Re: [galaxy-dev] galaxy local installation
Hello, Thank you very much for the quick answers. There were very useful. Now I hope I'm not bothering you with a couple more questions. I read more thoroughly the documentation for installing a production environment and I was wondering: 1. Is it possible to run the web server through apache but not as a proxy server? a. If so what are the steps exactly? I only found the explanation for a proxy server... 2. Will this kind of installation will work on red hat 6 enterprise server ? Cordialement / Regards, Edgar Fernandez De : Alistair Chilcott [mailto:alistair.chilc...@utas.edu.au] Envoyé : December-11-13 10:10 PM À : fernandez Edgar; galaxy-...@bx.psu.edu Objet : RE: galaxy local installation Edgar, I have been exploring similar outcomes and run into similar issues. I have recently found this post http://seqanswers.com/forums/showthread.php?t=23629 That I'm sure will prove helpful to you. This show how to get it working, including the dependancies and reference genomes .. advice on securing it is already on the galaxy websites. Another observation I would make is that the vast majority of help and advice you will find on the web relates to a galaxy environments built on Ubuntu, (12.04 LTS seem to be the version of choice). The instructions above will help you install it on SUSE but I found that having to translate the steps from Ubuntu to SUSE was occasionally problematic. Hope this helps. Regards, Alistair From: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of fernandez Edgar Sent: Thursday, 12 December 2013 4:31 AM To: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: [galaxy-dev] galaxy local installation Hello, My name is Edgar Fernandez. I'm a sys. admin. at University of Montreal. I've been ask by a teacher to check out Galaxy. So I've installed locally on my computer galaxy (I'm running openSUSE x86_64 but I'll install it on SUSE Linux ia64). I've executed the run.sh script and I've somewhat successfully made the website work. I say somewhat because I have a couple of issues: 1. The website is not well displayed (refer to the attachment) 2. I've changed the value of host to 0.0.0.0 in the universe_wsgi.ini file and it still launches to 127.0.0.1 I was also wondering if there is a step by step tutorial to install all the dependencies? I'm finding myself overwhelmed with all the different dependencies. 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy local installation
Hello Carl, The problem with the format of the website was resolved. However, I'm still wondering about the apache inquiry. Can it be done? Can I give apache the job of deploying the website instead of the run.sh script ? Furthermore, I do not want an apache proxy server, I just want apache to take care of the website Cordialement / Regards, Edgar Fernandez De : Carl Eberhard [mailto:carlfeberh...@gmail.com] Envoyé : December-12-13 5:25 PM À : fernandez Edgar Cc : Alistair Chilcott; galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy local installation Hello, Edgar - thanks for installing Galaxy! Regarding the screenshots: it looks like Galaxy's static css stylesheet isn't being loaded properly. Is this still occurring for you? Do you see anything when you try to go to http://localhost:8080/static/style/base.css in your browser? (You should see some text) Thanks, Carl On Thu, Dec 12, 2013 at 2:51 PM, fernandez Edgar edgar.fernan...@umontreal.camailto:edgar.fernan...@umontreal.ca wrote: Hello, Thank you very much for the quick answers. There were very useful. Now I hope I'm not bothering you with a couple more questions. I read more thoroughly the documentation for installing a production environment and I was wondering: 1. Is it possible to run the web server through apache but not as a proxy server? a. If so what are the steps exactly? I only found the explanation for a proxy server... 2. Will this kind of installation will work on red hat 6 enterprise server ? Cordialement / Regards, Edgar Fernandez De : Alistair Chilcott [mailto:alistair.chilc...@utas.edu.aumailto:alistair.chilc...@utas.edu.au] Envoyé : December-11-13 10:10 PM À : fernandez Edgar; galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Objet : RE: galaxy local installation Edgar, I have been exploring similar outcomes and run into similar issues. I have recently found this post http://seqanswers.com/forums/showthread.php?t=23629 That I'm sure will prove helpful to you. This show how to get it working, including the dependancies and reference genomes .. advice on securing it is already on the galaxy websites. Another observation I would make is that the vast majority of help and advice you will find on the web relates to a galaxy environments built on Ubuntu, (12.04 LTS seem to be the version of choice). The instructions above will help you install it on SUSE but I found that having to translate the steps from Ubuntu to SUSE was occasionally problematic. Hope this helps. Regards, Alistair From: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of fernandez Edgar Sent: Thursday, 12 December 2013 4:31 AM To: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: [galaxy-dev] galaxy local installation Hello, My name is Edgar Fernandez. I'm a sys. admin. at University of Montreal. I've been ask by a teacher to check out Galaxy. So I've installed locally on my computer galaxy (I'm running openSUSE x86_64 but I'll install it on SUSE Linux ia64). I've executed the run.sh script and I've somewhat successfully made the website work. I say somewhat because I have a couple of issues: 1. The website is not well displayed (refer to the attachment) 2. I've changed the value of host to 0.0.0.0 in the universe_wsgi.ini file and it still launches to 127.0.0.1 I was also wondering if there is a step by step tutorial to install all the dependencies? I'm finding myself overwhelmed with all the different dependencies. Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111tel: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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/
[galaxy-dev] creating a hierarchy of students teachers and courses
Hello galaxy team, First and foremost, I would like to thank you for your assistance with my galaxy installation with apache proxy. It works very well. Secondly, I would like your help with creating users, groups, roles and permissions that would allow me to: 1. differentiate a student from a teacher 2. differentiate a student in course A or in course B 3. teachers having read access to students' work 4. teachers sharing with students Right now, I just have created users. There is no group or roles or permissions or datasets. On another note, how can I disable the account of one specific user or a whole group ? 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] creating a hierarchy of students teachers and courses
Hello John, Thank you very much for your answer! It's sounds logical and do-able. However, I've thought of the following and I would like your opinion about it: (this is to create a workspace for each student which is accessible only by them and their teacher) 1. create a data library for each user (student, teacher and class) 2. the data library for each student will have the following permissions: a. modify library item = student private role (email address) b. access library = student private role (email address) and teacher private role c. add library item = student private role (email address) d. manage library permissions = student private role (email address) 3. the data library for each teacher will have the following permissions: a. modify library item = teacher private role (email address) b. access library = teacher private role (email address) c. add library item = teacher private role (email address) d. manage library permissions = teacher private role (email address) 4. the data library for each class will have the following permissions: a. modify library item = teacher private role (email address) b. access library = teacher private role (email address) c. add library item = teacher private role (email address) and all students privates roles d. manage library permissions = teacher private role (email address) Now, here's the one million dollar questions: Will the permission 4c permit to every student to drop some work into the class workspace but not cheap by seeing the work of another student ? Cordialement / Regards, Edgar Fernandez -Message d'origine- De : jmchil...@gmail.com [mailto:jmchil...@gmail.com] De la part de John Chilton Envoyé : January-15-14 12:12 PM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] creating a hierarchy of students teachers and courses Galaxy can do some these and maybe not others. This is a really big topic, and I hope you let us all know how progress on this goes - it is a really interesting use case. I can comment a little on each part of this, but they are all connected and there are different ways to approach each of these things. On Tue, Jan 14, 2014 at 12:03 PM, Fernandez Edgar edgar.fernan...@umontreal.ca wrote: Hello galaxy team, First and foremost, I would like to thank you for your assistance with my galaxy installation with apache proxy. It works very well. Secondly, I would like your help with creating users, groups, roles and permissions that would allow me to: 1. differentiate a student from a teacher Are you creating these accounts inside of Galaxy or using an external authentication method? Because if your are creating these accounts yourself - I would suggest using naming scheme to distinguish these: std_cls_lastname teach_cls_lastname Another idea to consider is to make all teachers admins. This provides a lot of extra functionality that can cover some additional requirements below and can serve as the basis for differentiating. 2. differentiate a student in course A or in course B You could use a naming scheme, or your could create a group and role for each course. It looks like there is an API for managing groups and roles. This can help automate some of this - it would be very laborious to do this through the UI I imagine. 3. teachers having read access to students' work This one is why I would give the teachers admin access - I think they could impersonate the students to access their work (set allow_user_impersonation = True in universe_wsgi.ini). It would mean that every teacher would have full access to every students work - if this is a problem you might want to consider standing up a Galaxy instance per class - there is some up front overhead with this - but it would make cleaning things up really easy. If these aren't realistic solutions, I think producing course documentation describing for students how to manually share their work with teachers is probably the best bet. Any user can share a history with any other user or produce links and e-mail these to the teacher. 4. teachers sharing with students I would look at having the teachers setup pages for individual courses or lesson plans. These can be made public and students would be able to import histories, datasets, and workflows right in from these. If more targeted sharing is needed again I think the best bet right now might just use Galaxy's history sharing capabilities. Right now, I just have created users. There is no group or roles or permissions or datasets. On another note, how can I disable the account of one specific user or a whole group ? To enable this functionality for individual users and groups in the UI you need to set
Re: [galaxy-dev] small suggestion: customize stuff
Hello y'all I was wondering if I did the right thing : I've modified the file user.py to reset the user's password to a length of 8 characters by doing: diff /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/user.py /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/ARCHIVES/user.py_20140120_15.3.14 1092c1092 for i in range(7): --- for i in range(15): I believe the sys admin would like this to be customizable in the universe_wsgi.ini file. As well for the reset capability could be accessible just by the administrator. I would like to apologies to galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu if I'm spamming your email. Please let me know if I should remove this to my threads. Cordialement / Regards, Edgar Fernandez ___ 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/
