Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)
Hi, This is a quick follow up about the instructions given by Aysam and Martin, which may help others (including me ;-). Indeed I upgraded our galaxy-dist to the last commit and the /client directory showed up. To get the instructions working I had to install as root some grunt related packages, otherwise it failed: including $ sudo apt-get install software-properties-common $ sudo apt-get install python-software-properties $ sudo apt-get update $ sudo npm -g install grunt $ sudo npm install -g grunt-cli Then I had the grunt watch working and could make the changes - *opening another shell session* (I say this because it is not evident for those who are not familiar with grunt). Yet the changes still do not show up in the browser. My guess is that the galaxy configuration model has changed too, with the creation of a config directory. I suppose that the use of the /client directory is specified in the new galaxy.ini file which replaces universe_wsgi.ini in / . More generally, I did not see instructions on how to move from the old .ini file*sss* at / to the new configuration model using the /config directory without crashing the production instance. Is it available somewhere in the wiki or in a discussion ? Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.org 2014-11-12 16:11 GMT+01:00 Aysam Guerler aysam.guer...@gmail.com: Hi Christophe, In order to apply the changes scripts have to be packed properly. Please follow these steps: 1. Go to the client/ directory and type 'npm install' 2. Now type 'grunt watch'. This will start a listener which captures code changes and repacks scripts automatically 3. Finally, make your changes to the code files in client/galaxy/scripts/mvc/upload and reload your browser Let me know if that works for you or if you have any other questions. Thanks, Sam ___ 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] customize the Upload File tool form (version 1.1.4)
Hi Christophe, In order to apply the changes scripts have to be packed properly. Please follow these steps: 1. Go to the client/ directory and type 'npm install' 2. Now type 'grunt watch'. This will start a listener which captures code changes and repacks scripts automatically 3. Finally, make your changes to the code files in client/galaxy/scripts/mvc/upload and reload your browser Let me know if that works for you or if you have any other questions. Thanks, Sam On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Hi, As we have arranged an sftp upload system through ftp port for our Galaxy instance, we would need to customize the Upload File tool form, so that a few more line explain how-to-do in the FTP section of the form, in addition to the This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at 127.0.0.1 using your Galaxy credentials (email address and password). I dug into /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js and /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js but the changes I tried into these files do not show up in the tool form. If someone can indicate the right way to intercept this content and enrich it as mentioned above, I would be grateful ! Cheers Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.org ___ 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/
Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)
I updated our wiki with this new build information. https://wiki.galaxyproject.org/Develop/JSA M. On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler aysam.guer...@gmail.com wrote: Hi Christophe, In order to apply the changes scripts have to be packed properly. Please follow these steps: 1. Go to the client/ directory and type 'npm install' 2. Now type 'grunt watch'. This will start a listener which captures code changes and repacks scripts automatically 3. Finally, make your changes to the code files in client/galaxy/scripts/mvc/upload and reload your browser Let me know if that works for you or if you have any other questions. Thanks, Sam On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Hi, As we have arranged an sftp upload system through ftp port for our Galaxy instance, we would need to customize the Upload File tool form, so that a few more line explain how-to-do in the FTP section of the form, in addition to the This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at 127.0.0.1 using your Galaxy credentials (email address and password). I dug into /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js and /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js but the changes I tried into these files do not show up in the tool form. If someone can indicate the right way to intercept this content and enrich it as mentioned above, I would be grateful ! Cheers Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.org ___ 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/ ___ 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] customize the Upload File tool form (version 1.1.4)
Aysam and Martin, Thanks for your help. I am not familiar with JS development. To make client crystal clear : /client stands for the home directory where Galaxy-dist is installed ? and client/galaxy/scripts/mvc/upload stands for ~/galaxy-dist/scripts/mvc/upload (assuming that the galaxy code is installed in galaxy-dis) ? right ? Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.org 2014-11-12 16:42 GMT+01:00 Martin Čech mar...@bx.psu.edu: I updated our wiki with this new build information. https://wiki.galaxyproject.org/Develop/JSA M. On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler aysam.guer...@gmail.com wrote: Hi Christophe, In order to apply the changes scripts have to be packed properly. Please follow these steps: 1. Go to the client/ directory and type 'npm install' 2. Now type 'grunt watch'. This will start a listener which captures code changes and repacks scripts automatically 3. Finally, make your changes to the code files in client/galaxy/scripts/mvc/upload and reload your browser Let me know if that works for you or if you have any other questions. Thanks, Sam On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Hi, As we have arranged an sftp upload system through ftp port for our Galaxy instance, we would need to customize the Upload File tool form, so that a few more line explain how-to-do in the FTP section of the form, in addition to the This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at 127.0.0.1 using your Galaxy credentials (email address and password). I dug into /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js and /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js but the changes I tried into these files do not show up in the tool form. If someone can indicate the right way to intercept this content and enrich it as mentioned above, I would be grateful ! Cheers Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.org ___ 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/ ___ 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] customize the Upload File tool form (version 1.1.4)
corrrect: /client is a directory within Galaxy root - it contains all the javascripts The build (grunt) process takes the /client directory and copies the scripts to /static/scripts directory within Galaxy root (and packs them and stuff) from where the files are served to the browser. If you want to make JS changes, make them in /client and propagate it via grunt. Make sure you have up to date version of Galaxy since the grunt building was added fairly recently. note: /scripts directory within Galaxy root has a different purpose, those are python scripts (API and stuff) M. On Wed, Nov 12, 2014 at 1:16 PM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Aysam and Martin, Thanks for your help. I am not familiar with JS development. To make client crystal clear : /client stands for the home directory where Galaxy-dist is installed ? and client/galaxy/scripts/mvc/upload stands for ~/galaxy-dist/scripts/mvc/upload (assuming that the galaxy code is installed in galaxy-dis) ? right ? Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.org 2014-11-12 16:42 GMT+01:00 Martin Čech mar...@bx.psu.edu: I updated our wiki with this new build information. https://wiki.galaxyproject.org/Develop/JSA M. On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler aysam.guer...@gmail.com wrote: Hi Christophe, In order to apply the changes scripts have to be packed properly. Please follow these steps: 1. Go to the client/ directory and type 'npm install' 2. Now type 'grunt watch'. This will start a listener which captures code changes and repacks scripts automatically 3. Finally, make your changes to the code files in client/galaxy/scripts/mvc/upload and reload your browser Let me know if that works for you or if you have any other questions. Thanks, Sam On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Hi, As we have arranged an sftp upload system through ftp port for our Galaxy instance, we would need to customize the Upload File tool form, so that a few more line explain how-to-do in the FTP section of the form, in addition to the This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at 127.0.0.1 using your Galaxy credentials (email address and password). I dug into /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js and /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js but the changes I tried into these files do not show up in the tool form. If someone can indicate the right way to intercept this content and enrich it as mentioned above, I would be grateful ! Cheers Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.org ___ 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/ ___ 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] customize the Upload File tool form (version 1.1.4)
Ok I just noticed the new client directory in Bitbucket and the accompanying trello cards. Make things more understandable... Thanks Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.org 2014-11-12 19:23 GMT+01:00 Martin Čech mar...@bx.psu.edu: corrrect: /client is a directory within Galaxy root - it contains all the javascripts The build (grunt) process takes the /client directory and copies the scripts to /static/scripts directory within Galaxy root (and packs them and stuff) from where the files are served to the browser. If you want to make JS changes, make them in /client and propagate it via grunt. Make sure you have up to date version of Galaxy since the grunt building was added fairly recently. note: /scripts directory within Galaxy root has a different purpose, those are python scripts (API and stuff) M. On Wed, Nov 12, 2014 at 1:16 PM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Aysam and Martin, Thanks for your help. I am not familiar with JS development. To make client crystal clear : /client stands for the home directory where Galaxy-dist is installed ? and client/galaxy/scripts/mvc/upload stands for ~/galaxy-dist/scripts/mvc/upload (assuming that the galaxy code is installed in galaxy-dis) ? right ? Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.org 2014-11-12 16:42 GMT+01:00 Martin Čech mar...@bx.psu.edu: I updated our wiki with this new build information. https://wiki.galaxyproject.org/Develop/JSA M. On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler aysam.guer...@gmail.com wrote: Hi Christophe, In order to apply the changes scripts have to be packed properly. Please follow these steps: 1. Go to the client/ directory and type 'npm install' 2. Now type 'grunt watch'. This will start a listener which captures code changes and repacks scripts automatically 3. Finally, make your changes to the code files in client/galaxy/scripts/mvc/upload and reload your browser Let me know if that works for you or if you have any other questions. Thanks, Sam On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Hi, As we have arranged an sftp upload system through ftp port for our Galaxy instance, we would need to customize the Upload File tool form, so that a few more line explain how-to-do in the FTP section of the form, in addition to the This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at 127.0.0.1 using your Galaxy credentials (email address and password). I dug into /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js and /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js but the changes I tried into these files do not show up in the tool form. If someone can indicate the right way to intercept this content and enrich it as mentioned above, I would be grateful ! Cheers Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.org ___ 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/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other
