Re: [galaxy-dev] BWA installation
Hi, מירב Sounds like you might want to try reindexing and make sure you have plenty of disk space - I have a .rbwt file from the last time I indexed using BWA version: 0.6.2-r126 and it works fine for me. On Sun, Jun 2, 2013 at 4:02 PM, מירב . mer...@gmail.com wrote: Thanks fo your answer, But when I am tring to use the bwa and to do Map with BWA for Illuminahttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 I'm getting this error: The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwt_restore_bwt] fail to open file '/home/user/extra_galaxy_project/bwa/data/hg18full/hg18full.fa.rbwt'. Abort! Aborted (core dumped) It seems like the .rbwt file is missing and cause the error?! 2013/5/30 Carl Eberhard carlfeberh...@gmail.com Hello, מירב It looks like the indexing system/format in 'bwa index' has changed and we haven't updated the wiki to reflect the changes. The reverse index (which includes the .r* files) are now part of the forward index. You should be fine to proceed. I'll update the wiki to reflect this. From https://github.com/lh3/bwa/blob/master/NEWS : Release 0.5.10 and 0.6.0 (12 November, 2011) The 0.6.0 release comes with two major changes. Firstly, the index data structure has been changed to support genomes longer than 4GB. The forward and reverse backward genome is now integrated in one index. On Thu, May 30, 2013 at 8:03 AM, מירב . mer...@gmail.com wrote: Hello all, I am trying to install BWA , I used the command: bwa index -a bwtsw /global_data/hg18full.fa and I got only 5 files insted of 8 The missing files are - rbwt - rpac - .rsa I didn't recieve any error message while running. thanks for your help merav ___ 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/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ 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] Adding a Tool for PANAMA
As part of a warmup, I added a tool for perming eQTL analysis using PANAMA( http://ml.sheffield.ac.uk/qtl/panama/). By default PANAMA writes to stderr and creates a PANAM_results.csv file in the same directory as the input files. I wrote a python wrapper https://bitbucket.org/saketkc/galaxy-central/src/3eb26205af5a0b77fa6177d5ecd1413ffd4d7a87/tools/eqtl_tools/panama_run.py?at=gsoc2013 for this. I however also came across how stderr text can be handled in Galaxy : http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C_.3Cregex.3E.2C_and_.3Cexit_code.3E_tag_sets and thus wrote a new XML : https://gist.github.com/saketkc/5697388 Apparently the above XML runs too, but I dont get back a CSV. Essentially I need to move the PANAMA_results.csv file to output1. Can this be done without using a wrapper at all , just using the XML files ? Is there a way to nest the commands in the XML so that I could do a move command after panama command , but how would the paths be specified ? Saket ___ 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] Adding a Tool for PANAMA
On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary sake...@gmail.com wrote: As part of a warmup, I added a tool for perming eQTL analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/). By default PANAMA writes to stderr and creates a PANAM_results.csv file in the same directory as the input files. I wrote ... XML : https://gist.github.com/saketkc/5697388 Apparently the above XML runs too, but I dont get back a CSV. Essentially I need to move the PANAMA_results.csv file to output1. Can this be done without using a wrapper at all , just using the XML files ? Is there a way to nest the commands in the XML so that I could do a move command after panama command , but how would the paths be specified ? Hi Saket, You could try this (two commands in one shell line), but catching error conditions would be a problem: commandpanama $expression_data $snp_data; mv PANAMA_results.csv $output1/command In cases like this where the underlying tool is too inflexible to accept an output filename, I would personally use a wrapper script which can handle moving things to the desired location, and raising a clear error if the file was not created. Peter ___ 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] Adding a Tool for PANAMA
Hi Saket If you want to redirect the executable's stdout to a new Galaxy dataset you've defined as $output, something like: gt; '$output' is a workable idiom for a command line AFAIK - you need to escape the redirection '' character or you'll confuse the xml parser. It's often possible to hack a complex command line (or use configfile to write a script!) but as Peter says, it all boils down to personal preference - they all work. Use whatever you find most convenient but remember you may need to maintain it :) On Mon, Jun 3, 2013 at 9:05 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary sake...@gmail.com wrote: As part of a warmup, I added a tool for perming eQTL analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/). By default PANAMA writes to stderr and creates a PANAM_results.csv file in the same directory as the input files. I wrote ... XML : https://gist.github.com/saketkc/5697388 Apparently the above XML runs too, but I dont get back a CSV. Essentially I need to move the PANAMA_results.csv file to output1. Can this be done without using a wrapper at all , just using the XML files ? Is there a way to nest the commands in the XML so that I could do a move command after panama command , but how would the paths be specified ? Hi Saket, You could try this (two commands in one shell line), but catching error conditions would be a problem: commandpanama $expression_data $snp_data; mv PANAMA_results.csv $output1/command In cases like this where the underlying tool is too inflexible to accept an output filename, I would personally use a wrapper script which can handle moving things to the desired location, and raising a clear error if the file was not created. Peter ___ 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] FW: order of menu items
Dear all, We have 2 different instances of Galaxy within our institute (a test and a production instance). The thing is that the two tool menus are not in the same order and we don't understand why because we've got the same configuration files on both instance. Test instance [cid:1A999B49-4E2D-4B03-A0C8-0F3E7459F730] Production instance: [cid:31D3C34C-1FF2-4ED9-8A0D-DF73DEE548A7] What could explain a difference in the order of the menu items? The thing is that I would like to get the NGS tools all together. Thank you in advance. Stephanie -- Stephanie Le Gras Bioinformatics engineer High throughput sequencing platform IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73 Tel. Solexa : +33 (0)3 88 65 32 97 attachment: Capture d¹écran 2013-06-03 à 14.03.09.pngattachment: Capture d¹écran 2013-06-03 à 14.03.32.png___ 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] FW: order of menu items
Hi Stephanie Try removing integrated_tool_panel.xml before you restart your galaxy server. There used to be a bug, where integrated_tool_panel.xml was not properly re-written after a restart. Regards, Hans-Rudolf On 06/03/2013 02:17 PM, Stephanie LE GRAS wrote: Dear all, We have 2 different instances of Galaxy within our institute (a test and a production instance). The thing is that the two tool menus are not in the same order and we don't understand why because we've got the same configuration files on both instance. Test instance Production instance: What could explain a difference in the order of the menu items? The thing is that I would like to get the NGS tools all together. Thank you in advance. Stephanie -- Stephanie Le Gras Bioinformatics engineer High throughput sequencing platform IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73 Tel. Solexa : +33 (0)3 88 65 32 97 ___ 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] FW: order of menu items
Thank you very much for your very fast answer!! It's worked! Stephanie Le 03/06/13 14:36, « Hans-Rudolf Hotz » h...@fmi.ch a écrit : Hi Stephanie Try removing integrated_tool_panel.xml before you restart your galaxy server. There used to be a bug, where integrated_tool_panel.xml was not properly re-written after a restart. Regards, Hans-Rudolf On 06/03/2013 02:17 PM, Stephanie LE GRAS wrote: Dear all, We have 2 different instances of Galaxy within our institute (a test and a production instance). The thing is that the two tool menus are not in the same order and we don't understand why because we've got the same configuration files on both instance. Test instance Production instance: What could explain a difference in the order of the menu items? The thing is that I would like to get the NGS tools all together. Thank you in advance. Stephanie -- Stephanie Le Gras Bioinformatics engineer High throughput sequencing platform IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73 Tel. Solexa : +33 (0)3 88 65 32 97 ___ 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] Problem with tool in R
I have a problem with a tool in R. I can't load the RPostgreSQL library that I get the following error: ERROR: carregando pacotes exigidos: dbi My xml is this: command interpreter=bashr_wrapper.sh $script_file/command configfiles configfile name=script_file library(RPostgreSQL) ... /configfile /configfiles I have this library installed at my system, what can I do? ___ 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] Tool Visibility
Suppose a tool didn't have any kind of configuration and therefore didn't need to be displayed in the Analyze Data part of Galaxy. Is there a way to modify tool_conf.xml so that a particular tool is only displayed in the Workflow editor? Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ ___ 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] Run galaxy on a specific SGE queue
Thanks Nate, In fact, our ~/.sge_request set workq by default. So, we have changed this parameter in ~/.sge_request file in order to change the working queue. Thanks again for your help, Sarah Nate Coraor a écrit : On May 22, 2013, at 11:36 AM, Sarah Maman wrote: Hi everyone, Galaxy is set up on our cluster, and so far everything is working just fine. However, we'd like to change the submission queue from the default to a specific one. To do so, we tryed to set on the universe_wsgi.ini file the default_cluster_job_runner parameter as following: default_cluster_job_runner = drmaa://-q test.q -l mem=8G -l h_vmem=10G/ When doing so, an error occured telling us the job has been rejected because 2 queues were specified: the workq (default one) and the test.q. Should be the queue setting this way ? What are we doing wrong ? Hi Sarah, Without knowing what's going on in your environment I can't say for sure, but I would guess that something else is (~/.sge_request?) is also attempting to set the queue. Are you able to use `qsub -q test.q` on the command line as the same user that runs Galaxy? Thanks, --nate thanks for your help, Sarah 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 Fax: +33(0)5.61.28.57.53 ___ 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/ -- --*-- 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)5.61.28.57.53 --*-- ___ 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] login to ftp server failed or Problem with ftp connexion to Galaxy
Dear Björn, Yes, this helps so much! Thanks a lot! Sincerely, Danni On May 31, 2013, at 3:34 PM, Björn Grüning wrote: Hi Danni, the following is copied from a Mail from Jennifer Jackson 2 days ago. For some reason this mail is not indexed from google, yet. Hope that helps, Björn Dear Galaxy Main Community, We apologize for recent FTP login issues, but are glad to report that a solution is now in place. May 29th 2013 FTP login resolution Issue: FTP login failed for user accounts newly created or that had passwords updated during the time frame May 20th - May 29th. Solution: Change your Galaxy password using the form on the Main instance at http://usegalaxy.org User - Preferences - Manage your information On the Manage User Information form, change your password Wait ~20 minutes for the server to update, then use FTP with the new credentials How to use FTP Upload Share notice: http://bit.ly/ftpmay29 Thanks for using Galaxy, The Galaxy Team --- To whom this may concern, This is Danni Yu, a Galaxy user starting to use Galaxy since 2011. I was able to upload large files through ftp in 2011 and 2012. Now, I am facing the same problem as the other users (such as Barbara Sixt on May 27, 2013 and Fabrice Besnard on May 22, 2013). The error message is 530 login incorrect. Ms. Jennifer Hillman-Jackson in Galaxy Support and Training team very kindly mentioned that Please feel free to contact us for an update if this is still a problem by next Friday on May 24, 2013. Since it is already Friday but the problem still exists, I am hoping to learn whether a solution has been provided. Thanks very much and Sincerely, Danni ___ 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] [galaxy-user] List of genomes
Hi All, Can some one tell me the parameters used in the Galaxy Mapping Illumina with Bowtie defined as the common settings? I was trying to replicate the results from Galaxy using my own desktop installation of Bowtie but they differ by a rather big margin. Thanks much, Yongde On Mon, Apr 29, 2013 at 1:06 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Yongde, The list of genomes is gathered from many sources and is comprehensive to facilitate external display functionality (at UCSC - main and microbial-, Ensembl, Wormbase, etc.). When assigning a dataset in a standard format to one of these sources, those available will appear as links within the dataset's box. Trackster (Galaxy's native visualization tool) is available to most common data formats, even in the absence of an assigned database, through the use of the Custom Reference Genome function (aka Custom Build). We think this is a great advantage, in particular for cases such as yours - since you don't have restrict yourself to external applications that happen to host your genome. Click on the link here and select Trackster to give it a test run: The Custom Reference Genome function is also intended to be used for smaller genomes such as this one when performing alignments and most other jobs - no pre-indexing of the genome is necessary. Simply load the genome in fasta format as a dataset and use it with tools, using a reference genome from the history. The rational is that these are many, small, easily indexed during the course of job processing, and provides immediate access to genomes that are either newly published, or not widely used, or simply too numerous as a whole class for us to practically process in full and keep current. We have detailed help about how to use the Custom Reference Genome method, including troubleshooting help should you need it, although in practice you will likely find this to be fairly simple with 2-3 preparatory steps, depending on the source. Most if not all of these can be done within Galaxy. http://wiki.galaxyproject.org/Support#Custom_reference_genome Hopefully this helps. If you do need more guidance, please let us know, Best, Jen Galaxy team On 4/29/13 9:01 AM, YBao wrote: Hi All, I was trying to map a set of data to a genome, Klebsiella pneumoniae subsp. Pneumoniae MGH 78578(31). While uploading the reads, I was able to find the reference genome as listed above. However, when I tried to map the data using wither bowtie or BWA, the pull down list did not include this genome. Can someone help or enlighten me as why it did not make into the list? Thanks Yongde -- Yongde Bao DNA Sciences Core Dept. of Microbiology, Immunology, and Cancer Biology UVA ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Traininghttp://galaxyproject.org -- Yongde Bao DNA Sciences Core Dept. of Microbiology, Immunology, and Cancer Biology UVA icficedh.png___ 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] storage utilisation on the main galaxy instance
Hi, I had storage utilisation of +60% and two days ago I decided to remove a large chunk of my data. I did this by clicking on the delete links for each of these datasets. Today I've logged in and see that my storage utilisation hasn't changed. Is there anything else that I need to do to free up the storage? many thanks, Nick ___ 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] Stable usegalaxy.org links for main Tool Shed repositories?
Hello all, Having asked this before, I knew the friendly and memorable alias http://usegalaxy.org/toolshed/ existed for the main Galaxy Tool Shed, http://toolshed.g2.bx.psu.edu Currently tools there have a unique stable shareable URL like this: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus (Due to the current frame based design, that redirects to a less pleasant URL) From a little experimentation, the following style aliases also work: http://usegalaxy.org/toolshed/view/devteam/ncbi_blast_plus Is that deliberate? Can it be relied on, and are these style URLs actually preference? If so, could the Tool Shed be enhanced to allow a default stem for the URL (rather than the current host name) to show these URLs instead? (Personally I find the usegalaxy.org based URLs more presentable compared to toolshed.g2.bx.psu.edu which feels less permanent.) Thanks, Peter ___ 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] Information for Galaxy Event Horizon
Hi Sarah, We'd be happy to put this on the Galaxy Event Horizon page on the wiki. Since the event is over, we would list it in the past events section. Is there a web page for the workshop or slides that we can link to? And, for future reference, wiki update requests can be sent directly to Galaxy Outreach outre...@galaxyproject.org. Thanks, Dave C. On Thu, May 30, 2013 at 7:18 AM, Sarah Maman sarah.ma...@toulouse.inra.frwrote: ** Dear all, Four days of training in genomics are occurring on our local instance of Galaxy (27-30 May). This training session takes place at INRA, Toulouse Auzeville, France, as part of a collaboration between Sigenae (http://www.sigenae.org/) and GenoToul bioinformatics platform (http://bioinfo.genotoul.fr/). This session is composed of four training days: - Galaxy first step - Reads alignment and SNP calling - RNAseq alignment and transcripts assemblies - sRNAseq Do you think it is possible to list our training session in your Galaxy Event Horizon? Sincerely, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAEhttp://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)5.61.28.57.53 --*-- ___ 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/ -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.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/
[galaxy-dev] mapping Summary from Bowtie
Dear Developers, I am running Bowtie2 through galaxy interface, previously it gives the the mapping summary and convert the format to sam.. but now it directly convert the fastq file to bam and doesnt give the mapping summary. how to get the mapping summary from bowtie2 using galaxy interface.. Thanks Sridhar ___ 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/
