Re: [galaxy-dev] API : Max retries exceeded
Hi, Just a little up ! I promise, it's the first and the last one :P But I really need a clue. This script is included in an automatic process to create account (LDAP) on our network, create directories (some for Galaxy, some for backup) and create galaxy libraries. The part of my script, which raise this error, just get the user id from his email. I didn't found other method to do that : users_in_galaxy=instance.users.get_users() for user_in_galaxy in users_in_galaxy: if ((user_in_galaxy[email].find(user))=0): userGalaxy = user_in_galaxy break Is it a parameter that can be set when we build the GalaxyInstance ? or is it an apache setting ? Thanks Gildas Le 11/09/2014 17:46, Gildas Le Corguille a écrit : Hi, I wrote a script which need to retrieve a list of all users on our production instance. It seems that we have too many users (325) :P bioblend.galaxy.client.ConnectionError: HTTPConnectionPool(host='galaxy.sb-roscoff.fr', port=8080): Max retries exceeded with url: /api/users?key=fd420zefff9a9df586210fd8c8452d98 (Caused by class 'socket.error': [Errno 111] Connection refused): None My script is running on an test instance which have less users. Is there a way to set this threshold ? Thanks Gildas PS : don't try my api_key, little hacker, it's a fake :P ___ 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] Main tool shed installation issues
Hello fellow Galaxy-Dev users, We are having an issue trying to install tools from the main tool shed. Trying to install bowtie2 (or any other tool for that matter) gives us the following error message : Error Traceback: ⇝ URLError: urlopen error [Errno -2] Name or service not known Looking further in the error traceback, the url not found in question is this one (in the case of bowtie2): https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b54596%2066changeset_revisions=a54de7e658f7 Indeed, copy pasting this URL into a browser gives me the Internal server error page. Anyone knows if this is a widespread issue? Thanks for your feedback! Yves ___ 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] Main tool shed installation issues
somehow a space (escaped) got into your id this is the correct url: https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b5459666changeset_revisions=a54de7e658f7 I will look around why it got there. On Tue, Sep 16, 2014 at 4:41 PM, Yves Gagnon yves.gag...@dnalandmarks.ca wrote: Hello fellow Galaxy-Dev users, We are having an issue trying to install tools from the main tool shed. Trying to install bowtie2 (or any other tool for that matter) gives us the following error message : *Error Traceback:* ⇝ URLError: urlopen error [Errno -2] Name or service not known Looking further in the error traceback, the url not found in question is this one (in the case of bowtie2): https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b54596%2066changeset_revisions=a54de7e658f7 Indeed, copy pasting this URL into a browser gives me the Internal server error page. Anyone knows if this is a widespread issue? Thanks for your feedback! Yves ___ 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] API : Max retries exceeded
Is there some small difference between your test and production instance? It seems like you client is trying to connect to port 8080 in production? Is this accessible? The error makes me think this is not a Galaxy problem but a firewall or proxy issue. Is your production instance served out on port 8080 or do you have some kind of proxy setup to serve content on port 80? It might be worth testing this script on the same server as Galaxy is running on as well to verify it is an issue like this. -John On Tue, Sep 16, 2014 at 3:35 AM, Gildas Le Corguille lecorgui...@sb-roscoff.fr wrote: Hi, Just a little up ! I promise, it's the first and the last one :P But I really need a clue. This script is included in an automatic process to create account (LDAP) on our network, create directories (some for Galaxy, some for backup) and create galaxy libraries. The part of my script, which raise this error, just get the user id from his email. I didn't found other method to do that : users_in_galaxy=instance.users.get_users() for user_in_galaxy in users_in_galaxy: if ((user_in_galaxy[email].find(user))=0): userGalaxy = user_in_galaxy break Is it a parameter that can be set when we build the GalaxyInstance ? or is it an apache setting ? Thanks Gildas Le 11/09/2014 17:46, Gildas Le Corguille a écrit : Hi, I wrote a script which need to retrieve a list of all users on our production instance. It seems that we have too many users (325) :P bioblend.galaxy.client.ConnectionError: HTTPConnectionPool(host='galaxy.sb-roscoff.fr', port=8080): Max retries exceeded with url: /api/users?key=fd420zefff9a9df586210fd8c8452d98 (Caused by class 'socket.error': [Errno 111] Connection refused): None My script is running on an test instance which have less users. Is there a way to set this threshold ? Thanks Gildas PS : don't try my api_key, little hacker, it's a fake :P ___ 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] Main tool shed installation issues
I tried installing this exact repo and changeset on the latest -central galaxy code and encountered no problems. What version of Galaxy are you using. Did you modify it? Martin On Tue, Sep 16, 2014 at 4:44 PM, Martin Čech mar...@bx.psu.edu wrote: somehow a space (escaped) got into your id this is the correct url: https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b5459666changeset_revisions=a54de7e658f7 I will look around why it got there. On Tue, Sep 16, 2014 at 4:41 PM, Yves Gagnon yves.gag...@dnalandmarks.ca wrote: Hello fellow Galaxy-Dev users, We are having an issue trying to install tools from the main tool shed. Trying to install bowtie2 (or any other tool for that matter) gives us the following error message : *Error Traceback:* ⇝ URLError: urlopen error [Errno -2] Name or service not known Looking further in the error traceback, the url not found in question is this one (in the case of bowtie2): https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b54596%2066changeset_revisions=a54de7e658f7 Indeed, copy pasting this URL into a browser gives me the Internal server error page. Anyone knows if this is a widespread issue? Thanks for your feedback! Yves ___ 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] Main tool shed installation issues
Hi Martin, I think that the escaped space was added because of the Interactive traceback display, I had to click a link to display the full URL. The original URL does not contain a space in the repository_id (URL: admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=126c0918b5459666changeset_revisions=a54de7e658f7) I think I pinpointed the issue now. It seems to be a proxy misconfiguration. When I enter the URL on my machine, I do not have any errors. When I do wget on the galaxy server machine, it is there that I have the Name or service not known error. Well, thank you for your quick answer! Yves From: Martin Čech mar...@bx.psu.edu To: Yves Gagnon yves.gag...@dnalandmarks.ca Cc: galaxy-dev galaxy-dev@lists.bx.psu.edu Date: 16/09/2014 04:50 PM Subject:Re: [galaxy-dev] Main tool shed installation issues Sent by:emulato...@gmail.com I tried installing this exact repo and changeset on the latest -central galaxy code and encountered no problems. What version of Galaxy are you using. Did you modify it? Martin On Tue, Sep 16, 2014 at 4:44 PM, Martin Čech mar...@bx.psu.edu wrote: somehow a space (escaped) got into your id this is the correct url: https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b5459666changeset_revisions=a54de7e658f7 I will look around why it got there. On Tue, Sep 16, 2014 at 4:41 PM, Yves Gagnon yves.gag...@dnalandmarks.ca wrote: Hello fellow Galaxy-Dev users, We are having an issue trying to install tools from the main tool shed. Trying to install bowtie2 (or any other tool for that matter) gives us the following error message : Error Traceback: ? URLError: urlopen error [Errno -2] Name or service not known Looking further in the error traceback, the url not found in question is this one (in the case of bowtie2): https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b54596%2066changeset_revisions=a54de7e658f7 Indeed, copy pasting this URL into a browser gives me the Internal server error page. Anyone knows if this is a widespread issue? Thanks for your feedback! Yves ___ 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] Dependencies within dependencies
I am trying to move the package_r_3_0_3 repository owned by devteam from the main toolshed to our local toolshed. This does not work as some dependencies required for package_r_3_0_3 are not exported (export capsule) and not included in the archive. For instance, package_freetype_2_5_2 and package_libpng_1_6_7 are present in the capsule and thus moved to the local toolshed, but not package_readline_6_2, package_cairo_1_12_14 and package_pixman_0_32_4. Is it a bug (I would expect a sort of recursivity in the export process) or did I miss some logics behind this ? And do we have to manually export-import the missing dependencies to the local toolshed ? Cheers Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 christophe.antoniew...@upmc.fr http://bio-dev.snv.jussieu.fr/ Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org http://www.sciencesenmarche.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/
Re: [galaxy-dev] Dependencies within dependencies
Hi Christophe - there's a trello card for this at https://trello.com/c/ClgcV0Sn - upvote and add your experiences please? On Wed, Sep 17, 2014 at 8:01 AM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: I am trying to move the package_r_3_0_3 repository owned by devteam from the main toolshed to our local toolshed. This does not work as some dependencies required for package_r_3_0_3 are not exported (export capsule) and not included in the archive. For instance, package_freetype_2_5_2 and package_libpng_1_6_7 are present in the capsule and thus moved to the local toolshed, but not package_readline_6_2, package_cairo_1_12_14 and package_pixman_0_32_4. Is it a bug (I would expect a sort of recursivity in the export process) or did I miss some logics behind this ? And do we have to manually export-import the missing dependencies to the local toolshed ? Cheers Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 christophe.antoniew...@upmc.fr http://bio-dev.snv.jussieu.fr/ Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org http://www.sciencesenmarche.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/
