Re: [galaxy-dev] ACTION needed: fix error in Cloud Cluster Galaxy Trackster DATE needed: needed for workshop on Wednesday 20 November

2013-11-18 Thread Young, Lynn (NIH/OD/ORS) [E] 
Hi Dannon,

I edited the file.

Will the system automatically recognize the change?

Warmly,
Lynn

From: Dannon Baker mailto:dannon.ba...@gmail.com>>
Date: Monday, November 18, 2013 1:06 PM
To: Lynn Young mailto:ly...@mail.nih.gov>>
Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: Re: [galaxy-dev] ACTION needed: fix error in Cloud Cluster Galaxy 
Trackster DATE needed: needed for workshop on Wednesday 20 November

This may be due to an incorrect reference to '/mnt/galaxyTools' in the galaxy 
user's .sge_request file.

If you're comfortable with ssh and editing files on the server, you can log in 
and edit the file (the path should be /mnt/galaxy instead), and you should be 
good to go.  Feel free to reply offline if you're not comfortable with this and 
would like me to take a look directly.


On Mon, Nov 18, 2013 at 8:41 AM, Young, Lynn (NIH/OD/ORS) [E] 
mailto:ly...@mail.nih.gov>> wrote:
Hi,

We're using Galaxy Cloud -> New Cloud Cluster to create instances of Galaxy for 
training on Wednesday 20 November.

When we try to view a bam file using Trackster, we get the following error:


/opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: bedtools: 
command not found
/opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: 
bedGraphToBigWig: command not found

Please let us know how to proceed.

Sincerely,

Lynn

Lynn Young, PhD | Informationist/Bioinformatics Scientist | National Institutes 
of Health Library | Office of Research Services | Building 10, Room B1L-306D | 
10 Center Drive | Bethesda, Maryland 20892-1150 | T. 301-594-6426 | F. 
301-402-0254 | E. 
ly...@mail.nih.gov<mailto:ly...@mail.nih.gov><mailto:ly...@mail.nih.gov<mailto:ly...@mail.nih.gov>>
 | http://twitter.com/bioinformatics1

Stay connected with the NIH Library
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Re: [galaxy-dev] ACTION needed: fix error in Cloud Cluster Galaxy Trackster DATE needed: needed for workshop on Wednesday 20 November

2013-11-18 Thread Dannon Baker 
I believe subsequent jobs should use the new paths automatically, yes.


On Mon, Nov 18, 2013 at 12:14 PM, Young, Lynn (NIH/OD/ORS) [E] <
ly...@mail.nih.gov> wrote:

> Hi Dannon,
>
> I edited the file.
>
> Will the system automatically recognize the change?
>
> Warmly,
> Lynn
>
> From: Dannon Baker mailto:dannon.ba...@gmail.com>>
> Date: Monday, November 18, 2013 1:06 PM
> To: Lynn Young mailto:ly...@mail.nih.gov>>
> Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" <
> galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>>
> Subject: Re: [galaxy-dev] ACTION needed: fix error in Cloud Cluster Galaxy
> Trackster DATE needed: needed for workshop on Wednesday 20 November
>
> This may be due to an incorrect reference to '/mnt/galaxyTools' in the
> galaxy user's .sge_request file.
>
> If you're comfortable with ssh and editing files on the server, you can
> log in and edit the file (the path should be /mnt/galaxy instead), and you
> should be good to go.  Feel free to reply offline if you're not comfortable
> with this and would like me to take a look directly.
>
>
> On Mon, Nov 18, 2013 at 8:41 AM, Young, Lynn (NIH/OD/ORS) [E] <
> ly...@mail.nih.gov<mailto:ly...@mail.nih.gov>> wrote:
> Hi,
>
> We're using Galaxy Cloud -> New Cloud Cluster to create instances of
> Galaxy for training on Wednesday 20 November.
>
> When we try to view a bam file using Trackster, we get the following error:
>
>
> /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13:
> bedtools: command not found
> /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13:
> bedGraphToBigWig: command not found
>
> Please let us know how to proceed.
>
> Sincerely,
>
> Lynn
>
> Lynn Young, PhD | Informationist/Bioinformatics Scientist | National
> Institutes of Health Library | Office of Research Services | Building 10,
> Room B1L-306D | 10 Center Drive | Bethesda, Maryland 20892-1150 | T.
> 301-594-6426 | F. 301-402-0254 | E. ly...@mail.nih.gov ly...@mail.nih.gov><mailto:ly...@mail.nih.gov<mailto:ly...@mail.nih.gov>>
> | http://twitter.com/bioinformatics1
>
> Stay connected with the NIH Library
> NIH Library:  http://nihlibrary.nih.gov<http://nihlibrary.nih.gov/> |
> Facebook:  http://www.facebook.com/nihlibrary | Twitter:
> http://www.twitter.com/nihlib<http://www.twitter.com/nihlib>
> _
> Amazing Research. Amazing Help.
>
> ___
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
>
___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] ACTION needed: fix error in Cloud Cluster Galaxy Trackster DATE needed: needed for workshop on Wednesday 20 November

2013-11-18 Thread Dannon Baker 
This may be due to an incorrect reference to '/mnt/galaxyTools' in the
galaxy user's .sge_request file.

If you're comfortable with ssh and editing files on the server, you can log
in and edit the file (the path should be /mnt/galaxy instead), and you
should be good to go.  Feel free to reply offline if you're not comfortable
with this and would like me to take a look directly.


On Mon, Nov 18, 2013 at 8:41 AM, Young, Lynn (NIH/OD/ORS) [E] <
ly...@mail.nih.gov> wrote:

> Hi,
>
> We're using Galaxy Cloud -> New Cloud Cluster to create instances of
> Galaxy for training on Wednesday 20 November.
>
> When we try to view a bam file using Trackster, we get the following error:
>
>
> /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13:
> bedtools: command not found
> /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13:
> bedGraphToBigWig: command not found
>
> Please let us know how to proceed.
>
> Sincerely,
>
> Lynn
>
> Lynn Young, PhD | Informationist/Bioinformatics Scientist | National
> Institutes of Health Library | Office of Research Services | Building 10,
> Room B1L-306D | 10 Center Drive | Bethesda, Maryland 20892-1150 | T.
> 301-594-6426 | F. 301-402-0254 | E. ly...@mail.nih.gov ly...@mail.nih.gov> | http://twitter.com/bioinformatics1
>
> Stay connected with the NIH Library
> NIH Library:  http://nihlibrary.nih.gov |
> Facebook:  http://www.facebook.com/nihlibrary | Twitter:
> http://www.twitter.com/nihlib
> _
> Amazing Research. Amazing Help.
>
> ___
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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[galaxy-dev] ACTION needed: fix error in Cloud Cluster Galaxy Trackster DATE needed: needed for workshop on Wednesday 20 November

2013-11-18 Thread Young, Lynn (NIH/OD/ORS) [E] 
Hi,

We're using Galaxy Cloud -> New Cloud Cluster to create instances of Galaxy for 
training on Wednesday 20 November.

When we try to view a bam file using Trackster, we get the following error:


/opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: bedtools: 
command not found
/opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: 
bedGraphToBigWig: command not found

Please let us know how to proceed.

Sincerely,

Lynn

Lynn Young, PhD | Informationist/Bioinformatics Scientist | National Institutes 
of Health Library | Office of Research Services | Building 10, Room B1L-306D | 
10 Center Drive | Bethesda, Maryland 20892-1150 | T. 301-594-6426 | F. 
301-402-0254 | E. ly...@mail.nih.gov | 
http://twitter.com/bioinformatics1

Stay connected with the NIH Library
NIH Library:  http://nihlibrary.nih.gov | Facebook: 
 http://www.facebook.com/nihlibrary | Twitter:  
http://www.twitter.com/nihlib
_
Amazing Research. Amazing Help.

___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/