Re: [galaxy-user] Error / Nebula and RepeatMasker
and spaces rather ## than tabs. Remove the header and replace the whitespaces with tab #set $standard_file = $output_basename + '.out' #os.system(tail -n +4 $standard_file | tr -s ' ' '\t' $output_std;) ## Delete all temporary files #os.system(rm $dirname -r; * For the tool FilterControl, our cluster is configured to kill jobs that use more than 4Go of memory. I don't achieve to modify qsub options in my Galaxy instance, so I'he changed this option -Xmx6g in -Xmx4g. Maybe some treatment won't run by lake of memory .. If you have any idea on how to add option on Galaxy qsub, could you please help me ? I would like to add these options to qsub : qsub -l mem=6G -l h_vmem=8G * ChIPMunk :Sorry, but all ChIPMunk files (xml, pl; sh) didn't have execution rights... So I just do chmod a+x on these files and ChIPMunk tool is OK in my Galaxy instance Thanks a lot for all your explanations, Alban, Marie-Stephane and Bjoern . Thanks in advance for qsub and IntersectBed tool (test file), Sarah alermine a écrit : Hi Sarah, I'll try to debug, point per point: - Here is the error I get when running the tool FilterControl *** glibc detected *** java: double free or corruption (!prev): 0x7fe56800ecd0 *** I think here you have a misconfiguration of the memory of your java install (according to the need of the tool) If you look at the FilterControlPeaks.sh file, the java is called with the option -Xmx6g. So your java install have to be allowed to use 6G as memory (by default it's 1024M) - Here is the error I get when running the tool IntersectBed /work/galaxy/database/pbs/galaxy_4129.sh: line 13: Erreur de syntaxe près du symbole inattendu « ;; » /work/galaxy/database/pbs/galaxy_4129.sh: line 13: `bedtools intersect -f 0.05 I don't understand this one, The intersectBed tool is only composed of a xml which simply call bedtools.. Check the command by typing 'bedtools intersect' in a terminal, if it sends you back the option list, the Galaxy tool should work.. If not, you have to check your bedtools install - Here is the error I get when running the tool ChIPmunk (thanks Alban for you help (ChIPMunk v2 is used and all librairies are found) but here is a new error, maybe a problem of dirname ?) mv: impossible d'évaluer « /work/galaxy/database/job_working_directory/004/4132/galaxy_dataset_5992.dat_0.xml.png »: Aucun fichier ou dossier de ce type mv: impossible d'évaluer « /work/gala Here, I think that the error is due to the ChIPMunk execution which doesn't work. You can try the ChIPMunk execution this way: Find the line containing: ruby $CHIPMUNK_BIN_DIR/run_chiphorde.rb $LOG $motifs $MODE yes 1.0 s:$inputfile 100 10 1 4 /dev/null 2 /dev/null Add a line with: echo ruby $CHIPMUNK_BIN_DIR/run_chiphorde.rb $LOG $motifs $MODE yes 1.0 s:$inputfile 100 10 1 4 /dev/null 2 /dev/null ~/ChIPMunk.log Then try to launch the command in ~/ChIPMunk.log in a terminal and look at the output. If ChIPMunk has run, the error comes from next step (i.e. the parseChipmunkOutput.pl script). Else, try to debug ChIPMunk, and then the tool will work. - Here is the error I get when running the tool PeaksToBed readline() on closed filehandle FILE at /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 124 (#1) (W closed) The filehandle you're reading from got itself closed sometime before now. Check your control flow. Use of uninitialized value $fields[1] in concatenation (.) or string at For this one, edit the PeaksToBed.pl script this way: The 3 lines: use strict; use warnings; use diagnostics; becomes: #use strict; #use warnings; #use diagnostics; Galaxy doesn't really love to have the return of a script (even if it's not an error). Here the perl scripts gives you warnings that are understood as errors by Galaxy. Hope It will help you, don't hesitate if you need more.. ++, 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 1 févr. 2013 à 14:41, Sarah Maman sarah.ma...@toulouse.inra.fr a écrit : Thanks Bjoern, In your xml file, I 've specified the interpreter : command replace by command interpreter=bash but the problem is not solved (; is supported by our cluster) because the command is runned with an error ;; (double ;) instead of ; (simple ;) : `bash /my/path/to/RepeatMasker -parallel 8 -species fungi -dir /work/tmp/tmprRrJh2 -gff /my/path/to/galaxy/database/files/005/dataset_5979.dat/dev/null 2 /dev/null; cp /my/path/to/work/tmp/tmprRrJh2/dataset_5979.dat.tbl /my/path/to/galaxy/database/job_working_directory/004/4135
Re: [galaxy-user] Error / Nebula and RepeatMasker
Hi Sarah, I'll try to debug, point per point: - Here is the error I get when running the tool FilterControl *** glibc detected *** java: double free or corruption (!prev): 0x7fe56800ecd0 *** I think here you have a misconfiguration of the memory of your java install (according to the need of the tool) If you look at the FilterControlPeaks.sh file, the java is called with the option -Xmx6g. So your java install have to be allowed to use 6G as memory (by default it's 1024M) - Here is the error I get when running the tool IntersectBed /work/galaxy/database/pbs/galaxy_4129.sh: line 13: Erreur de syntaxe près du symbole inattendu « ;; » /work/galaxy/database/pbs/galaxy_4129.sh: line 13: `bedtools intersect -f 0.05 I don't understand this one, The intersectBed tool is only composed of a xml which simply call bedtools.. Check the command by typing 'bedtools intersect' in a terminal, if it sends you back the option list, the Galaxy tool should work.. If not, you have to check your bedtools install - Here is the error I get when running the tool ChIPmunk (thanks Alban for you help (ChIPMunk v2 is used and all librairies are found) but here is a new error, maybe a problem of dirname ?) mv: impossible d'évaluer « /work/galaxy/database/job_working_directory/004/4132/galaxy_dataset_5992.dat_0.xml.png »: Aucun fichier ou dossier de ce type mv: impossible d'évaluer « /work/gala Here, I think that the error is due to the ChIPMunk execution which doesn't work. You can try the ChIPMunk execution this way: Find the line containing: ruby $CHIPMUNK_BIN_DIR/run_chiphorde.rb $LOG $motifs $MODE yes 1.0 s:$inputfile 100 10 1 4 /dev/null 2 /dev/null Add a line with: echo ruby $CHIPMUNK_BIN_DIR/run_chiphorde.rb $LOG $motifs $MODE yes 1.0 s:$inputfile 100 10 1 4 /dev/null 2 /dev/null ~/ChIPMunk.log Then try to launch the command in ~/ChIPMunk.log in a terminal and look at the output. If ChIPMunk has run, the error comes from next step (i.e. the parseChipmunkOutput.pl script). Else, try to debug ChIPMunk, and then the tool will work. - Here is the error I get when running the tool PeaksToBed readline() on closed filehandle FILE at /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 124 (#1) (W closed) The filehandle you're reading from got itself closed sometime before now. Check your control flow. Use of uninitialized value $fields[1] in concatenation (.) or string at For this one, edit the PeaksToBed.pl script this way: The 3 lines: use strict; use warnings; use diagnostics; becomes: #use strict; #use warnings; #use diagnostics; Galaxy doesn't really love to have the return of a script (even if it's not an error). Here the perl scripts gives you warnings that are understood as errors by Galaxy. Hope It will help you, don't hesitate if you need more.. ++, 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 1 févr. 2013 à 14:41, Sarah Maman sarah.ma...@toulouse.inra.fr a écrit : Thanks Bjoern, In your xml file, I 've specified the interpreter : command replace by command interpreter=bash but the problem is not solved (; is supported by our cluster) because the command is runned with an error ;; (double ;) instead of ; (simple ;) : `bash /my/path/to/RepeatMasker -parallel 8 -species fungi -dir /work/tmp/tmprRrJh2 -gff /my/path/to/galaxy/database/files/005/dataset_5979.dat/dev/null 2 /dev/null; cp /my/path/to/work/tmp/tmprRrJh2/dataset_5979.dat.tbl /my/path/to/galaxy/database/job_working_directory/004/4135/galaxy_dataset_5999.dat; cp /work/tmp/tmprRrJh2/dataset_5979.dat.out.gff None; cp /work/tmp/tmprRrJh2/dataset_5979.dat.masked None; tail -n +4 /work/tmp/tmprRrJh2/dataset_5979.dat.out | tr -s ' ' '\t' /my/path/to/galaxy/database/job_working_directory/004/4135/galaxy_dataset_5998.dat; rm /work/tmp/tmprRrJh2 -r;; cd /my/path/to/galaxy/galaxy-dist; /my/path/to/galaxy/galaxy-dist/set_metadata.sh /my/path/to/galaxy/database/files /my/path/to/galaxy/database/job_working_directory/004/4135 . /my/path/to/galaxy/galaxy-dist/universe_wsgi.ini /work/tmp/tmpi0u8TZ /my/path/to/galaxy/database/job_working_directory/004/4135/galaxy.json /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_in_HistoryDatasetAssociation_6156_Lp_2X3, /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_kwds_HistoryDatasetAssociation_6156_emJ62i, /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_out_HistoryDatasetAssociation_6156_Dgw3la, /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_results_HistoryDatasetAssociation_6156_aTCjOU,
Re: [galaxy-user] nebula suite / _chiphorde.log not found
Hi Sarah, It seems that Chipmunk is not well executed (reason why it can't found the log file). 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 Tell me if it works.. ++, 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 7 janv. 2013 à 17:13, Sarah Maman sarah.ma...@toulouse.inra.fr a écrit : Hello, I 've integrated nebula suite in my local instance of galaxy but here is the error message received when running ChipMunk analysis : Galaxy cannot stat a file _chiphorde.log in the job working directory. Do you have any idea ? Thanks in advance, Sarah ChiMunk_Log.jpg ___ 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.
