I have the software for our SGE cluster (eg. Bowtie) in /mnt/ngswork/galaxy/sw/bin And I've set the PATH environment in the galaxy user's .bashrc export PATH="/mnt/ngswork/galaxy/sw/bin:$PATH" When I echo $PATH via qsub as galaxy I do see my path in STDIN.o on the job runner node /mnt/ngswork/galaxy/sw/bin:/tmp/41.1.default.q:/usr/local/bin:/bin:/usr/bin But I always see /bin/sh: bowtie: not found As an error message. How can I get the path set correctly? Brad -- Brad Langhorst New England Biolabs langhorst@neb.com
On Dec 1, 2011, at 8:55 PM, Langhorst, Brad wrote:
I have the software for our SGE cluster (eg. Bowtie) in /mnt/ngswork/galaxy/sw/bin And I've set the PATH environment in the galaxy user's .bashrc
export PATH="/mnt/ngswork/galaxy/sw/bin:$PATH"
When I echo $PATH via qsub as galaxy I do see my path in STDIN.o on the job runner node
/mnt/ngswork/galaxy/sw/bin:/tmp/41.1.default.q:/usr/local/bin:/bin:/usr/bin But I always see /bin/sh: bowtie: not found
As an error message.
How can I get the path set correctly?
Hi Brad, I'd suggest putting it in ~/.sge_request rather than ~/.bashrc. This will ensure that running jobs differently (qsub vs. the DRMAA API) won't affect setting $PATH or other environment variables. See past discussions on the list for more on .sge_request: http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=search_page&node=815885&query=sge_request --nate
Brad -- Brad Langhorst New England Biolabs langhorst@neb.com
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Or you could create a directory in tool-deps called bowtie under bowtie create a default directory and in default create an env.sh file which set yours path correctly. -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Friday, December 02, 2011 7:42 AM To: Langhorst, Brad Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] PATH env variable for SGE jobs On Dec 1, 2011, at 8:55 PM, Langhorst, Brad wrote:
I have the software for our SGE cluster (eg. Bowtie) in /mnt/ngswork/galaxy/sw/bin And I've set the PATH environment in the galaxy user's .bashrc
export PATH="/mnt/ngswork/galaxy/sw/bin:$PATH"
When I echo $PATH via qsub as galaxy I do see my path in STDIN.o on the job runner node
/mnt/ngswork/galaxy/sw/bin:/tmp/41.1.default.q:/usr/local/bin:/bin:/us r/bin But I always see /bin/sh: bowtie: not found
As an error message.
How can I get the path set correctly?
Hi Brad, I'd suggest putting it in ~/.sge_request rather than ~/.bashrc. This will ensure that running jobs differently (qsub vs. the DRMAA API) won't affect setting $PATH or other environment variables. See past discussions on the list for more on .sge_request: http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=search_page&node=815885&query=sge_request --nate
Brad -- Brad Langhorst New England Biolabs langhorst@neb.com
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I had a similar problem where $PATH doesn't appear to be getting read but mine was with the EMBOSS packages. I cheated a bit and just put the full path for the executables in the command: perl -npi -e 's:<command>:<command>/usr/local/bin/:' emboss_*.xml --Russell
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev- bounces@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Saturday, 3 December 2011 4:42 a.m. To: Langhorst, Brad Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] PATH env variable for SGE jobs
On Dec 1, 2011, at 8:55 PM, Langhorst, Brad wrote:
I have the software for our SGE cluster (eg. Bowtie) in /mnt/ngswork/galaxy/sw/bin And I've set the PATH environment in the galaxy user's .bashrc
export PATH="/mnt/ngswork/galaxy/sw/bin:$PATH"
When I echo $PATH via qsub as galaxy I do see my path in STDIN.o on the job runner node
/mnt/ngswork/galaxy/sw/bin:/tmp/41.1.default.q:/usr/local/bin:/bin:/us r/bin But I always see /bin/sh: bowtie: not found
As an error message.
How can I get the path set correctly?
Hi Brad,
I'd suggest putting it in ~/.sge_request rather than ~/.bashrc. This will ensure that running jobs differently (qsub vs. the DRMAA API) won't affect setting $PATH or other environment variables.
See past discussions on the list for more on .sge_request:
http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=searc h_page&node=815885&query=sge_request
--nate
Brad -- Brad Langhorst New England Biolabs langhorst@neb.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:
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participants (4)
-
Chorny, Ilya -
Langhorst, Brad -
Nate Coraor -
Smithies, Russell