ACTION needed: fix error in Cloud Cluster Galaxy Trackster DATE needed: needed for workshop on Wednesday 20 November
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. lynny@mail.nih.gov<mailto:lynny@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.
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] < lynny@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. lynny@mail.nih.gov<mailto: lynny@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.
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Hi Dannon, I edited the file. Will the system automatically recognize the change? Warmly, Lynn From: Dannon Baker <dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>> Date: Monday, November 18, 2013 1:06 PM To: Lynn Young <lynny@mail.nih.gov<mailto:lynny@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] <lynny@mail.nih.gov<mailto:lynny@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. lynny@mail.nih.gov<mailto:lynny@mail.nih.gov><mailto:lynny@mail.nih.gov<mailto:lynny@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/
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] < lynny@mail.nih.gov> wrote:
Hi Dannon,
I edited the file.
Will the system automatically recognize the change?
Warmly, Lynn
From: Dannon Baker <dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>> Date: Monday, November 18, 2013 1:06 PM To: Lynn Young <lynny@mail.nih.gov<mailto:lynny@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] < lynny@mail.nih.gov<mailto:lynny@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. lynny@mail.nih.gov<mailto: lynny@mail.nih.gov><mailto:lynny@mail.nih.gov<mailto:lynny@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/
participants (2)
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Dannon Baker -
Young, Lynn (NIH/OD/ORS) [E]