Re: [galaxy-user] [Ticket#2013010710000031] Installation de ChipMunk sur Genotoul
Thanks Alban for your answer, Our admin system has tested to run ChIPMunk externally but didn't received the same error message. In fact, pretty.rb lib is found. It seems to be a difference between chiphorde version : we have run_chiphorde4.rb instead of run_chiphorde.rb Do you think that we have to install your version or thaht we just need to rename some files? Your error message when running ruby run_chiphorde4.rb is : LLIB 08 Jan 09:10:17 [ytilib] ytilib required, working directory /usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts LLIB 08 Jan 09:10:17 [ytilib] use_chiphorde4.rb started, usage motif_template ChIPHorde-engine-params LLIB 08 Jan 09:10:17 [ytilib] run_chiphorde4.rb Thanks in advance, Sarah Support a écrit : Bonjour, Voilà ce que j'obtiens quand je lance la commande qu'il demande: ruby run_chiphorde4.rb LLIB 08 Jan 09:10:17 [ytilib] ytilib required, working directory /usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts LLIB 08 Jan 09:10:17 [ytilib] use_chiphorde4.rb started, usage motif_template ChIPHorde-engine-params LLIB 08 Jan 09:10:17 [ytilib] run_chiphorde4.rb Je n'obtiens donc pas l'erreur dont il parle. Par ailleurs voici le chemin de la librairie: /usr/lib/ruby/1.8/rexml/formatters/pretty.rb, mais il semble la trouver. Je continue à chercher avec ce que tu m'as envoyé. Mais il est possible que ce soit un problème de version puisqu'il semble qu'ils aient renommé les fichiers Cordialement, Marie-Stephane Trotard Génopole - Plateforme bio-informatique Centre INRA de Toulouse - Unité de BIA Chemin de Borde-Rouge - AUZEVILLE BP 52627 - 31326 CASTANET-TOLOSAN CEDEX tél. : +33 (0)5 61 28 54 27 Support : support.genop...@toulouse.inra.fr 08.01.2013 09:05 - Sarah Maman a écrit: Bonjour Marie-Stephane, A priori, il manquerait une librairie : I think that there's some ruby libraries missing. Please try to run ChIPMunk externally this way: ruby /path/to/ChIPMunk/run_chiphorde.rb If you receive this kind of error message, it means that it missed one library to work: ChIPMunk/ytilib/hack1.rb:1:in `require': no such file to load -- rexml/formatters/pretty (LoadError) from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/hack1.rb:1 from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44:in `require' from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44 from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3:in `require' from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3 I already had the problem and the missing library was this one: http://www.ruby-doc.org/stdlib-1.9.3/libdoc/rexml/rdoc/REXML/Formatters/Pretty.html Merci d'avance, Sarah Support a écrit : Bonjour, Il me semble que je l'avais installé en même temps que FindPeaks: /usr/local/bioinfo/src/ChIPMunk/current Parles-tu d'un autre logiciel? D'un version? Cordialement, Marie-Stephane Trotard Génopole - Plateforme bio-informatique Centre INRA de Toulouse - Unité de BIA Chemin de Borde-Rouge - AUZEVILLE BP 52627 - 31326 CASTANET-TOLOSAN CEDEX tél. : +33 (0)5 61 28 54 27 Support : support.genop...@toulouse.inra.fr 07.01.2013 14:35 - sarah.ma...@toulouse.inra.fr a écrit: A user filled out the contact form on bioinfo.genotoul.fr. ###master_email-line-plain_mailsubject## E-Mail: sarah.ma...@toulouse.inra.fr Priority: Very low Your Message: Bonjour, Il me semble, sauf erreur de ma part, que ChipMunk n est pas installé sur Genotoul. Est-il possible, s il vous plaît, de l installer. TrÚs cordialement, Sarah Maman -- This message was created automatically. ___ 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] [Ticket#2013010710000031] Installation de ChipMunk sur Genotoul
Thanks to Marie-Stephane to have found that this error is due to a diifference of verion. Alban, could you please tell us which version (2 or 3) do you use in your Galaxy tools, in order to install this version on our cluster ? Thanks in advance, Sarah Sarah Maman a écrit : Thanks Alban for your answer, Our admin system has tested to run ChIPMunk externally but didn't received the same error message. In fact, pretty.rb lib is found. It seems to be a difference between chiphorde version : we have run_chiphorde4.rb instead of run_chiphorde.rb Do you think that we have to install your version or thaht we just need to rename some files? Your error message when running ruby run_chiphorde4.rb is : LLIB 08 Jan 09:10:17 [ytilib] ytilib required, working directory /usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts LLIB 08 Jan 09:10:17 [ytilib] use_chiphorde4.rb started, usage motif_template ChIPHorde-engine-params LLIB 08 Jan 09:10:17 [ytilib] run_chiphorde4.rb Thanks in advance, Sarah Support a écrit : Bonjour, Voilà ce que j'obtiens quand je lance la commande qu'il demande: ruby run_chiphorde4.rb LLIB 08 Jan 09:10:17 [ytilib] ytilib required, working directory /usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts LLIB 08 Jan 09:10:17 [ytilib] use_chiphorde4.rb started, usage motif_template ChIPHorde-engine-params LLIB 08 Jan 09:10:17 [ytilib] run_chiphorde4.rb Je n'obtiens donc pas l'erreur dont il parle. Par ailleurs voici le chemin de la librairie: /usr/lib/ruby/1.8/rexml/formatters/pretty.rb, mais il semble la trouver. Je continue à chercher avec ce que tu m'as envoyé. Mais il est possible que ce soit un problème de version puisqu'il semble qu'ils aient renommé les fichiers Cordialement, Marie-Stephane Trotard Génopole - Plateforme bio-informatique Centre INRA de Toulouse - Unité de BIA Chemin de Borde-Rouge - AUZEVILLE BP 52627 - 31326 CASTANET-TOLOSAN CEDEX tél. : +33 (0)5 61 28 54 27 Support : support.genop...@toulouse.inra.fr 08.01.2013 09:05 - Sarah Maman a écrit: Bonjour Marie-Stephane, A priori, il manquerait une librairie : I think that there's some ruby libraries missing. Please try to run ChIPMunk externally this way: ruby /path/to/ChIPMunk/run_chiphorde.rb If you receive this kind of error message, it means that it missed one library to work: ChIPMunk/ytilib/hack1.rb:1:in `require': no such file to load -- rexml/formatters/pretty (LoadError) from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/hack1.rb:1 from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44:in `require' from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44 from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3:in `require' from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3 I already had the problem and the missing library was this one: http://www.ruby-doc.org/stdlib-1.9.3/libdoc/rexml/rdoc/REXML/Formatters/Pretty.html Merci d'avance, Sarah Support a écrit : Bonjour, Il me semble que je l'avais installé en même temps que FindPeaks: /usr/local/bioinfo/src/ChIPMunk/current Parles-tu d'un autre logiciel? D'un version? Cordialement, Marie-Stephane Trotard Génopole - Plateforme bio-informatique Centre INRA de Toulouse - Unité de BIA Chemin de Borde-Rouge - AUZEVILLE BP 52627 - 31326 CASTANET-TOLOSAN CEDEX tél. : +33 (0)5 61 28 54 27 Support : support.genop...@toulouse.inra.fr 07.01.2013 14:35 - sarah.ma...@toulouse.inra.fr a écrit: A user filled out the contact form on bioinfo.genotoul.fr. ###master_email-line-plain_mailsubject## E-Mail: sarah.ma...@toulouse.inra.fr Priority: Very low Your Message: Bonjour, Il me semble, sauf erreur de ma part, que ChipMunk n est pas installé sur Genotoul. Est-il possible, s il vous plaît, de l installer. TrÚs cordialement, Sarah Maman -- This message was created automatically. ___ 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] [Ticket#2013010710000031] Installation de ChipMunk sur Genotoul
Hi, You have to use ChIPMunk v2 with Nebula (I don't think its compatible with the v3) ++, Alban -- Alban Lermine Unité 900: INSERM - Mines ParisTech - Institut Curie Bioinformatics and Computational Systems Biology of Cancer 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel: +33 (0) 1 56 24 69 84 Le 8 janv. 2013 à 10:10, Sarah Maman sarah.ma...@toulouse.inra.fr a écrit : Thanks to Marie-Stephane to have found that this error is due to a diifference of verion. Alban, could you please tell us which version (2 or 3) do you use in your Galaxy tools, in order to install this version on our cluster ? Thanks in advance, Sarah Sarah Maman a écrit : Thanks Alban for your answer, Our admin system has tested to run ChIPMunk externally but didn't received the same error message. In fact, pretty.rb lib is found. It seems to be a difference between chiphorde version : we have run_chiphorde4.rb instead of run_chiphorde.rb Do you think that we have to install your version or thaht we just need to rename some files? Your error message when running ruby run_chiphorde4.rb is : LLIB 08 Jan 09:10:17 [ytilib]ytilib required, working directory /usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts LLIB 08 Jan 09:10:17 [ytilib]use_chiphorde4.rb started, usage motif_template ChIPHorde-engine-params LLIB 08 Jan 09:10:17 [ytilib]run_chiphorde4.rb Thanks in advance, Sarah Support a écrit : Bonjour, Voilà ce que j'obtiens quand je lance la commande qu'il demande: ruby run_chiphorde4.rb LLIB 08 Jan 09:10:17 [ytilib] ytilib required, working directory /usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts LLIB 08 Jan 09:10:17 [ytilib] use_chiphorde4.rb started, usage motif_template ChIPHorde-engine-params LLIB 08 Jan 09:10:17 [ytilib] run_chiphorde4.rb Je n'obtiens donc pas l'erreur dont il parle. Par ailleurs voici le chemin de la librairie: /usr/lib/ruby/1.8/rexml/formatters/pretty.rb, mais il semble la trouver. Je continue à chercher avec ce que tu m'as envoyé. Mais il est possible que ce soit un problème de version puisqu'il semble qu'ils aient renommé les fichiers Cordialement, Marie-Stephane Trotard Génopole - Plateforme bio-informatique Centre INRA de Toulouse - Unité de BIA Chemin de Borde-Rouge - AUZEVILLE BP 52627 - 31326 CASTANET-TOLOSAN CEDEX tél. : +33 (0)5 61 28 54 27 Support : support.genop...@toulouse.inra.fr 08.01.2013 09:05 - Sarah Maman a écrit: Bonjour Marie-Stephane, A priori, il manquerait une librairie : I think that there's some ruby libraries missing. Please try to run ChIPMunk externally this way: ruby /path/to/ChIPMunk/run_chiphorde.rb If you receive this kind of error message, it means that it missed one library to work: ChIPMunk/ytilib/hack1.rb:1:in `require': no such file to load -- rexml/formatters/pretty (LoadError) from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/hack1.rb:1 from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44:in `require' from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44 from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3:in `require' from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3 I already had the problem and the missing library was this one: http://www.ruby-doc.org/stdlib-1.9.3/libdoc/rexml/rdoc/REXML/Formatters/Pretty.html Merci d'avance, Sarah Support a écrit : Bonjour, Il me semble que je l'avais installé en même temps que FindPeaks: /usr/local/bioinfo/src/ChIPMunk/current Parles-tu d'un autre logiciel? D'un version? Cordialement, Marie-Stephane Trotard Génopole - Plateforme bio-informatique Centre INRA de Toulouse - Unité de BIA Chemin de Borde-Rouge - AUZEVILLE BP 52627 - 31326 CASTANET-TOLOSAN CEDEX tél. : +33 (0)5 61 28 54 27 Support : support.genop...@toulouse.inra.fr 07.01.2013 14:35 - sarah.ma...@toulouse.inra.fr a écrit: A user filled out the contact form on bioinfo.genotoul.fr. ###master_email-line-plain_mailsubject## E-Mail: sarah.ma...@toulouse.inra.fr Priority: Very low Your Message: Bonjour, Il me semble, sauf erreur de ma part, que ChipMunk n est pas installé sur Genotoul. Est-il possible, s il vous plaît, de l installer. TrÚs cordialement, Sarah Maman -- This message was created automatically. ___ 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.
