Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg
Have you installed SGE on the same machine? If so, then you should be able to do a locate libdrmaa.so, which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so - libdrmaa.so.1.0 You may also want to try updatedb (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use dpkg on Ubuntu/Debian and yum on Centos to manipulate packages. -Scott - Original Message - I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the $DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg
I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this: echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so -Scott - Original Message - Have you installed SGE on the same machine? If so, then you should be able to do a locate libdrmaa.so, which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so - libdrmaa.so.1.0 You may also want to try updatedb (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use dpkg on Ubuntu/Debian and yum on Centos to manipulate packages. -Scott - Original Message - I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the $DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg
Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0 I guess that would be it. For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine? -Greg On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus scottmcma...@gatech.eduwrote: I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this: *echo $DRMAA_LIBRARY_PATH* /usr/lib/libdrmaa.so -Scott -- Have you installed SGE on the same machine? If so, then you should be able to do a locate libdrmaa.so, which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so - libdrmaa.so.1.0 You may also want to try updatedb (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use dpkg on Ubuntu/Debian and yum on Centos to manipulate packages. -Scott -- I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the $DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg
And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable? The normal nodes running jobs don't need this, right? Thanks, -Greg On Mon, Nov 5, 2012 at 3:12 PM, greg margeem...@gmail.com wrote: Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0 I guess that would be it. For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine? -Greg On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus scottmcma...@gatech.edu wrote: I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this: echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so -Scott Have you installed SGE on the same machine? If so, then you should be able to do a locate libdrmaa.so, which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so - libdrmaa.so.1.0 You may also want to try updatedb (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use dpkg on Ubuntu/Debian and yum on Centos to manipulate packages. -Scott I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg
On Nov 5, 2012, at 3:15 PM, greg wrote: And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable? The normal nodes running jobs don't need this, right? Hi Greg, That's correct. If you're starting Galaxy with an init script, I'd put the export there. --nate Thanks, -Greg On Mon, Nov 5, 2012 at 3:12 PM, greg margeem...@gmail.com wrote: Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0 I guess that would be it. For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine? -Greg On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus scottmcma...@gatech.edu wrote: I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this: echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so -Scott Have you installed SGE on the same machine? If so, then you should be able to do a locate libdrmaa.so, which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so - libdrmaa.so.1.0 You may also want to try updatedb (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use dpkg on Ubuntu/Debian and yum on Centos to manipulate packages. -Scott I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg
Well, I want it to ultimately run under Apache. Does it still make sense to go in an init script? thanks again, Greg On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor n...@bx.psu.edu wrote: On Nov 5, 2012, at 3:15 PM, greg wrote: And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable? The normal nodes running jobs don't need this, right? Hi Greg, That's correct. If you're starting Galaxy with an init script, I'd put the export there. --nate Thanks, -Greg On Mon, Nov 5, 2012 at 3:12 PM, greg margeem...@gmail.com wrote: Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0 I guess that would be it. For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine? -Greg On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus scottmcma...@gatech.edu wrote: I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this: echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so -Scott Have you installed SGE on the same machine? If so, then you should be able to do a locate libdrmaa.so, which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so - libdrmaa.so.1.0 You may also want to try updatedb (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use dpkg on Ubuntu/Debian and yum on Centos to manipulate packages. -Scott I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg
On Nov 5, 2012, at 3:26 PM, greg wrote: Well, I want it to ultimately run under Apache. Does it still make sense to go in an init script? thanks again, Yes, even when running behind Apache, you'll need an init script (or similar method) to start the Galaxy server. --nate Greg On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor n...@bx.psu.edu wrote: On Nov 5, 2012, at 3:15 PM, greg wrote: And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable? The normal nodes running jobs don't need this, right? Hi Greg, That's correct. If you're starting Galaxy with an init script, I'd put the export there. --nate Thanks, -Greg On Mon, Nov 5, 2012 at 3:12 PM, greg margeem...@gmail.com wrote: Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0 I guess that would be it. For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine? -Greg On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus scottmcma...@gatech.edu wrote: I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this: echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so -Scott Have you installed SGE on the same machine? If so, then you should be able to do a locate libdrmaa.so, which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so - libdrmaa.so.1.0 You may also want to try updatedb (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use dpkg on Ubuntu/Debian and yum on Centos to manipulate packages. -Scott I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this
Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg
On Nov 5, 2012, at 3:40 PM, greg wrote: Ok, that makes sense. Would you mind sharing how you set up your init script? What goes in it, where you place it? There are some sample init scripts in the contrib/ directory of the distribution. You should be able to place the export near the top, where other variables are set. --nate Thanks again, Greg On Mon, Nov 5, 2012 at 3:33 PM, Nate Coraor n...@bx.psu.edu wrote: On Nov 5, 2012, at 3:26 PM, greg wrote: Well, I want it to ultimately run under Apache. Does it still make sense to go in an init script? thanks again, Yes, even when running behind Apache, you'll need an init script (or similar method) to start the Galaxy server. --nate Greg On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor n...@bx.psu.edu wrote: On Nov 5, 2012, at 3:15 PM, greg wrote: And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable? The normal nodes running jobs don't need this, right? Hi Greg, That's correct. If you're starting Galaxy with an init script, I'd put the export there. --nate Thanks, -Greg On Mon, Nov 5, 2012 at 3:12 PM, greg margeem...@gmail.com wrote: Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0 I guess that would be it. For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine? -Greg On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus scottmcma...@gatech.edu wrote: I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this: echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so -Scott Have you installed SGE on the same machine? If so, then you should be able to do a locate libdrmaa.so, which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so - libdrmaa.so.1.0 You may also want to try updatedb (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use dpkg on Ubuntu/Debian and yum on Centos to manipulate packages. -Scott I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] cluster install
It's reasonably easy to set up Galaxy to use external authentication. We modeled our authentication after the way MSI folks did it as posted on the galaxy-dev list a while ago. We use SSO (Single Sign On) with mod_auth_tkt SSO tied into an LDAP back-end used for our cluster. I'd be happy to share the details beyond the LDAP authentication discussion you can find in the Galaxy list archives [1] if necessary. In addition, this sort of question is more appropriate to the galaxy-dev, but not the galaxy-user list. Regards, Alex -- Oleksandr Moskalenko, Ph.D. Biological Applications Support High Performance Computing Center University of Florida 1. http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002660.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002667.html On Oct 26, 2011, at 12:29 PM, Joshua Udall wrote: Dear Galaxy - We would like to install and instance of Galaxy on our campus cluster. The install process looks very straight forward, but tying it in with our authentication system for the current, functioning cluster may not be as simple. It appears that galaxy is easy to install if there are limited users on a local machine or on a cluster where galaxy is the main use of the cluster (so it handles all the user accounts). Where would I direct our IT admin group to get more assistance with customizing the authentication process with our existing, function cluster? -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307 Fax: 801-422-0008 USA ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
