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

[Louise-Amélie Schmitt]

Le 29/08/2011 18:54, Nate Coraor a écrit :

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.


Ok, thanks a lot for all this information! :)

Best,
L-A


--nate


Thanks,
L-A


--nate


Thanks
L-A
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[galaxy-dev] set metadata step

[Shantanu Pavgi]

Hi,

There is a 'set_metadata_externally' setting in universe_wsgi.ini file.  What 
is involved in this step? Is it run for every dataset/output being generated in 
the galaxy? 

--
Thanks,
Shantanu.
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Re: [galaxy-dev] set metadata step

[Nate Coraor]

Shantanu Pavgi wrote:
> 
> Hi,
> 
> There is a 'set_metadata_externally' setting in universe_wsgi.ini file.  What 
> is involved in this step? Is it run for every dataset/output being generated 
> in the galaxy? 

Hi Shantanu,

Metadata is always detected/set on all job outputs.  This setting simply
controls whether the metadata setting occurs within the Galaxy server
process or in a new process.  It's highly recommended to always set this
= True, and it will probably become the default in the future.

--nate

> 
> --
> Thanks,
> Shantanu.
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Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

[Louise-Amélie Schmitt]

I just changed it and ran into an error, so I modified the line and it 
now works fine:

$__app__.security.encode_id( '%s' % $input1.id )
What was the 'file.' originally for?



Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit :

Thanks a lot!

I found another way to do it but it is awfully more complicated so 
I'll change as soon as I have some time.


Best,
L-A


Le 23/08/2011 19:49, Nate Coraor a écrit :

Louise-Amélie Schmitt wrote:

Hi,

I would need to make a tool that can get the API dataset id out of
the input dataset of the tool, how can I do that?

Hi L-A,

Pass in as an argument:

 $__app__.security.encode_id( 'file.%s' % $input1.id )

Where 'input1' is the param name of your input.

--nate


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Re: [galaxy-dev] set metadata step

[Shantanu Pavgi]

On Aug 30, 2011, at 9:16 AM, Nate Coraor wrote:

> Shantanu Pavgi wrote:
>> 
>> Hi,
>> 
>> There is a 'set_metadata_externally' setting in universe_wsgi.ini file.  
>> What is involved in this step? Is it run for every dataset/output being 
>> generated in the galaxy? 
> 
> Hi Shantanu,
> 
> Metadata is always detected/set on all job outputs.  This setting simply
> controls whether the metadata setting occurs within the Galaxy server
> process or in a new process.  It's highly recommended to always set this
> = True, and it will probably become the default in the future.
> 
> --nate
> 

Thanks Nate. So is this something in the core galaxy code and independent of 
tool wrappers? 

--
Shantanu. 
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Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

[Nate Coraor]

Louise-Amélie Schmitt wrote:
> I just changed it and ran into an error, so I modified the line and
> it now works fine:
> $__app__.security.encode_id( '%s' % $input1.id )
> What was the 'file.' originally for?

On the API side, a library or history's "contents" are all identified by
ID, so:

http://server/api/libraries//contents/

That content ID can refer to a dataset (file) or folder, but if this was not
'file.' or 'folder.', when the framework decoded it, it would just get
a numeric ID and wouldn't know to which type it refered.  So instead of using
just the ID, it uses the encoded form of 'file.' and 'folder.'.  This
was extended to histories even though there isn't a concept of folders in
histories.

So just encoding the ID is going to give you the encoded
HistoryDatasetAssociation id, but that ID won't be the dataset's API id.
For example, using the default id_secret in universe_wsgi.ini, if I
upload a dataset to a fresh instance of Galaxy, its encoded ID (the
encoded value of '1') is:

f2db41e1fa331b3e

As you can see in the 'display' URL for the dataset:

http://server/datasets/f2db41e1fa331b3e/display/

But that ID won't work for the history API:

% ./display.py  http://server/api/histories/f597429621d6eb2b/contents
Collection Members
--
#1: /api/histories/f597429621d6eb2b/contents/cc1c6c1afcb4fd4e
  name: 1.bed
  type: file
  id: cc1c6c1afcb4fd4e

f597429621d6eb2b is the encoding of '2' with the default id_secret since this
dataset is in history ID 2.  cc1c6c1afcb4fd4e is the encoding of 'file.1'.

--nate

> 
> 
> 
> Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit :
> >Thanks a lot!
> >
> >I found another way to do it but it is awfully more complicated so
> >I'll change as soon as I have some time.
> >
> >Best,
> >L-A
> >
> >
> >Le 23/08/2011 19:49, Nate Coraor a écrit :
> >>Louise-Amélie Schmitt wrote:
> >>>Hi,
> >>>
> >>>I would need to make a tool that can get the API dataset id out of
> >>>the input dataset of the tool, how can I do that?
> >>Hi L-A,
> >>
> >>Pass in as an argument:
> >>
> >> $__app__.security.encode_id( 'file.%s' % $input1.id )
> >>
> >>Where 'input1' is the param name of your input.
> >>
> >>--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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> >and other Galaxy lists, please use the interface at:
> >
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> 
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> 
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Re: [galaxy-dev] set metadata step

[Nate Coraor]

Shantanu Pavgi wrote:
> 
> On Aug 30, 2011, at 9:16 AM, Nate Coraor wrote:
> 
> > Shantanu Pavgi wrote:
> >> 
> >> Hi,
> >> 
> >> There is a 'set_metadata_externally' setting in universe_wsgi.ini file.  
> >> What is involved in this step? Is it run for every dataset/output being 
> >> generated in the galaxy? 
> > 
> > Hi Shantanu,
> > 
> > Metadata is always detected/set on all job outputs.  This setting simply
> > controls whether the metadata setting occurs within the Galaxy server
> > process or in a new process.  It's highly recommended to always set this
> > = True, and it will probably become the default in the future.
> > 
> > --nate
> > 
> 
> Thanks Nate. So is this something in the core galaxy code and independent of 
> tool wrappers? 

Yes.  It runs after the tool has finished executing.

> 
> --
> Shantanu. 
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Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

[Louise-Amélie Schmitt]

Le 30/08/2011 16:51, Nate Coraor a écrit :

Louise-Amélie Schmitt wrote:

I just changed it and ran into an error, so I modified the line and
it now works fine:
$__app__.security.encode_id( '%s' % $input1.id )
What was the 'file.' originally for?

On the API side, a library or history's "contents" are all identified by
ID, so:

 http://server/api/libraries//contents/

That content ID can refer to a dataset (file) or folder, but if this was not
'file.' or 'folder.', when the framework decoded it, it would just get
a numeric ID and wouldn't know to which type it refered.  So instead of using
just the ID, it uses the encoded form of 'file.' and 'folder.'.  This
was extended to histories even though there isn't a concept of folders in
histories.

So just encoding the ID is going to give you the encoded
HistoryDatasetAssociation id, but that ID won't be the dataset's API id.
For example, using the default id_secret in universe_wsgi.ini, if I
upload a dataset to a fresh instance of Galaxy, its encoded ID (the
encoded value of '1') is:

 f2db41e1fa331b3e

As you can see in the 'display' URL for the dataset:

 http://server/datasets/f2db41e1fa331b3e/display/

But that ID won't work for the history API:

 % ./display.py  http://server/api/histories/f597429621d6eb2b/contents
 Collection Members
 --
 #1: /api/histories/f597429621d6eb2b/contents/cc1c6c1afcb4fd4e
   name: 1.bed
   type: file
   id: cc1c6c1afcb4fd4e

f597429621d6eb2b is the encoding of '2' with the default id_secret since this
dataset is in history ID 2.  cc1c6c1afcb4fd4e is the encoding of 'file.1'.

--nate


This really confuses me. I'll try to explain why:

I have a script that runs two workflows one after the other. The ids in 
the results of workflow 1 are stored in a database, along with some 
parameters for workflow 2.


Then, I run workflow 2 on workflow 1's results. In this workflow I have 
a tool that queries the database to get the parameters it needs, so it 
compares the input ids with those stored previously.


If I use this line:

$__app__.security.encode_id( 'file.%s' % $input1.id )

It does not match the output ids of workflow 1, so I cannot access the 
corresponding parameters.

But if I use this:

$__app__.security.encode_id( '%s' % $input1.id )

the ids match and I get the appropriate database entry.

What I understood of it:
There must be something wrong somewhere, since I'm clearly manipulating 
"file." free stuff and it works just fine. Those same ids are passed to 
workflow 2 and it runs properly, on the appropriate datasets.


Did I miss anything? Did I do something wrong?

L-A




Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit :

Thanks a lot!

I found another way to do it but it is awfully more complicated so
I'll change as soon as I have some time.

Best,
L-A


Le 23/08/2011 19:49, Nate Coraor a écrit :

Louise-Amélie Schmitt wrote:

Hi,

I would need to make a tool that can get the API dataset id out of
the input dataset of the tool, how can I do that?

Hi L-A,

Pass in as an argument:

 $__app__.security.encode_id( 'file.%s' % $input1.id )

Where 'input1' is the param name of your input.

--nate


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Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

[Nate Coraor]

Louise-Amélie Schmitt wrote:
> Le 30/08/2011 16:51, Nate Coraor a écrit :
> >Louise-Amélie Schmitt wrote:
> >>I just changed it and ran into an error, so I modified the line and
> >>it now works fine:
> >>$__app__.security.encode_id( '%s' % $input1.id )
> >>What was the 'file.' originally for?
> >On the API side, a library or history's "contents" are all identified by
> >ID, so:
> >
> > http://server/api/libraries//contents/
> >
> >That content ID can refer to a dataset (file) or folder, but if this was not
> >'file.' or 'folder.', when the framework decoded it, it would just 
> >get
> >a numeric ID and wouldn't know to which type it refered.  So instead of using
> >just the ID, it uses the encoded form of 'file.' and 'folder.'.  This
> >was extended to histories even though there isn't a concept of folders in
> >histories.
> >
> >So just encoding the ID is going to give you the encoded
> >HistoryDatasetAssociation id, but that ID won't be the dataset's API id.
> >For example, using the default id_secret in universe_wsgi.ini, if I
> >upload a dataset to a fresh instance of Galaxy, its encoded ID (the
> >encoded value of '1') is:
> >
> > f2db41e1fa331b3e
> >
> >As you can see in the 'display' URL for the dataset:
> >
> > http://server/datasets/f2db41e1fa331b3e/display/
> >
> >But that ID won't work for the history API:
> >
> > % ./display.py  
> > http://server/api/histories/f597429621d6eb2b/contents
> > Collection Members
> > --
> > #1: /api/histories/f597429621d6eb2b/contents/cc1c6c1afcb4fd4e
> >   name: 1.bed
> >   type: file
> >   id: cc1c6c1afcb4fd4e
> >
> >f597429621d6eb2b is the encoding of '2' with the default id_secret since this
> >dataset is in history ID 2.  cc1c6c1afcb4fd4e is the encoding of 'file.1'.
> >
> >--nate
> 
> This really confuses me. I'll try to explain why:
> 
> I have a script that runs two workflows one after the other. The ids
> in the results of workflow 1 are stored in a database, along with
> some parameters for workflow 2.
> 
> Then, I run workflow 2 on workflow 1's results. In this workflow I
> have a tool that queries the database to get the parameters it
> needs, so it compares the input ids with those stored previously.
> 
> If I use this line:
> 
> $__app__.security.encode_id( 'file.%s' % $input1.id )
> 
> It does not match the output ids of workflow 1, so I cannot access
> the corresponding parameters.
> But if I use this:
> 
> $__app__.security.encode_id( '%s' % $input1.id )
> 
> the ids match and I get the appropriate database entry.
> 
> What I understood of it:
> There must be something wrong somewhere, since I'm clearly
> manipulating "file." free stuff and it works just fine. Those same
> ids are passed to workflow 2 and it runs properly, on the
> appropriate datasets.
> 
> Did I miss anything? Did I do something wrong?

Ah, no, the workflow API is using the encoded id without 'file.', and
specifies the source by using the format:

==

Since the type is provided as a parameter it isn't included in the
encoded id.  This is more ideal since the encoded id will match what's
in the UI, so let me think about how we can do this in the history and
library APIs without having ugly URLs.

--nate

> 
> L-A
> 
> >>
> >>
> >>Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit :
> >>>Thanks a lot!
> >>>
> >>>I found another way to do it but it is awfully more complicated so
> >>>I'll change as soon as I have some time.
> >>>
> >>>Best,
> >>>L-A
> >>>
> >>>
> >>>Le 23/08/2011 19:49, Nate Coraor a écrit :
> Louise-Amélie Schmitt wrote:
> >Hi,
> >
> >I would need to make a tool that can get the API dataset id out of
> >the input dataset of the tool, how can I do that?
> Hi L-A,
> 
> Pass in as an argument:
> 
>  $__app__.security.encode_id( 'file.%s' % $input1.id )
> 
> Where 'input1' is the param name of your input.
> 
> --nate
> 
> >___
> >Please keep all replies on the list by using "reply all"
> >in your mail client.  To manage your subscriptions to this
> >and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
> >>>___
> >>>Please keep all replies on the list by using "reply all"
> >>>in your mail client.  To manage your subscriptions to this
> >>>and other Galaxy lists, please use the interface at:
> >>>
> >>>http://lists.bx.psu.edu/
> >>___
> >>Please keep all replies on the list by using "reply all"
> >>in your mail client.  To manage your subscriptions to this
> >>and other Galaxy lists, please use the interface at:
> >>
> >>  http://lists.bx.psu.edu/
> >>
> 
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[galaxy-dev] Tools requiring java can't find java

[Chorny, Ilya]

This is probably a question for our sys admin but when I  run tools such as 
GATK I get an error java command not found. I can execute java from the command 
line and it works. Further I can grab the drmaa submission script (ie 
galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any 
thoughts?

Thanks,

Ilya


Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.com
Website: www.illumina.com


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Re: [galaxy-dev] Tools requiring java can't find java

[George Marselis]

Yes, your java path is not set, because you are using an non-login shell. 
Indeed, you should be talking to your sysadmins.


George Marselis, systems administrator
Building #2, Level 4, room 4327
Computational Bioscience Research Center, KAUST
Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a

From: "Chorny, Ilya" mailto:icho...@illumina.com>>
Date: Tue, 30 Aug 2011 19:23:42 +0300
To: "galaxy-dev@lists.bx.psu.edu" 
mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: [galaxy-dev] Tools requiring java can't find java

This is probably a question for our sys admin but when I  run tools such as 
GATK I get an error java command not found. I can execute java from the command 
line and it works. Further I can grab the drmaa submission script (ie 
galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any 
thoughts?

Thanks,

Ilya


Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.com
Website: www.illumina.com


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Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

[Louise-Amélie Schmitt]

Le 30/08/2011 18:00, Nate Coraor a écrit :

Louise-Amélie Schmitt wrote:

Le 30/08/2011 16:51, Nate Coraor a écrit :

Louise-Amélie Schmitt wrote:

I just changed it and ran into an error, so I modified the line and
it now works fine:
$__app__.security.encode_id( '%s' % $input1.id )
What was the 'file.' originally for?

On the API side, a library or history's "contents" are all identified by
ID, so:

 http://server/api/libraries//contents/

That content ID can refer to a dataset (file) or folder, but if this was not
'file.' or 'folder.', when the framework decoded it, it would just get
a numeric ID and wouldn't know to which type it refered.  So instead of using
just the ID, it uses the encoded form of 'file.' and 'folder.'.  This
was extended to histories even though there isn't a concept of folders in
histories.

So just encoding the ID is going to give you the encoded
HistoryDatasetAssociation id, but that ID won't be the dataset's API id.
For example, using the default id_secret in universe_wsgi.ini, if I
upload a dataset to a fresh instance of Galaxy, its encoded ID (the
encoded value of '1') is:

 f2db41e1fa331b3e

As you can see in the 'display' URL for the dataset:

 http://server/datasets/f2db41e1fa331b3e/display/

But that ID won't work for the history API:

 % ./display.py   http://server/api/histories/f597429621d6eb2b/contents
 Collection Members
 --
 #1: /api/histories/f597429621d6eb2b/contents/cc1c6c1afcb4fd4e
   name: 1.bed
   type: file
   id: cc1c6c1afcb4fd4e

f597429621d6eb2b is the encoding of '2' with the default id_secret since this
dataset is in history ID 2.  cc1c6c1afcb4fd4e is the encoding of 'file.1'.

--nate

This really confuses me. I'll try to explain why:

I have a script that runs two workflows one after the other. The ids
in the results of workflow 1 are stored in a database, along with
some parameters for workflow 2.

Then, I run workflow 2 on workflow 1's results. In this workflow I
have a tool that queries the database to get the parameters it
needs, so it compares the input ids with those stored previously.

If I use this line:

$__app__.security.encode_id( 'file.%s' % $input1.id )

It does not match the output ids of workflow 1, so I cannot access
the corresponding parameters.
But if I use this:

$__app__.security.encode_id( '%s' % $input1.id )

the ids match and I get the appropriate database entry.

What I understood of it:
There must be something wrong somewhere, since I'm clearly
manipulating "file." free stuff and it works just fine. Those same
ids are passed to workflow 2 and it runs properly, on the
appropriate datasets.

Did I miss anything? Did I do something wrong?

Ah, no, the workflow API is using the encoded id without 'file.', and
specifies the source by using the format:

 ==

Since the type is provided as a parameter it isn't included in the
encoded id.  This is more ideal since the encoded id will match what's
in the UI, so let me think about how we can do this in the history and
library APIs without having ugly URLs.

--nate


Ah ok, I get it :)

Thanks for all the information!

Best,
L-A


L-A



Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit :

Thanks a lot!

I found another way to do it but it is awfully more complicated so
I'll change as soon as I have some time.

Best,
L-A


Le 23/08/2011 19:49, Nate Coraor a écrit :

Louise-Amélie Schmitt wrote:

Hi,

I would need to make a tool that can get the API dataset id out of
the input dataset of the tool, how can I do that?

Hi L-A,

Pass in as an argument:

 $__app__.security.encode_id( 'file.%s' % $input1.id )

Where 'input1' is the param name of your input.

--nate


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Re: [galaxy-dev] Tools requiring java can't find java

[Chorny, Ilya]

How do I set my path in a non login shell?

From: George Marselis [mailto:george.marse...@kaust.edu.sa]
Sent: Tuesday, August 30, 2011 9:40 AM
To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Tools requiring java can't find java

Yes, your java path is not set, because you are using an non-login shell. 
Indeed, you should be talking to your sysadmins.


George Marselis, systems administrator
Building #2, Level 4, room 4327
Computational Bioscience Research Center, KAUST
Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a

From: "Chorny, Ilya" mailto:icho...@illumina.com>>
Date: Tue, 30 Aug 2011 19:23:42 +0300
To: "galaxy-dev@lists.bx.psu.edu" 
mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: [galaxy-dev] Tools requiring java can't find java

This is probably a question for our sys admin but when I  run tools such as 
GATK I get an error java command not found. I can execute java from the command 
line and it works. Further I can grab the drmaa submission script (ie 
galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any 
thoughts?

Thanks,

Ilya


Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.com
Website: www.illumina.com


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Re: [galaxy-dev] Tools requiring java can't find java

[Chris Fields]

The following has a bit of advice on that:

http://www.admon.org/difference-between-login-shell-and-non-login-shell/

chris

On Aug 30, 2011, at 1:03 PM, Chorny, Ilya wrote:

> How do I set my path in a non login shell?
>  
> From: George Marselis [mailto:george.marse...@kaust.edu.sa] 
> Sent: Tuesday, August 30, 2011 9:40 AM
> To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Tools requiring java can't find java
>  
> Yes, your java path is not set, because you are using an non-login shell. 
> Indeed, you should be talking to your sysadmins. 
>  
> 
> George Marselis, systems administrator
> Building #2, Level 4, room 4327
> Computational Bioscience Research Center, KAUST
> Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a
>  
> From: "Chorny, Ilya" 
> Date: Tue, 30 Aug 2011 19:23:42 +0300
> To: "galaxy-dev@lists.bx.psu.edu" 
> Subject: [galaxy-dev] Tools requiring java can't find java
>  
> This is probably a question for our sys admin but when I  run tools such as 
> GATK I get an error java command not found. I can execute java from the 
> command line and it works. Further I can grab the drmaa submission script (ie 
> galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any 
> thoughts?
>  
> Thanks,
>  
> Ilya
>  
>  
> Ilya Chorny Ph.D.
> Bioinformatics Scientist I
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Work: 858.202.4582
> Email: icho...@illumina.com
> Website: www.illumina.com
>  
>  
> ___
> 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] Tools requiring java can't find java

[Chris Fields]

Gah, wrong link, apologies (the other one is okay, if a bit wonky):

http://www.linuxfromscratch.org/blfs/view/cvs/postlfs/profile.html

chrus

On Aug 30, 2011, at 1:12 PM, Chris Fields wrote:

> The following has a bit of advice on that:
> 
> http://www.admon.org/difference-between-login-shell-and-non-login-shell/
> 
> chris
> 
> On Aug 30, 2011, at 1:03 PM, Chorny, Ilya wrote:
> 
>> How do I set my path in a non login shell?
>> 
>> From: George Marselis [mailto:george.marse...@kaust.edu.sa] 
>> Sent: Tuesday, August 30, 2011 9:40 AM
>> To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu
>> Subject: Re: [galaxy-dev] Tools requiring java can't find java
>> 
>> Yes, your java path is not set, because you are using an non-login shell. 
>> Indeed, you should be talking to your sysadmins. 
>> 
>> 
>> George Marselis, systems administrator
>> Building #2, Level 4, room 4327
>> Computational Bioscience Research Center, KAUST
>> Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a
>> 
>> From: "Chorny, Ilya" 
>> Date: Tue, 30 Aug 2011 19:23:42 +0300
>> To: "galaxy-dev@lists.bx.psu.edu" 
>> Subject: [galaxy-dev] Tools requiring java can't find java
>> 
>> This is probably a question for our sys admin but when I  run tools such as 
>> GATK I get an error java command not found. I can execute java from the 
>> command line and it works. Further I can grab the drmaa submission script 
>> (ie galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. 
>> Any thoughts?
>> 
>> Thanks,
>> 
>> Ilya
>> 
>> 
>> Ilya Chorny Ph.D.
>> Bioinformatics Scientist I
>> Illumina, Inc.
>> 9885 Towne Centre Drive
>> San Diego, CA 92121
>> Work: 858.202.4582
>> Email: icho...@illumina.com
>> Website: www.illumina.com
>> 
>> 
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> 
>> http://lists.bx.psu.edu/
> 


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[galaxy-dev] August 30, 2011 Galaxy Development News Brief

[Jennifer Jackson]

August 30, 2011 Galaxy Development News Brief


http://galaxyproject.org/wiki/News%20Briefs/2011_08_30


Source: http://getgalaxy.org

new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 949e4f5fa03a


What's New
ISMB/ECCB, BOSC, and 3DSIG 2011 Slides
Recent Publications
GalaxyProject.org
Wiki
Tool Shed
Upcoming Events
Updated & Improved
Data
Tools
Visualization (Trackster)
Workflows
API
Source
Quotas
Bug Fixes


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