[galaxy-user] Mark Your Calendars: Galaxy Developers Conference 25-26 May 2011, in the Netherlands

[Dave Clements]

Hello all,

This year's Galaxy Developers Conference will be held May 25-26, 2011 in the
Netherlands.  The meeting will feature two full days of presentations,
workshops, and conversations by and for Galaxy community members.  Please
mark your calendars.

We are in the final stages of making arrangements, and a full meeting
announcement will be published in the coming weeks.

Thanks,

Dave C.

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Re: [galaxy-user] Galaxy--upload data file

[Jennifer Jackson]

Hi Farhat,

This is reasonable suggestion, I'll pass this along to the development 
team for consideration.


Thanks for using Galaxy!

Jen
Galaxy team

On 1/19/11 10:50 AM, Farhat Habib wrote:

Would it be possible to configure Galaxy to simply refuse to upload
files greater than 2 GB since almost no browsers seem to support it? A
large number of people seem to run into this issue.

-Farhat



On Wed, Jan 19, 2011 at 9:02 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote:

Hello Takako,

The best way to load data locally is to use the the method described
here:

https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles

Please let us know if we can help more,

Best,

Jen
Galaxy team

On 1/18/11 4:18 PM, Nan Deng wrote:

Hi,

I installed Galaxy locally, and just start to use it, and I want
to use
it to align my short reads with fastq format using Tophat. The first
thing I need to do is uploading my data file. If the data is
small then
that's no problem, but my data is about 5G, so when I upload, it
took
very long time (it is still uploading). Is it normal? and could
you let
me know how long it will take? I think since both Galaxy and my
data are
on my local machine, it should be very easy to let Galaxy know
where the
data is rather than uploading for such a long time.

Thanks

Nan



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Re: [galaxy-user] Galaxy--upload data file

[Farhat Habib]

Would it be possible to configure Galaxy to simply refuse to upload files
greater than 2 GB since almost no browsers seem to support it? A large
number of people seem to run into this issue.

-Farhat



On Wed, Jan 19, 2011 at 9:02 PM, Jennifer Jackson  wrote:

> Hello Takako,
>
> The best way to load data locally is to use the the method described here:
>
> https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
>
> Please let us know if we can help more,
>
> Best,
>
> Jen
> Galaxy team
>
> On 1/18/11 4:18 PM, Nan Deng wrote:
>
>> Hi,
>>
>> I installed Galaxy locally, and just start to use it, and I want to use
>> it to align my short reads with fastq format using Tophat. The first
>> thing I need to do is uploading my data file. If the data is small then
>> that's no problem, but my data is about 5G, so when I upload, it took
>> very long time (it is still uploading). Is it normal? and could you let
>> me know how long it will take? I think since both Galaxy and my data are
>> on my local machine, it should be very easy to let Galaxy know where the
>> data is rather than uploading for such a long time.
>>
>> Thanks
>>
>> Nan
>>
>>
>>
>> ___
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>> galaxy-user@lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>
>
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> Jennifer Jackson
> http://usegalaxy.org
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Re: [galaxy-user] Galaxy--upload data file

[Jennifer Jackson]

Hello Takako,

The best way to load data locally is to use the the method described here:
https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles

Please let us know if we can help more,

Best,

Jen
Galaxy team

On 1/18/11 4:18 PM, Nan Deng wrote:

Hi,

I installed Galaxy locally, and just start to use it, and I want to use
it to align my short reads with fastq format using Tophat. The first
thing I need to do is uploading my data file. If the data is small then
that's no problem, but my data is about 5G, so when I upload, it took
very long time (it is still uploading). Is it normal? and could you let
me know how long it will take? I think since both Galaxy and my data are
on my local machine, it should be very easy to let Galaxy know where the
data is rather than uploading for such a long time.

Thanks

Nan



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Re: [galaxy-user] file uploads

[Jennifer Jackson]

Hello Takako,

The best way to load data locally is to use the the method described here:
https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles

Please let us know if we can help more,

Best,

Jen
Galaxy team

On 12/19/10 11:08 PM, 望月 孝子 wrote:

Dear  galaxy-user,

When we want to use sam files in our local Galaxy server, we can copy the files in our local Galaxy server  
to "~/galaxy_dist/database/files/000/" to appear in "history" column in Galaxy window by 
"cp" command written in attempted script.  The step, which is recognizing file guess long time.
Could you please tell me if you know the methods, which are the data appear in 
"history" column faster.

Best regards,

Takako Mochizuki


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Re: [galaxy-user] Run tools/Workflow from command line

[Jennifer Jackson]

Hello Sonali,

Here is a link to a wiki help page where the API handles that James 
mentions are explained:

https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster

And a link to the Tool Shed, in case you wish to donate a Java wrapper:
http://community.g2.bx.psu.edu/

Best,

Jen
Galaxy team

On 1/19/11 1:13 AM, Sonali Amonkar wrote:

Hi Jen,

I got the answer from James regarding the API question(Thank you James!, your 
answer was exactly what I wanted to know), however I did not get his reply on 
mail so pasting the inline content for reference.

Can you also let me know what the release plan for the HTTP API functionality 
is? If it is being implemented currently, is there a tentative time by when you 
are looking into releasing it?

Warm Regards,
Sonali Amonkar

(From James Taylor-2)

Excerpts from Sonali Amonkar's message of Sun Jan 16 17:17:14 + 2011:


I agree what you mentioned on Tools. Does Galaxy have any provision
for executing Workflows from command line too?


Currently I don't think this is implemented, but the plan is that this
would be done through the API.


At initial glance I was unable to figure out what the scripts are
for(am basically not familiar with Python). Until I try to figure that
out, can you just let me know whether, in the first place, if Galaxy
does provide (or has a Beta version planned of) some API library (say
Galaxy.tar) which I can pick up and put in my Java project and then
create workflows&  tools?


Galaxy is primarily a web application, and the API provided is REST /
HTTP based. The python scripts are command line wrappers for accessing
this. If you want to use the API from a Java application, you would just
access it directly through the web. We do not provide any special
support for Java, but you are welcome to contribute and API wrapper.

Thanks,
James
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-Original Message-
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Friday, January 14, 2011 9:23 PM
To: Sonali Amonkar
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Run tools/Workflow from command line

Hi Sonali,

Roman sent you the info for the API (thanks!) and here is some information 
about the command line usage.

Basically, any of the tools can be run from the command line.
Example:

python<  output file>

All of the tool dependencies would need to be in place:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies

Sort of related to this question, but also to a prior question:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax

I don't know if you have this already, but this is a google search link for the 
Galaxy wiki at bitbucket. Add in your own search terms to locate documents - 
these will cover in detail most of these sort of topics.
http://www.google.com/search?q=site%3Ahttp%3A%2F%2Fbitbucket.org%2Fgalaxy%2Fgalaxy-central%2Fwiki

You can also search prior mailing list posts, using google or Nabble at GMOD 
(GMOD only has most recent posts).
http://www.google.com/search?q=site%3Ahttp%3A%2F%2Flists.bx.psu.edu%2Fpipermail
http://gmod.org/wiki/Galaxy#Mailing_Lists

Best,

Jen
Galaxy team

On 1/14/11 1:50 AM, Sonali Amonkar wrote:

Hi,

1.Does Galaxy provide command line execution of Workflows / tools?

2.Does Galaxy provide API of its own, which can be imported as a
library in another program and used for executing certain workflows?

Thanks for your time.

Regards,

Sonali Amonkar

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Re: [galaxy-user] Run tools/Workflow from command line

[Sonali Amonkar]

Hi Jen,

I got the answer from James regarding the API question(Thank you James!, your 
answer was exactly what I wanted to know), however I did not get his reply on 
mail so pasting the inline content for reference.

Can you also let me know what the release plan for the HTTP API functionality 
is? If it is being implemented currently, is there a tentative time by when you 
are looking into releasing it? 

Warm Regards,
Sonali Amonkar

(From James Taylor-2)

Excerpts from Sonali Amonkar's message of Sun Jan 16 17:17:14 + 2011: 

> I agree what you mentioned on Tools. Does Galaxy have any provision 
> for executing Workflows from command line too? 

Currently I don't think this is implemented, but the plan is that this 
would be done through the API. 

> At initial glance I was unable to figure out what the scripts are 
> for(am basically not familiar with Python). Until I try to figure that 
> out, can you just let me know whether, in the first place, if Galaxy 
> does provide (or has a Beta version planned of) some API library (say 
> Galaxy.tar) which I can pick up and put in my Java project and then 
> create workflows & tools? 

Galaxy is primarily a web application, and the API provided is REST / 
HTTP based. The python scripts are command line wrappers for accessing 
this. If you want to use the API from a Java application, you would just 
access it directly through the web. We do not provide any special 
support for Java, but you are welcome to contribute and API wrapper. 

Thanks, 
James 
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-Original Message-
From: Jennifer Jackson [mailto:j...@bx.psu.edu] 
Sent: Friday, January 14, 2011 9:23 PM
To: Sonali Amonkar
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Run tools/Workflow from command line

Hi Sonali,

Roman sent you the info for the API (thanks!) and here is some information 
about the command line usage.

Basically, any of the tools can be run from the command line.
Example:

python   < output file>

All of the tool dependencies would need to be in place:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies

Sort of related to this question, but also to a prior question:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax

I don't know if you have this already, but this is a google search link for the 
Galaxy wiki at bitbucket. Add in your own search terms to locate documents - 
these will cover in detail most of these sort of topics.
http://www.google.com/search?q=site%3Ahttp%3A%2F%2Fbitbucket.org%2Fgalaxy%2Fgalaxy-central%2Fwiki

You can also search prior mailing list posts, using google or Nabble at GMOD 
(GMOD only has most recent posts).
http://www.google.com/search?q=site%3Ahttp%3A%2F%2Flists.bx.psu.edu%2Fpipermail
http://gmod.org/wiki/Galaxy#Mailing_Lists

Best,

Jen
Galaxy team

On 1/14/11 1:50 AM, Sonali Amonkar wrote:
> Hi,
>
> 1.Does Galaxy provide command line execution of Workflows / tools?
>
> 2.Does Galaxy provide API of its own, which can be imported as a 
> library in another program and used for executing certain workflows?
>
> Thanks for your time.
>
> Regards,
>
> Sonali Amonkar
>
> DISCLAIMER == This e-mail may contain privileged and 
> confidential information which is the property of Persistent Systems 
> Ltd. It is intended only for the use of the individual or entity to 
> which it is addressed. If you are not the intended recipient, you are 
> not authorized to read, retain, copy, print, distribute or use this 
> message. If you have received this communication in error, please 
> notify the sender and delete all copies of this message. Persistent 
> Systems Ltd. does not accept any liability for virus infected mails.
>
>
>
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[galaxy-user] Galaxy--upload data file

[Nan Deng]

 Hi,

 I installed Galaxy locally, and just start to use it, and I want to use it 
to align my short reads with fastq format using Tophat. The first thing I need 
to do is uploading my data file. If the data is small then that's no problem, 
but my data is about 5G, so when I upload, it took very long time (it is still 
uploading). Is it normal? and could you let me know how long it will take? I 
think since both Galaxy and my data are on my local machine, it should be very 
easy to let Galaxy know where the data is rather than uploading for such a long 
time.

Thanks

Nan
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