[galaxy-user] "Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

% input_dbkey ) +chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey ) But I always have the same error message. Could you please help us ? Thanks in advance, Sarah // -- --*-- Sarah Maman INRA - GenPhySE - SIGENAE http://www.sigenae.org/ Chemin de Bo

Re: [galaxy-user] How to share an history with a SPECIFIC user ?

me" which is in the History options menu: -- James Taylor, Assistant Professor, Biology/CS, Emory University On Mon, Jun 3, 2013 at 11:22 AM, Sarah Maman wrote: Hello Jennifer, I would like to share only with a specific user but when I use the meth 3 with the email address into la

Re: [galaxy-user] How to share an history with a SPECIFIC user ?

Also please include the exact full name of the history in your account that you are trying to share. Thanks, Jen Galaxy team On 6/3/13 8:22 AM, Sarah Maman wrote: Hello Jennifer, I would like to share only with a specific user but when I use the meth 3 with the email address into last sectio

Re: [galaxy-user] How to share an history with a SPECIFIC user ?

places it in the list of all "Shared Histories" where everyone using that server can see it 3 - "share" with just a user by entering in their email address into last section Hopefully this helps, Jen Galaxy team On 6/3/13 6:58 AM, Sarah Maman wrote: Hello, My question is

[galaxy-user] How to share an history with a SPECIFIC user ?

Hello, My question is about sharing histories _with a specific user._ The share is not effective for a specific one but for all users logged in our local instance. Could you please help me ? Thank you in advance, Sarah -- --*-- Sarah Maman INRA - LGC - SIGENAE http

[galaxy-user] Information for Galaxy Event Horizon

alaxy Event Horizon"? Sincerely, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.6

Re: [galaxy-user] Error / Nebula - Chipmunk

Hi Alban, After a few weeks on other work, I try again the integration of your suite Nebula in my local instance of Galaxy. If possible, could you please help me to understand why the script "parseChipmunkOutput.pl " doesn't found results in my Galaxy instance. Here are the steps performed:

Re: [galaxy-user] Error / Nebula and RepeatMasker

-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel: +33 (0) 1 56 24 69 84 Le 5 févr. 2013 à 14:53, Sarah Maman <mailto:sarah.ma...@toulouse.inra.fr>> a écrit : Hi Alban, Marie-Stephane and Bjoern, * _*For IntersectBed tool,*_ running is OK. I've just deleted &q

Re: [galaxy-user] Error / Nebula and RepeatMasker

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 hesit

Re: [galaxy-user] Error / Nebula and RepeatMasker

at jeu. janv. 31 14:39:16 CET 2013 /work/galaxy/database/pbs/galaxy_4134.sh: line 13: Erreur de syntaxe près du symbole inattendu « ;; » /work/galaxy/database/pbs/galaxy_4134.sh: line 13: `RepeatMasker -parallel 8 -speci Do you have any ideas ? Thank you in advance for yo

[galaxy-user] Error / Nebula and RepeatMasker

eur de syntaxe près du symbole inattendu « ;; » /work/galaxy/database/pbs/galaxy_4134.sh: line 13: `RepeatMasker -parallel 8 -speci/ Do you have any ideas ? Thank you in advance for your help, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de

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

Re: [galaxy-user] [Ticket#2013010710000031] Installation de ChipMunk sur Genotoul

rmatique 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 lib

[galaxy-user] How to share a dataset without sharing my history ?

Hello, I would like to know how to share a single dataset without sharing my history through a local instance of Galaxy (with a LDAP identification) ? Thanks in advance, Sarah maman ___ The Galaxy User list should be used for the

Re: [galaxy-user] Datasets permanently deleted

-0500 summary: Fix for populating the tool panel and generating the integrated_tool_panel.xml file. This behavior is not reproduce on your public server. Thanks, Sarah Maman Jeremy Goecks a écrit : Sarah, I can't reproduce this behavior on a local instance or on our public server.

[galaxy-user] Datasets permanently deleted

e any solution to drop these datasets in "saved datasets" ? Thanks in advance, Sarah Maman ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please

Re: [galaxy-user] MarkupSafe cannot be fetched

ys.stderr.write('entree dans bwa wapper')" in comment to avoid to display SAM file in red. Faithfully, Sarah Maman Sarah Maman a écrit : Hi, This problem bellow is solved thanks to an eccho on $PATH and $DRMAA_LIBRARY_PATH. I have modified ~/.bash_profile file to define these

Re: [galaxy-user] MarkupSafe cannot be fetched

: BWA run on single-end An error occurred running this job: entree dans bwa for illumina BWA Version: 0.6.1-r104 BWA run on single-end dataEpilog : job finished at ven avr 6 14:16:01 CEST 2012 entree dans bwa wapper Thanks in advance, Sarah Maman Sarah Maman a écrit : Hi Nate, When I operate

[galaxy-user] MarkupSafe cannot be fetched

ilog : job finished at ven avr 6 14:04:13 CEST 2012 Could you please help me ? Thanks in advance, Sarah Maman ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.or

[galaxy-user] universe_wsgi.ini and .htaccess file

Dear, I would like to protect Galaxy installed on my own server , with an .htaccess file. Unfortunalty, my .htaccess file seems not to be read. Only universe_wsgi.ini seems to be read. How can I modify universe_wsgi.ini to add an .htaccess ? Thanks in advance, Sarah MAMAN

[galaxy-user] Login error + admin rights

ah.ma...@inra.toulouse.fr) is a mistake. Could you please delete the second one ? Thank you in advance, Sarah MAMAN -- Sarah Maman INRA - LGC - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Tax: +33(0)5.61.28.