I had a similar problem where $PATH doesn't appear to be getting read but mine was with the EMBOSS packages. I cheated a bit and just put the full path for the executables in the command:
perl -npi -e 's:<command>:<command>/usr/local/bin/:' emboss_*.xml --Russell > -----Original Message----- > From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev- > boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor > Sent: Saturday, 3 December 2011 4:42 a.m. > To: Langhorst, Brad > Cc: galaxy-dev@lists.bx.psu.edu > Subject: Re: [galaxy-dev] PATH env variable for SGE jobs > > On Dec 1, 2011, at 8:55 PM, Langhorst, Brad wrote: > > > I have the software for our SGE cluster (eg. Bowtie) in > > /mnt/ngswork/galaxy/sw/bin And I've set the PATH environment in the > > galaxy user's .bashrc > > > > export PATH="/mnt/ngswork/galaxy/sw/bin:$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 > > langho...@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: > > > > 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/ ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= ___________________________________________________________ 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/
