Re: [galaxy-dev] GalaxyCloudman + CADDSuite

[Marcel Schumann]

Hi Brad, hi Enis,

ok, so one possible way should thus be to use the  _cleanup_ec2() 
function before creating an AMI via the amazon console and the second 
option perhaps is this share-a-cluster functionality.


About the latter: sorry, I tried to find out what it really does, but 
did not find any documentation of it. So, how does this share-a-cluster 
functionality work in principle? If it does not create AMI, does it just 
create snapshots of the individual disks that users have to mount 
(manually) or ... ?
My point here is: I need to make a modified version of GalaxyCloudman 
available (i.e. one that contains the CADDSuite tools). I do not just 
want to share an _instance_ (a running cluster) but a cloudman image (as 
an AMI or by some other means) that includes all my tools, so that other 
users can easily start their own server.


If you do indeed have a description of this somewhere that I just did 
not find, then I am sorry but would be grateful for a link ;-)



Cheers,
Marcel


On 12/1/11 10:04 PM, Brad Chapman wrote:


Marcel;


well, I know I do not have to create a new AMI if I want to reuse an
instance myself.

However, I would like to share the modified GalaxyCloudman version with
other people and therefore I do have to create an AMI.


What Enis was suggesting is using the share-a-cluster functionality
built into CloudMan. This bundles your data volumes as snapshots and
prepares a sharable cluster than anyone can initiate.

In the CloudMan interface, there is a little green button next to the
cluster name that enables this. That is definitely the easiest way to
share and distribute modified CloudMan versions.


Ok, I will try to make this work somehow ... but I guess there are no
immediate clues as to what could have gone wrong? Or do you have any
ideas what I should try?


After CloudMan boots once, you need to clean up some files before
preparing an AMI. This is the automated code we use to clean up for
prepping CloudMan compatible AMIs:

https://github.com/chapmanb/cloudbiolinux/blob/master/cloudbio/cloudman.py#L87

Be careful if you run that directly. It runs immediately before bundling
and removes the ssh keys (so you don't have a backdoor to the AMI you
are distributing) so you want to do it as the last thing. It also
assumes you have unmounted all of the associated Galaxy data libraries.

Hope this helps,
Brad




--
Marcel Schumann

University of Tuebingen
Wilhelm Schickard Institute for Computer Science
Division for Applied Bioinformatics
Room C313, Sand 14, D-72076 Tuebingen

phone:  +49 (0)7071-29 70437
fax:  +49 (0)7071-29 5152
email:  schum...@informatik.uni-tuebingen.de
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Re: [galaxy-dev] GalaxyCloudman + CADDSuite

[Enis Afgan]

Hi Marcel,

On Thu, Dec 1, 2011 at 10:35 PM, Marcel Schumann <
schum...@informatik.uni-tuebingen.de> wrote:

> Hi Brad, hi Enis,
>
> ok, so one possible way should thus be to use the  _cleanup_ec2() function
> before creating an AMI via the amazon console and the second option perhaps
> is this share-a-cluster functionality.
>
> About the latter: sorry, I tried to find out what it really does, but did
> not find any documentation of it. So, how does this share-a-cluster
> functionality work in principle? If it does not create AMI, does it just
> create snapshots of the individual disks that users have to mount
> (manually) or ... ?
> My point here is: I need to make a modified version of GalaxyCloudman
> available (i.e. one that contains the CADDSuite tools). I do not just want
> to share an _instance_ (a running cluster) but a cloudman image (as an AMI
> or by some other means) that includes all my tools, so that other users can
> easily start their own server.
>
The share-an-instance functionality creates snapshot the data volume
(/mnt/galaxyData) so any tool that is installed on that file system will
get bundled into the shared instance. Also, any modifications that you make
to you galaxy configuration (e.g., galaxy_tools.xml) become part of the
shared instance. When a user then starts a new cluster and provides the
cluster share string (this is available on the shared cluster after you
share it), they will get access to an exact replica of your cluster. Like,
I mentioned earlier, unless you are modifing system libraries there is
absolutely no reason to create a new AMI. Simply contain your
customizations to the file system and use cluster sharing functionality.
Try it and see if it does what you need it to do.

>
> If you do indeed have a description of this somewhere that I just did not
> find, then I am sorry but would be grateful for a link ;-)
>
> Sorry but there's no functionality about this feature on the wiki.
However, there is a pretty detailed description of the functionality and
the process on the cloudman console after you click the green share a
cluster button. I'll work on preparing some additional documentation on
this topic.

Enis

>
> Cheers,
> Marcel
>
>
>
> On 12/1/11 10:04 PM, Brad Chapman wrote:
>
>>
>> Marcel;
>>
>>  well, I know I do not have to create a new AMI if I want to reuse an
>>> instance myself.
>>>
>>> However, I would like to share the modified GalaxyCloudman version with
>>> other people and therefore I do have to create an AMI.
>>>
>>
>> What Enis was suggesting is using the share-a-cluster functionality
>> built into CloudMan. This bundles your data volumes as snapshots and
>> prepares a sharable cluster than anyone can initiate.
>>
>> In the CloudMan interface, there is a little green button next to the
>> cluster name that enables this. That is definitely the easiest way to
>> share and distribute modified CloudMan versions.
>>
>>  Ok, I will try to make this work somehow ... but I guess there are no
>>> immediate clues as to what could have gone wrong? Or do you have any
>>> ideas what I should try?
>>>
>>
>> After CloudMan boots once, you need to clean up some files before
>> preparing an AMI. This is the automated code we use to clean up for
>> prepping CloudMan compatible AMIs:
>>
>> https://github.com/chapmanb/**cloudbiolinux/blob/master/**
>> cloudbio/cloudman.py#L87
>>
>> Be careful if you run that directly. It runs immediately before bundling
>> and removes the ssh keys (so you don't have a backdoor to the AMI you
>> are distributing) so you want to do it as the last thing. It also
>> assumes you have unmounted all of the associated Galaxy data libraries.
>>
>> Hope this helps,
>> Brad
>>
>>
>
> --
> Marcel Schumann
>
> University of Tuebingen
> Wilhelm Schickard Institute for Computer Science
> Division for Applied Bioinformatics
> Room C313, Sand 14, D-72076 Tuebingen
>
> phone:  +49 (0)7071-29 70437
> fax:  +49 (0)7071-29 5152
> email:  
> schum...@informatik.uni-**tuebingen.de
>
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Re: [galaxy-dev] GalaxyCloudman + CADDSuite

[Brad Chapman]

Marcel;

> well, I know I do not have to create a new AMI if I want to reuse an 
> instance myself.
> 
> However, I would like to share the modified GalaxyCloudman version with 
> other people and therefore I do have to create an AMI.

What Enis was suggesting is using the share-a-cluster functionality
built into CloudMan. This bundles your data volumes as snapshots and
prepares a sharable cluster than anyone can initiate.

In the CloudMan interface, there is a little green button next to the
cluster name that enables this. That is definitely the easiest way to
share and distribute modified CloudMan versions.

> Ok, I will try to make this work somehow ... but I guess there are no 
> immediate clues as to what could have gone wrong? Or do you have any 
> ideas what I should try?

After CloudMan boots once, you need to clean up some files before
preparing an AMI. This is the automated code we use to clean up for
prepping CloudMan compatible AMIs:

https://github.com/chapmanb/cloudbiolinux/blob/master/cloudbio/cloudman.py#L87

Be careful if you run that directly. It runs immediately before bundling
and removes the ssh keys (so you don't have a backdoor to the AMI you
are distributing) so you want to do it as the last thing. It also
assumes you have unmounted all of the associated Galaxy data libraries.

Hope this helps,
Brad

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Re: [galaxy-dev] GalaxyCloudman + CADDSuite

[Marcel Schumann]

Hi Enis,

well, I know I do not have to create a new AMI if I want to reuse an 
instance myself.


However, I would like to share the modified GalaxyCloudman version with 
other people and therefore I do have to create an AMI.


Ok, I will try to make this work somehow ... but I guess there are no 
immediate clues as to what could have gone wrong? Or do you have any 
ideas what I should try?



Cheers,
Marcel


On 12/1/11 10:45 AM, Enis Afgan wrote:

Hi Marcel,

However, when I create an AMI, terminate the cluster and create a new

cluster using the new AMI, both /mnt/galaxyData and /mnt/galaxyTools do not
exist anymore, i.e. /dev/sdg3 and /dev/sdg4 are not mounted automatically.
If I mount those two devices manually, everything runs smoothly again.

So, is there anything that I might have forgotten to do while creating the
AMI? Is there a way to make sure that those devices will be mounted
automatically?

It is not necessary to create a new AMI when wanting to customize your

cluster. Instead, on the admin interface - after you have modified the file
systems, there is an option to persist static file systems (galaxyTools&
galaxyIndices). Once the process is completed and you restart the cluster,
just continue to use the same AMI. CloudMan will use the new, customized,
data snapshots at runtime.

Let us know how it goes,
Enis



Regards,
Marcel



On 11/30/11 3:57 PM, Enis Afgan wrote:


Hi Marcel,
It would be best to use 'galaxy' user to add any tools. To do so, after
you've logged in as ubuntu user, simply execute:
sudo su galaxy
and you will become galaxy user. You can then make the desired
modifications.

Good luck,
Enis

On Wed, Nov 30, 2011 at 3:42 PM, Greg Von Kuster   wrote:

  Hello Marcel,



--
Marcel Schumann

University of Tuebingen
Wilhelm Schickard Institute for Computer Science
Division for Applied Bioinformatics
Room C313, Sand 14, D-72076 Tuebingen

phone:  +49 (0)7071-29 70437
fax:  +49 (0)7071-29 5152
email:  
schum...@informatik.uni-**tuebingen.de






--
Marcel Schumann

University of Tuebingen
Wilhelm Schickard Institute for Computer Science
Division for Applied Bioinformatics
Room C313, Sand 14, D-72076 Tuebingen

phone:  +49 (0)7071-29 70437
fax:  +49 (0)7071-29 5152
email:  schum...@informatik.uni-tuebingen.de
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Re: [galaxy-dev] GalaxyCloudman + CADDSuite

[Enis Afgan]

Hi Marcel,

On Thu, Dec 1, 2011 at 11:28 AM, Marcel Schumann <
schum...@informatik.uni-tuebingen.de> wrote:

> Hi Enis,
>
> well, I know I do not have to create a new AMI if I want to reuse an
> instance myself.
>
> However, I would like to share the modified GalaxyCloudman version with
> other people and therefore I do have to create an AMI.
>
Unless you modify the system packages (i.e., your customizations are not
self contained), you still don't have to create a new AMI to share a
cluster. There is the share-a-cluster option (icon next to the cluster
name). Just wanted to make sure you were aware of the functionality...


> Ok, I will try to make this work somehow ... but I guess there are no
> immediate clues as to what could have gone wrong? Or do you have any ideas
> what I should try?
>
CloudMan sets up the system at runtime so it performs changes that then get
persisted when you create the AMI. So, it is necessary to reverse those
changes before creating the AMI so that next time a cluster is started, the
startup procedure proceeds as before. Did you see what's in the cloudman
log (/mnt/cm/paster.log) on your customized AMI? That's probably the
easiest place to start and we can work from there.

Enis



>
> Cheers,
> Marcel
>
>
>
> On 12/1/11 10:45 AM, Enis Afgan wrote:
>
>> Hi Marcel,
>>
>> However, when I create an AMI, terminate the cluster and create a new
>>
>>> cluster using the new AMI, both /mnt/galaxyData and /mnt/galaxyTools do
>>> not
>>> exist anymore, i.e. /dev/sdg3 and /dev/sdg4 are not mounted
>>> automatically.
>>> If I mount those two devices manually, everything runs smoothly again.
>>>
>>> So, is there anything that I might have forgotten to do while creating
>>> the
>>> AMI? Is there a way to make sure that those devices will be mounted
>>> automatically?
>>>
>>> It is not necessary to create a new AMI when wanting to customize your
>>>
>> cluster. Instead, on the admin interface - after you have modified the
>> file
>> systems, there is an option to persist static file systems (galaxyTools&
>> galaxyIndices). Once the process is completed and you restart the cluster,
>> just continue to use the same AMI. CloudMan will use the new, customized,
>> data snapshots at runtime.
>>
>> Let us know how it goes,
>> Enis
>>
>>
>>  Regards,
>>> Marcel
>>>
>>>
>>>
>>> On 11/30/11 3:57 PM, Enis Afgan wrote:
>>>
>>>  Hi Marcel,
 It would be best to use 'galaxy' user to add any tools. To do so, after
 you've logged in as ubuntu user, simply execute:
 sudo su galaxy
 and you will become galaxy user. You can then make the desired
 modifications.

 Good luck,
 Enis

 On Wed, Nov 30, 2011 at 3:42 PM, Greg Von Kuster
 wrote:

  Hello Marcel,


>>> --
>>> Marcel Schumann
>>>
>>> University of Tuebingen
>>> Wilhelm Schickard Institute for Computer Science
>>> Division for Applied Bioinformatics
>>> Room C313, Sand 14, D-72076 Tuebingen
>>>
>>> phone:  +49 (0)7071-29 70437
>>> fax:  +49 (0)7071-29 5152
>>> email:  schum...@informatik.uni-**tueb**ingen.de <
>>> schumann@informatik.**uni-tuebingen.de
>>> >
>>>
>>>
>>
>
> --
> Marcel Schumann
>
> University of Tuebingen
> Wilhelm Schickard Institute for Computer Science
> Division for Applied Bioinformatics
> Room C313, Sand 14, D-72076 Tuebingen
>
> phone:  +49 (0)7071-29 70437
> fax:  +49 (0)7071-29 5152
> email:  
> schum...@informatik.uni-**tuebingen.de
>
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Re: [galaxy-dev] GalaxyCloudman + CADDSuite

[Enis Afgan]

Hi Marcel,

However, when I create an AMI, terminate the cluster and create a new
> cluster using the new AMI, both /mnt/galaxyData and /mnt/galaxyTools do not
> exist anymore, i.e. /dev/sdg3 and /dev/sdg4 are not mounted automatically.
> If I mount those two devices manually, everything runs smoothly again.
>
> So, is there anything that I might have forgotten to do while creating the
> AMI? Is there a way to make sure that those devices will be mounted
> automatically?
>
> It is not necessary to create a new AMI when wanting to customize your
cluster. Instead, on the admin interface - after you have modified the file
systems, there is an option to persist static file systems (galaxyTools &
galaxyIndices). Once the process is completed and you restart the cluster,
just continue to use the same AMI. CloudMan will use the new, customized,
data snapshots at runtime.

Let us know how it goes,
Enis


> Regards,
> Marcel
>
>
>
> On 11/30/11 3:57 PM, Enis Afgan wrote:
>
>> Hi Marcel,
>> It would be best to use 'galaxy' user to add any tools. To do so, after
>> you've logged in as ubuntu user, simply execute:
>> sudo su galaxy
>> and you will become galaxy user. You can then make the desired
>> modifications.
>>
>> Good luck,
>> Enis
>>
>> On Wed, Nov 30, 2011 at 3:42 PM, Greg Von Kuster  wrote:
>>
>>  Hello Marcel,
>>>
>>> In the future, please send all questions like this to the galaxy-dev
>>> mailing list, as doing so will streamline the process of getting a timely
>>> answer.  I believe Enis is best able to answer your questions.
>>>
>>> Thanks!
>>>
>>>
>>> On Nov 30, 2011, at 9:29 AM, Marcel Schumann wrote:
>>>
>>>  Hi Greg,

 I'm currently trying to create a GalaxyCloudman version that includes

>>> CADDSuite.
>>>
 Thus, I launched GalaxyCloudman as described in your wiki and tried to

>>> modify it afterwards.
>>>

 Well, starting cloudman worked without any problems... so far, so good

>>> :-)
>>>
 As described on
   http://wiki.g2.bx.psu.edu/**Admin/Cloud/Customize%**
 20Galaxy%20Cloud
 I could then log-in via ssh as user 'ubuntu' (not as user 'galaxy').
 However, all files of the galaxy installation belong to user and group

>>> 'galaxy'.
>>>

 Thus my question: How should users be able to customize cloudman? Is

>>> there some trick by which I can log-in as 'galaxy' or do you have any
>>> other
>>> idea how to make this work ? ;-)
>>>

 Sorry Greg, if you are not the correct contact in this case, but I found

>>> not specific contact or mailing list for cloudman. Perhaps, you could
>>> just
>>> forward this mail in that case ...
>>>


 Cheers,
 Marcel


 --
 Marcel Schumann

 University of Tuebingen
 Wilhelm Schickard Institute for Computer Science
 Division for Applied Bioinformatics
 Room C313, Sand 14, D-72076 Tuebingen

 phone:  +49 (0)7071-29 70437
 fax:  +49 (0)7071-29 5152
 email:  
 schum...@informatik.uni-**tuebingen.de

>>>
>>> Greg Von Kuster
>>> Galaxy Development Team
>>> g...@bx.psu.edu
>>>
>>>
>>>
>>>
>>>
>>
>
> --
> Marcel Schumann
>
> University of Tuebingen
> Wilhelm Schickard Institute for Computer Science
> Division for Applied Bioinformatics
> Room C313, Sand 14, D-72076 Tuebingen
>
> phone:  +49 (0)7071-29 70437
> fax:  +49 (0)7071-29 5152
> email:  
> schum...@informatik.uni-**tuebingen.de
>
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Re: [galaxy-dev] GalaxyCloudman + CADDSuite

[Marcel Schumann]

Hi Enis and Dannon,

thanks for the reply.
Yes, I should have tried 'sudo su' ... this works.

Ok, integrating CADDSuite was no problem at all after this and 
everything seems to run well.


However, when I create an AMI, terminate the cluster and create a new 
cluster using the new AMI, both /mnt/galaxyData and /mnt/galaxyTools do 
not exist anymore, i.e. /dev/sdg3 and /dev/sdg4 are not mounted 
automatically.

If I mount those two devices manually, everything runs smoothly again.

So, is there anything that I might have forgotten to do while creating 
the AMI? Is there a way to make sure that those devices will be mounted 
automatically?



Regards,
Marcel


On 11/30/11 3:57 PM, Enis Afgan wrote:

Hi Marcel,
It would be best to use 'galaxy' user to add any tools. To do so, after
you've logged in as ubuntu user, simply execute:
sudo su galaxy
and you will become galaxy user. You can then make the desired
modifications.

Good luck,
Enis

On Wed, Nov 30, 2011 at 3:42 PM, Greg Von Kuster  wrote:


Hello Marcel,

In the future, please send all questions like this to the galaxy-dev
mailing list, as doing so will streamline the process of getting a timely
answer.  I believe Enis is best able to answer your questions.

Thanks!


On Nov 30, 2011, at 9:29 AM, Marcel Schumann wrote:


Hi Greg,

I'm currently trying to create a GalaxyCloudman version that includes

CADDSuite.

Thus, I launched GalaxyCloudman as described in your wiki and tried to

modify it afterwards.


Well, starting cloudman worked without any problems... so far, so good

:-)

As described on
   http://wiki.g2.bx.psu.edu/Admin/Cloud/Customize%20Galaxy%20Cloud
I could then log-in via ssh as user 'ubuntu' (not as user 'galaxy').
However, all files of the galaxy installation belong to user and group

'galaxy'.


Thus my question: How should users be able to customize cloudman? Is

there some trick by which I can log-in as 'galaxy' or do you have any other
idea how to make this work ? ;-)


Sorry Greg, if you are not the correct contact in this case, but I found

not specific contact or mailing list for cloudman. Perhaps, you could just
forward this mail in that case ...



Cheers,
Marcel


--
Marcel Schumann

University of Tuebingen
Wilhelm Schickard Institute for Computer Science
Division for Applied Bioinformatics
Room C313, Sand 14, D-72076 Tuebingen

phone:  +49 (0)7071-29 70437
fax:  +49 (0)7071-29 5152
email:  schum...@informatik.uni-tuebingen.de


Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu









--
Marcel Schumann

University of Tuebingen
Wilhelm Schickard Institute for Computer Science
Division for Applied Bioinformatics
Room C313, Sand 14, D-72076 Tuebingen

phone:  +49 (0)7071-29 70437
fax:  +49 (0)7071-29 5152
email:  schum...@informatik.uni-tuebingen.de
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Re: [galaxy-dev] GalaxyCloudman + CADDSuite

[Enis Afgan]

Hi Marcel,
It would be best to use 'galaxy' user to add any tools. To do so, after
you've logged in as ubuntu user, simply execute:
sudo su galaxy
and you will become galaxy user. You can then make the desired
modifications.

Good luck,
Enis

On Wed, Nov 30, 2011 at 3:42 PM, Greg Von Kuster  wrote:

> Hello Marcel,
>
> In the future, please send all questions like this to the galaxy-dev
> mailing list, as doing so will streamline the process of getting a timely
> answer.  I believe Enis is best able to answer your questions.
>
> Thanks!
>
>
> On Nov 30, 2011, at 9:29 AM, Marcel Schumann wrote:
>
> > Hi Greg,
> >
> > I'm currently trying to create a GalaxyCloudman version that includes
> CADDSuite.
> > Thus, I launched GalaxyCloudman as described in your wiki and tried to
> modify it afterwards.
> >
> > Well, starting cloudman worked without any problems... so far, so good
> :-)
> > As described on
> >   http://wiki.g2.bx.psu.edu/Admin/Cloud/Customize%20Galaxy%20Cloud
> > I could then log-in via ssh as user 'ubuntu' (not as user 'galaxy').
> > However, all files of the galaxy installation belong to user and group
> 'galaxy'.
> >
> > Thus my question: How should users be able to customize cloudman? Is
> there some trick by which I can log-in as 'galaxy' or do you have any other
> idea how to make this work ? ;-)
> >
> > Sorry Greg, if you are not the correct contact in this case, but I found
> not specific contact or mailing list for cloudman. Perhaps, you could just
> forward this mail in that case ...
> >
> >
> > Cheers,
> > Marcel
> >
> >
> > --
> > Marcel Schumann
> >
> > University of Tuebingen
> > Wilhelm Schickard Institute for Computer Science
> > Division for Applied Bioinformatics
> > Room C313, Sand 14, D-72076 Tuebingen
> >
> > phone:  +49 (0)7071-29 70437
> > fax:  +49 (0)7071-29 5152
> > email:  schum...@informatik.uni-tuebingen.de
>
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
>
>
>
>
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Re: [galaxy-dev] GalaxyCloudman + CADDSuite

[Dannon Baker]

Marcel,

After logging in as the ubuntu user, simply 'sudo su galaxy', and then make any 
modifications you want.  If you do change the tools volume, remember to use the 
cloudman admin panel and select "persist changes to the file system: 
galaxyTools".

-Dannon



On Nov 30, 2011, at 9:42 AM, Greg Von Kuster wrote:

> Hello Marcel,
> 
> In the future, please send all questions like this to the galaxy-dev mailing 
> list, as doing so will streamline the process of getting a timely answer.  I 
> believe Enis is best able to answer your questions.
> 
> Thanks!
> 
> 
> On Nov 30, 2011, at 9:29 AM, Marcel Schumann wrote:
> 
>> Hi Greg,
>> 
>> I'm currently trying to create a GalaxyCloudman version that includes 
>> CADDSuite.
>> Thus, I launched GalaxyCloudman as described in your wiki and tried to 
>> modify it afterwards.
>> 
>> Well, starting cloudman worked without any problems... so far, so good :-)
>> As described on
>>  http://wiki.g2.bx.psu.edu/Admin/Cloud/Customize%20Galaxy%20Cloud
>> I could then log-in via ssh as user 'ubuntu' (not as user 'galaxy').
>> However, all files of the galaxy installation belong to user and group 
>> 'galaxy'.
>> 
>> Thus my question: How should users be able to customize cloudman? Is there 
>> some trick by which I can log-in as 'galaxy' or do you have any other idea 
>> how to make this work ? ;-)
>> 
>> Sorry Greg, if you are not the correct contact in this case, but I found not 
>> specific contact or mailing list for cloudman. Perhaps, you could just 
>> forward this mail in that case ...
>> 
>> 
>> Cheers,
>> Marcel
>> 
>> 
>> -- 
>> Marcel Schumann
>> 
>> University of Tuebingen
>> Wilhelm Schickard Institute for Computer Science
>> Division for Applied Bioinformatics
>> Room C313, Sand 14, D-72076 Tuebingen
>> 
>> phone:  +49 (0)7071-29 70437
>> fax:  +49 (0)7071-29 5152
>> email:  schum...@informatik.uni-tuebingen.de
> 
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
> 
> 
> 
> 
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> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/

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Re: [galaxy-dev] GalaxyCloudman + CADDSuite

[Greg Von Kuster]

Hello Marcel,

In the future, please send all questions like this to the galaxy-dev mailing 
list, as doing so will streamline the process of getting a timely answer.  I 
believe Enis is best able to answer your questions.

Thanks!


On Nov 30, 2011, at 9:29 AM, Marcel Schumann wrote:

> Hi Greg,
> 
> I'm currently trying to create a GalaxyCloudman version that includes 
> CADDSuite.
> Thus, I launched GalaxyCloudman as described in your wiki and tried to modify 
> it afterwards.
> 
> Well, starting cloudman worked without any problems... so far, so good :-)
> As described on
>   http://wiki.g2.bx.psu.edu/Admin/Cloud/Customize%20Galaxy%20Cloud
> I could then log-in via ssh as user 'ubuntu' (not as user 'galaxy').
> However, all files of the galaxy installation belong to user and group 
> 'galaxy'.
> 
> Thus my question: How should users be able to customize cloudman? Is there 
> some trick by which I can log-in as 'galaxy' or do you have any other idea 
> how to make this work ? ;-)
> 
> Sorry Greg, if you are not the correct contact in this case, but I found not 
> specific contact or mailing list for cloudman. Perhaps, you could just 
> forward this mail in that case ...
> 
> 
> Cheers,
> Marcel
> 
> 
> -- 
> Marcel Schumann
> 
> University of Tuebingen
> Wilhelm Schickard Institute for Computer Science
> Division for Applied Bioinformatics
> Room C313, Sand 14, D-72076 Tuebingen
> 
> phone:  +49 (0)7071-29 70437
> fax:  +49 (0)7071-29 5152
> email:  schum...@informatik.uni-tuebingen.de

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




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