Re: [galaxy-user] generating a new fasta from a pileup
Hi John, That would be totally fantastic - many thanks! Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk On 30 Jul 2011, at 16:35, John Nash wrote: I have some code which can do most of the requested things. Let me figure out how to galaxy around it, and I'll submit it. John Sent from my mobile device On 2011-07-30, at 12:47 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello David, Generating a consensus fasta sequence from a BAM or Pile-up file is not yet possible in Galaxy. To date, the Tool Shed also does not have a wrapped/novel tool for this function either. If you or another user were to create such a wrapped tool, it would be most welcome. As would a tool that would replace the corresponding region of the reference genome with the variant fasta sequence to create a novel reference for alignments. Both great ideas that have been discussed a few times on the list and here among our team. If you wanted to open a bitbucket ticket, that would be one way to share exactly what you had in mind and give you a ticket to watch for if/when tools like this are added. Or, I can open one (or possibly two, one for each function) for you, just let me know. https://bitbucket.org/galaxy/galaxy-central/issues?status=newstatus=open Thanks for the great feedback, sorry there wasn't a solution (yet!), Best, Jen Galaxy team On 7/22/11 12:56 PM, David Matthews wrote: Hi On a separate issue, I have been having trouble generating a corrected fasta file based on a pileup. I have a dataset that is a resequenced genome and I want to correct the fasta file based on the consensus and then re run the alignments to see how it affects things. However, I cannot for the life of me figure out how to do it in Galaxy. Any help appreciated! David ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ 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/ ___ 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/ ___ 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/
[galaxy-user] mi-tools- tools_fabfile.py permissions requirements (local install)
Enis, a few things we came across: a, local install R - not the correct download url, rpy - will this be fixed? permissions: the script seems to use sudo and galaxy interchangeably, which creates an issue with permissions writing to folders. Is there a way to install as galaxy user only? If we do need the switching between sudo and galaxy - is there a set of directory permissions you suggest for the original galaxy-dist install and the galaxyToools folder? b, as a second category of questions: are there any tools that do not work on the standard cloud install? (skipped over entirely or installed but do not work?) best, joe ___ 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] mi-tools- tools_fabfile.py permissions requirements (local install)
Note: Local install questions are normally directed to the galaxy-dev list (CC'd) rather than galaxy-user On Mon, Aug 1, 2011 at 3:21 PM, Joseph Hargitai joseph.hargi...@einstein.yu.edu wrote: Enis, a few things we came across: a, local install R - not the correct download url, Which URL are you talking about? The wiki page on dependencies http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies correctly links to the R project as http://www.r-project.org/ rpy - will this be fixed? What needs to be fixed? Moving Galaxy to rpy2? https://bitbucket.org/galaxy/galaxy-central/issue/103/upgrade-rpy-to-latest-version permissions: the script seems to use sudo and galaxy interchangeably, which creates an issue with permissions writing to folders. Is there a way to install as galaxy user only? Do you mean installing Galaxy without admin rights (i.e. without using sudo)? If we do need the switching between sudo and galaxy - is there a set of directory permissions you suggest for the original galaxy-dist install and the galaxyToools folder? Good question - having manually reset permissions on a test server while debugging driving mappings, I'd like to know what they should be. Are you planing on using the Linux user group functionality as part of your setup? e.g. Both your personal account and the Galaxy user account could be part of a Galaxy admin group. b, as a second category of questions: are there any tools that do not work on the standard cloud install? (skipped over entirely or installed but do not work?) By that do you mean of the standard tool set in the main repository? (Because there will be lots of Galaxy tools in the Tool Shed which are not in the standard cloud install). Peter ___ 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] Troubles with Bowtie alignement of sRNA dataset (against precursor of mirBase)
Hello Christian, I found this FAQ on the IGV web site. They may be the best resource for resolving display issues if they continue. Comparing results between IGV and Galaxy's visualization tool Trackster can help you to determine the root cause of the problem. http://www.broadinstitute.org/software/igv/BAM http://www.broadinstitute.org/igv/FAQ Hopefully this helps point you in the right direction, Best, Jen Galaxy team On 7/31/11 6:04 PM, Cristian Rojas wrote: Hi people, I have a litle problem with Bowtie alignments. I am tryin to align sRNA Illumina dataset to hairpin mirbase. The problem is that after the steps (detailed below) I only obtain reads of 15-18nt, and I know that I have a lot of microRNAs (20-22nt) in my data. Beside the size problem, I realized that when the reads and the reference (the precursor in any case) the sequences don't match as I would expect. The sequential steps that I've made: - Groom - Clip (adaptor elimination) - Bowtie against hairpin database (mirBase precursor) - SAM-to-BAM - Download Bam and Bai files - Open in IGV the file and the hairpin database May be I am doing something really bad, but I dont know. Any help/suggestion/tip? Thanks in advance ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ 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/
