[galaxy-user] Extract genomic DNA-strand information is not recognized

Hello, I am trying to extract sequences from a FASTA file containing genomic information. The coordinates are in a tab-delimited format, which is recognized as BED format by Galaxy (meaning that the 6th column is correctly interpreted as 6. Strand). However, upon running "Fetch sequences" , Ex

[galaxy-user] Operate on genomic intervals

files with different names in the chromosome column? Thanks a lot in advance, Sarah ___ 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

Re: [galaxy-user] macs14 with Galaxy

Hi Hersh, you can find a working wrapper for macs 1.4. when you follow the link in the comments there: https://bitbucket.org/galaxy/galaxy-central/issue/573/enable-macs-v14 Best regards, Sarah On 07/07/2011 10:19 AM, Hersh wrote: Hi, Has anyone tried configuring latest version of macs

[galaxy-user] Application error

and get the same problem occurring each time. Could you please help me find a fix for this? Cheers, Sarah Traceback (most recent call last): File "/Users/allabyrg/Desktop/galaxy-dist/tools/rgenetics/rgFastQC.py", line 141, in assert os.path.isfile(opts.executable),'##rg

[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.

[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] 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

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

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

[galaxy-user] MegaBLAST output

out that problem, so I'm also waiting on details on that question, but for now, I'd just like to know what to make of the output... best, Sarah ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other fe

Re: [galaxy-user] MegaBLAST output

n, that I should NOT identify my representative sequence file to updated GI numbers using another pipeline, and then bring the file of GI numbers to Galaxy to fetch taxonomic assignments? (which I would do because of the nice neat columns for each taxonomic level Galaxy puts out) Sarah On Mon, Apr

Re: [galaxy-user] MegaBLAST output

s the correct match is the listed GI value minus 1 (ie, in NCBI, gi|324034994 is not 527nt long, but 324034993 IS 527nt long). On Mon, Apr 23, 2012 at 11:05 AM, Peter Cock wrote: > On Mon, Apr 23, 2012 at 5:56 PM, Sarah Hicks wrote: >> I am having trouble finding information on the Me

Re: [galaxy-user] MegaBLAST output

on't know which to pick. Is this problem well understood, yet? On Tue, Apr 24, 2012 at 10:52 AM, Peter Cock wrote: > On Mon, Apr 23, 2012 at 11:41 PM, Sarah Hicks wrote: >> Peter, you requested an example, here are the first five hits for my >> first query sequence (OTU#0) >&g

Re: [galaxy-user] MegaBLAST output

Thanks for the update! I am not in a huge rush, but I was worried I had not been describing the problem clearly, as it took quite a while to explain to colleagues here :) best On Tue, Apr 24, 2012 at 3:24 PM, Jennifer Jackson wrote: > Hi Sarah, > > We appreciate all of the information

Re: [galaxy-user] MegaBLAST output

Ok, I'll work on installing this... On Tue, Apr 24, 2012 at 4:08 PM, Jennifer Jackson wrote: > Thanks Peter, > > Excellent point. From there, the "Cut" tool could be used to reorganize the > output to exactly match that of the 13-column regular megablast output. So, > no external data needed, no

[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] 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] New reference genome in Bowtie

Dear All, I was wondering if it would be possible to add Mycobacterium tuberculosis H37Rv as a reference genome to the list of built-in indexes in the Map with Bowtie for Illumina (version 1.1.2) tool. Thank you, Sarah ___ The Galaxy User

Re: [galaxy-user] New reference genome in Bowtie

Thanks Jen! That solved my problem. Sarah On 8/22/2012 10:59 AM, Jennifer Jackson wrote: Hello Sarah, We can add this genome to the list to be indexed for Bowtie. Meanwhile, quickest way to work with small genomes immediately is as a custom genome. Simply load the genome into your history in

[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] [Ticket#2013010710000031] Installation de ChipMunk sur Genotoul

tilib] use_chiphorde4.rb started, usage 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

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

[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] Error / Nebula and RepeatMasker

ou dossier de ce type cp: impossible d'évaluer « /work/tmp/tmpga_QOo/dataset_5979.dat.masked »: Aucun fichier ou dossier de ce type tail: impossible d'ouvrir « /work/tmp/tmpga_QOo/dataset_5979.dat.out » en lecture: Aucun fichier ou dossier de ce type Do you have any idea ? Thanks i

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

me 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

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

Thanks a lot Alban for these explanations , Everything is OK. ++, Sarah alermine a écrit : Hi all, * _*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 ch

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

tput.pl script). Do you have any idea ? Thanks in advance, Sarah Here is your last message : - 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

[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

[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

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

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 section, my history is not shared. I need to publish AND share with a mail , in order to see my history in shared data . It seems to be a bug ? Thanks in advance, Sarah

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

Jennifer, I agree with you : it's work in the public Main Galaxy instance but it doesn't in my local instance of galaxy. Maybe a problem of version ? Would you like to test in my local instance ? Thanks in advance, Sarah Jennifer Jackson a écrit : Hi Sarah, I am unable to dupl

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

Thanks a lot, it's OK now ;-) Sarah James Taylor a écrit : Sarah, when you share with a specfic user, it will not show up under the "Shared Data" section since that is only for published items. The person you share it with should see it under "Histories Shared with

[galaxy-user] server problem?

line? Please advise, at your earliest convenience-- I have a room full of impatient newbie hackers ;) Thank you! --Sarah Sarah Schaack, PhD *Assistant Professor, Reed College* *Fulbright Scholar, Centre for Bioinformatics and Biotechnology, University

[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

[galaxy-user] Cufflinks error with illumina igenome .GTF for annnotation

add annotations to the already completed analysis would be terrific. Thanks! Sarah ___ 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 rep