Re: [galaxy-dev] show stopper for my galaxy installation
Hello Eric, It works great! Thank you! Is it possible to use the same logic to overwrite an input parameters to a job. For example, trimmomatic executes by default with the input parameters -threads 6”. Can I change that parameter to threads 4? Cordialement / Regards, Edgar Fernandez De : Eric Rasche [mailto:e...@tamu.edu] Envoyé : January-22-15 3:05 PM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] show stopper for my galaxy installation The tool to fetch data isn't being run on your submit node but instead on the cluster, which is the problem. It's a fairly easy to solve problem: * In your job_conf you'll need to define a way to run jobs locally (either via local runner, or via a special queue dedicated to your submit node) * Then you'll need to specify that the upload tool is forced to that job runner. Something like this (untested, probably invalid xml... ) plugins workers=4 plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner / !-- your torque runner here -- /plugins destinations default=cluster destination id=local runner=local !-- your cluster dest here -- /destinations tools !-- we force the upload tool to the local job runner, thereby bypassing the issue of internet access on the cluster nodes -- tool id=upload1 destination=local / /tools Cheers, Eric 2015-01-22 13:51 GMT-06:00 Fernandez Edgar edgar.fernan...@umontreal.camailto:edgar.fernan...@umontreal.ca: Hello gents, I started this new thread because I have a showstopper for my installation of galaxy. Here’s my situation: 1. I have a galaxy server that has internet access. 2. My galaxy server is also my torque server and my only torque submit node. 3. I have three torque compute nodes that DOESN’T have internet access. Now, I’ve tried uploading a file (larger than 2Gb) via and URL and it fails. However, I’ve added my galaxy server as a compute node and re-tried to upload the same file and I made sure the job will run on that machine and it works. Now, my compute nodes are in a network that is completely protected from the outside world. So no internet access. What are my option in this case? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication • Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edumailto:e...@tamu.edu rasche.e...@yandex.rumailto:rasche.e...@yandex.ru ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] show stopper for my galaxy installation
Hello guys! I’m impressed! You guys really thought of everything! This is amazing! I’ll try it and give you some news asap. I’m so impressed that I used too many exclamation points in this email!!! Cordialement / Regards, Edgar Fernandez De : Eric Rasche [mailto:e...@tamu.edu] Envoyé : January-22-15 3:05 PM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] show stopper for my galaxy installation The tool to fetch data isn't being run on your submit node but instead on the cluster, which is the problem. It's a fairly easy to solve problem: * In your job_conf you'll need to define a way to run jobs locally (either via local runner, or via a special queue dedicated to your submit node) * Then you'll need to specify that the upload tool is forced to that job runner. Something like this (untested, probably invalid xml... ) plugins workers=4 plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner / !-- your torque runner here -- /plugins destinations default=cluster destination id=local runner=local !-- your cluster dest here -- /destinations tools !-- we force the upload tool to the local job runner, thereby bypassing the issue of internet access on the cluster nodes -- tool id=upload1 destination=local / /tools Cheers, Eric 2015-01-22 13:51 GMT-06:00 Fernandez Edgar edgar.fernan...@umontreal.camailto:edgar.fernan...@umontreal.ca: Hello gents, I started this new thread because I have a showstopper for my installation of galaxy. Here’s my situation: 1. I have a galaxy server that has internet access. 2. My galaxy server is also my torque server and my only torque submit node. 3. I have three torque compute nodes that DOESN’T have internet access. Now, I’ve tried uploading a file (larger than 2Gb) via and URL and it fails. However, I’ve added my galaxy server as a compute node and re-tried to upload the same file and I made sure the job will run on that machine and it works. Now, my compute nodes are in a network that is completely protected from the outside world. So no internet access. What are my option in this case? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication • Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edumailto:e...@tamu.edu rasche.e...@yandex.rumailto:rasche.e...@yandex.ru ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] show stopper for my galaxy installation
The tool to fetch data isn't being run on your submit node but instead on the cluster, which is the problem. It's a fairly easy to solve problem: - In your job_conf you'll need to define a way to run jobs locally (either via local runner, or via a special queue dedicated to your submit node) - Then you'll need to specify that the upload tool is forced to that job runner. Something like this (untested, probably invalid xml... ) plugins workers=4 plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner / !-- your torque runner here -- /plugins destinations default=cluster destination id=local runner=local !-- your cluster dest here -- /destinations tools !-- we force the upload tool to the local job runner, thereby bypassing the issue of internet access on the cluster nodes -- tool id=upload1 destination=local / /tools Cheers, Eric 2015-01-22 13:51 GMT-06:00 Fernandez Edgar edgar.fernan...@umontreal.ca: Hello gents, I started this new thread because I have a showstopper for my installation of galaxy. Here’s my situation: 1. I have a galaxy server that has internet access. 2. My galaxy server is also my torque server and my only torque submit node. 3. I have three torque compute nodes that DOESN’T have internet access. Now, I’ve tried uploading a file (larger than 2Gb) via and URL and it *fails*. However, I’ve added my galaxy server as a compute node and re-tried to upload the same file and I made sure the job will run on that machine and it *works*. Now, my compute nodes are in a network that is completely protected from the outside world. So no internet access. What are my option in this case? Cordialement / Regards, *Edgar Fernandez* System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication ( Bur. : *1-514-343-6111 poste 16568* *Université de Montréal* PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu rasche.e...@yandex.ru ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
