working within our Galaxy
>  instance.  I have modified our Nginx configuration based on the more
>  advanced
>  configuration under "Sending files using nginx" on the nginxProxy page in
>  the
>  wiki.  The IGV viewer component in Galaxy does not display the results 
>  from
>  a
>  BAM file in either the web or local instance of IGV.  I have tested with
>  IGV1.5 and with version 2.03.  Neither produce a visual representation of
>  the
>  sequence. When attempting to use the web option we get the same error
>  provided in the original post as noted below.  Has anyone gotten this to
>  work
>  with Nginx-0.8.53 or any of the newer versions?
> >>> 
> >>> Hi Iry,
> >>> 
> >>> Have you checked to make sure that your nginx server is serving the file
> >>> for download, as opposed to the internal Galaxy web server?  In the
> >>> original email, it looked like nginx was being bypassed entirely (due to
> >>> serving on port 8080 - Galaxy's intenal server's default port). 

[galaxy-dev] Galaxy is Hiring

[Dave Clements]

Hello all

The Galaxy Project is growing and has open positions in both the Penn State
and Emory groups (http://wiki.g2.bx.psu.edu/News/Galaxy%20is%20Hiring).

*Penn State: System administrators/analysts*

The Nekrutenko Lab  at the Huck Institutes
of Life Sciences  at Penn State
is currently recruiting system
analysts/administrators with experience in
building and maintaining complex performance compute environments. The areas
of immediate need include:

   - Storage balancing and tiered storage
   - Virtualization
   - Schedulers
   - Deployment of Galaxy instances and dependence management
   - Relational databases and query optimization
   - User management

A minimum of 5 year experience with UNIX/Linux system administration is
required. Applicants should submit a CV and list of references to
j...@galaxyproject.org.


*Emory: Software Engineers and Post-Docs*

The Taylor Lab  in the
Biologyand Mathematics
& Computer Science  at Emory
Universityis looking for software
engineers  and postdoctoral
scholarsto work on the
Galaxy project.

We are seeking software engineers
with expertise in distributed
computing and systems programming, web-based
visualization and visual analytics, informatics and data analysis and
integration, and bioinformatics application areas such as re-sequencing, de
novo assembly, metagenomics, transcriptome analysis and epigenetics. These
are full time positions located in Atlanta, GA. See the official
postingfor full details.
Postdoctoral applicants
should have expertise in
Bioinformatics and Computational Biology and
research interests that complement but extend the lab's current
interests:
The Galaxy project; distributed and high-performance computing for data
intensive science; vertebrate functional genomics; and genomics and
epigenomic mechanisms of gene regulation, the role of transcription factors
and chromatin structure in global gene expression, development, and
differentiation. See the
announcementfor full
details.


If any of these positions describe you then please consider applying.

Thanks,

Dave C.


-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://galaxyproject.org/wiki/
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Re: [galaxy-dev] Setting the output label based on input parameters?

[Nikhil Joshi]

Hi Ross,

Yes, I did try that... but what I want is string parameter that changes
based on whether or not you've checked a checkbox (or a way to change the
label of the output based on whether or not the checkbox was checked).  So
my idea below did work, but it seems like a hack.  Which is why I was
wondering if there was a better way.

- Nik.

On Mon, Aug 29, 2011 at 2:55 AM, Ross  wrote:

> >> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB 
> >> wrote:
> >>>
> >>> I meant to say label="${input}" or label="${input.value}.
> >>>
>
> Nikhil, did you try as Shaun and others have suggested? Any available
> string parameter can be used in a label as far as I can tell.
>
> This is a common idiom - ask for a string ('title') to describe the
> job/output for posterity, then in an output:
>
>  label="${title}.myext"/>
>
> There's even a built in ${on_string} if you just want the file name
> plus some history ids?
>
>
> On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi  wrote:
> > It looks like the Cheetah syntax only is parsed within the 
> > tags so I figured out a way to do it... but it seems hackish.  I
> > basically changed the string values of truevalue and falsevalue within
> the
> > parameter to be an English sentence that would become the label for the
> > output.  I.e., in the input section:
> >
> >  > falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/>
> >
> > and in the output section:
> >
> > 
> >
> > This seems wrong to do, but it does work.  If anyone has a better method,
> > please let me know!
> >
> > - Nik.
> >
> > On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi 
> wrote:
> >>
> >> It's actually a boolean checkbox. so I basically want the label to
> >> change based upon whether or not the checkbox is checked.  Is there any
> way
> >> to do that?  Again, I've tried using the Cheetah syntax to do the #if
> #end
> >> inside the  tags but that didn't work.
> >>
> >> - Nik.
> >>
> >> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB 
> >> wrote:
> >>>
> >>> I meant to say label="${input}" or label="${input.value}.
> >>>
> >>> If it's a select field then you can change the option values to the
> text
> >>> you want to add to your output label.
> >>>
> >>> Shaun
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> Quoting Kanwei Li  on Wed, 24 Aug 2011 20:34:57
> -0400:
> >>>
>  Hi Nikhil,
> 
>  The tool templates are Cheetah templates, so you can do things like:
> 
>  
>  %if param == True:
>    
>  %else
>   
>  %endif
>  
> 
>  Thanks,
> 
>  K
> 
>  On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi 
>  wrote:
> 
> > Hi all,
> >
> > Is there a way to set the label of the output based on the input
> > parameters?  Perhaps by using the  tag?  Basically, I want
> the
> > output label to be different if the user sets a particular parameter
> to
> > be
> > true.
> >
> >
>
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Re: [galaxy-dev] Setting the output label based on input parameters?

[Ross]

Most times I need a user supplied label substring. I'm not sure how
else to conditionally set a string to a predetermined value other than
with boolean true/false strings or select parameter values.

One even more ugly option is to use a (strictly speaking now
deprecated) post job exec hook to change the output dataset name based
on some logic - but if the boolean works, I'd recommend moving on :)

On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi  wrote:
> Hi Ross,
>
> Yes, I did try that... but what I want is string parameter that changes
> based on whether or not you've checked a checkbox (or a way to change the
> label of the output based on whether or not the checkbox was checked).  So
> my idea below did work, but it seems like a hack.  Which is why I was
> wondering if there was a better way.
>
> - Nik.
>
> On Mon, Aug 29, 2011 at 2:55 AM, Ross  wrote:
>>
>> >> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB 
>> >> wrote:
>> >>>
>> >>> I meant to say label="${input}" or label="${input.value}.
>> >>>
>>
>> Nikhil, did you try as Shaun and others have suggested? Any available
>> string parameter can be used in a label as far as I can tell.
>>
>> This is a common idiom - ask for a string ('title') to describe the
>> job/output for posterity, then in an output:
>>
>> > label="${title}.myext"/>
>>
>> There's even a built in ${on_string} if you just want the file name
>> plus some history ids?
>>
>>
>> On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi  wrote:
>> > It looks like the Cheetah syntax only is parsed within the 
>> > tags so I figured out a way to do it... but it seems hackish.  I
>> > basically changed the string values of truevalue and falsevalue within
>> > the
>> > parameter to be an English sentence that would become the label for the
>> > output.  I.e., in the input section:
>> >
>> > > > falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/>
>> >
>> > and in the output section:
>> >
>> > 
>> >
>> > This seems wrong to do, but it does work.  If anyone has a better
>> > method,
>> > please let me know!
>> >
>> > - Nik.
>> >
>> > On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi 
>> > wrote:
>> >>
>> >> It's actually a boolean checkbox. so I basically want the label to
>> >> change based upon whether or not the checkbox is checked.  Is there any
>> >> way
>> >> to do that?  Again, I've tried using the Cheetah syntax to do the #if
>> >> #end
>> >> inside the  tags but that didn't work.
>> >>
>> >> - Nik.
>> >>
>> >> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB 
>> >> wrote:
>> >>>
>> >>> I meant to say label="${input}" or label="${input.value}.
>> >>>
>> >>> If it's a select field then you can change the option values to the
>> >>> text
>> >>> you want to add to your output label.
>> >>>
>> >>> Shaun
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> Quoting Kanwei Li  on Wed, 24 Aug 2011 20:34:57
>> >>> -0400:
>> >>>
>>  Hi Nikhil,
>> 
>>  The tool templates are Cheetah templates, so you can do things like:
>> 
>>  
>>  %if param == True:
>>    
>>  %else
>>   
>>  %endif
>>  
>> 
>>  Thanks,
>> 
>>  K
>> 
>>  On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi 
>>  wrote:
>> 
>> > Hi all,
>> >
>> > Is there a way to set the label of the output based on the input
>> > parameters?  Perhaps by using the  tag?  Basically, I want
>> > the
>> > output label to be different if the user sets a particular parameter
>> > to
>> > be
>> > true.
>> >
>> >
>
>



-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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Re: [galaxy-dev] migrate the database schema from 80 to 81

[Jack Zhu]

Hi Nate,

Thanks for the fix.  Everything is working great now.

Jack


On 29 August 2011 09:33, Nate Coraor  wrote:
> Jack Zhu wrote:
>> Hi all,
>>
>> I have problems with updating my local instance of Galaxy.
>> Specifically I can not migrate the database schema from 80 to 81:
>
> Hi Jack,
>
> Thanks for reporting this issue.  It has been fixed in changeset
> 5951:62d51750d7df.
>
> --nate
>
>>
>> --
>> $$ sh manage_db.sh upgrade
>>
>> 80 -> 81...
>>
>> Migration script to add a 'tool_version' column to the hda/ldda tables.
>>
>> Traceback (most recent call last):
>>   File "./scripts/manage_db.py", line 63, in 
>>     main( repository=repo, url=db_url )
>>   File 
>> "/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py",
>> line 150, in main
>>     ret = command_func(**kwargs)
>>   File 
>> "/home/zhujack/bin/galaxy/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/zhujack/bin/galaxy/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/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>> line 184, in runchange
>>     change.run(self.engine, step)
>>   File 
>> "/home/zhujack/bin/galaxy/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/0081_add_tool_version_to_hda_ldda.py",
>> line 17, in upgrade
>>     metadata.reflect()
>>   File 
>> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py",
>> line 1733, in reflect
>>     Table(name, self, **reflect_opts)
>>   File 
>> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py",
>> line 108, in __call__
>>     return type.__call__(self, name, metadata, *args, **kwargs)
>>   File 
>> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py",
>> line 236, in __init__
>>     _bind_or_error(metadata).reflecttable(self, 
>> include_columns=include_columns)
>>   File 
>> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>> line 1265, in reflecttable
>>     self.dialect.reflecttable(conn, table, include_columns)
>>   File 
>> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py",
>> line 1673, in reflecttable
>>     only=include_columns)
>>   File 
>> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py",
>> line 2139, in reflect
>>     self._add_column(table, line, charset, only)
>>   File 
>> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py",
>> line 2227, in _add_column
>>     type_instance = col_type(*type_args, **type_kw)
>>   File 
>> "/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py",
>> line 569, in __init__
>>     super(MSBigInteger, self).__init__(display_width, **kw)
>> TypeError: super(type, obj): obj must be an instance or subtype of type
>> --
>>
>> Your help will be greatly appreciated.
>>
>> Jack
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