Re: [galaxy-dev] [galaxy-user] Around Pittsburgh on April 6? Attend the Intro to Galaxy Sessions @ Pitt
For those wanting to see this online, have you had a chance to check out the very good online tutorials at usegalaxy.org? Getting these taped and posted online is usually much, much more difficult in practice than in theory. If these workshops do get taped and posted, then kudos to all those that make it so. If they don't, then I still say kudos to those who make the workshops happen. Organizing these events involves a lot of behind-the-scene work. Thanks Dave, Dan, Carrie, and anyone else involved. Sincerely, Christopher Bottoms - Informatics Research Core Facility University of Missouri 113 Bond Life Sciences Center Columbia, MO 65211 573-884-8151 http://ircf.rnet.missouri.edu From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Saha, Rinku Sent: Thursday, March 31, 2011 2:32 PM To: Dave Clements; Galaxy Dev List; Galaxy User List Cc: Carrie Iwema; Dan Blankenberg Subject: Re: [galaxy-user] Around Pittsburgh on April 6? Attend the Intro to Galaxy Sessions @ Pitt Hi Will this we available as a webiner or webcast for us who are located out side of Penn state. If so it would be really great for us. Kind Regards Rinku Saha University of Arkansas Medical Sciences Little Rock,AR From: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Dave Clements [cleme...@galaxyproject.org] Sent: Thursday, March 31, 2011 2:19 PM To: Galaxy Dev List; Galaxy User List Cc: Carrie Iwema; Dan Blankenberg Subject: [galaxy-user] Around Pittsburgh on April 6? Attend the Intro to Galaxy Sessions @ Pitt Hello all, Dan Blankenberg will be giving two workshops on Galaxy at the University of Pittsburgh on April 6. The presentations are open to the public. See below for details and please contact Dan, or Carrie Iwema at Pitt, if you have any questions. Thanks, Dave C. Intro to Galaxy http://galaxy.psu.edu/ Dan Blankenberg, PhD Center for Comparative Genomics Bioinformatics Penn State University Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples more... Wednesday 6th April 10 am - 12 pmIntro to Galaxy (general interest) 2 pm - 4 pmWorking w/NGS Data (advanced users) University of Pittsburgh Falk Library Conference Room B You are welcome to bring your laptop. Carrie L. Iwema, PhD, MLS Information Specialist in Molecular Biology Health Sciences Library System University of Pittsburgh 200 Scaife Hall 3550 Terrace St Pittsburgh, PA 15261 412-383-6887tel:412-383-6887 412-648-8819tel:412-648-8819 (fax) iw...@pitt.edumailto:iw...@pitt.edu www.hsls.pitt.edu/molbiohttp://www.hsls.pitt.edu/molbio -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.orghttp://getgalaxy.org/ http://usegalaxy.org/ Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.. ___ 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/
Re: [galaxy-dev] Default value for data_column not working?
On Fri, Apr 1, 2011 at 3:55 PM, Kanwei Li kan...@gmail.com wrote: Hi Peter, I don't see your attempt to use default in the example given. A bit more detail? -K Hi Kanwei, My example tool is now here: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 As per the original email, I have three parameters which are column numbers, and I want the defaults to be columns 1, 2 and 12. However, on my Galaxy installation they all default to the first column. I have tried giving the default values as 1, 2, and 12, and also as c1, c2 and c12 - neither works: https://bitbucket.org/peterjc/galaxy-central/changeset/374143be8e45 If you need more information, let me know. Thanks, Peter P.S. Bug filed here: https://bitbucket.org/galaxy/galaxy-central/issue/507/ ___ 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/
Re: [galaxy-dev] Inquiring
Dear Nate, Thanks a lot, I will check them. Best Wishes, Yan On Fri, Apr 1, 2011 at 11:07 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Thanks for your information, I will use it next times. By the way, how do we know the status of Galaxy's database (mysql)? I can't make sure if the database starts normally. Do you mean the database server itself? If you can connect with the 'mysql' command line interface, it's up. If you are worried about corruption, you can check the MySQL logs or use 'mysqlcheck'. --nate Best Wishes, Yan On Fri, Apr 1, 2011 at 10:48 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Your suggestion is very important for us. You are right, there is other instance of Galaxy to use the socket. I found the ps and kill them, but they are still there, then I using screen -wipe to remove it (I use screen to run the galaxy). It works. Is there any possibly for Galaxy to auto release the previous port and reuse it in the future version? It does this now. You would need to reconnect to the screen (using 'screen -r') and stop Galaxy with CTRL-C. Note that screen is not necessary. You can start and stop Galaxy in the background with: Start: % sh run.sh --daemon Stop: % sh run.sh --stop-daemon --nate Have a nice weekend! Best Wishes, Yan On Fri, Apr 1, 2011 at 10:37 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, I can't start my galaxy and got the following information, could you please let me know how we can fix it as soon as possible? We were running the system, it was down last night suddenly. Hope we can fix it today. File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 151, in server_wrapper **context.local_conf) ... File /usr/lib/python2.6/SocketServer.py, line 411, in server_bind self.socket.bind(self.server_address) File string, line 1, in bind socket.error: [Errno 98] Address already in use Something (possibly another instance of Galaxy) is already listening on the port you are trying to start Galaxy on. You can determine what that process is with 'lsof -i :PORT' where PORT is the port number you connect to Galaxy on. You may need to use sudo for this to succeed. Assuming it's another Galaxy instance, you can probably find it with 'ps auxwww | grep universe' and then kill that process. --nate Looking forward to hearing from you. Best Wishes, Yan ___ 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/
[galaxy-dev] Freebayes
I'm trying to run Freebayes SNP calling on a bam file from a BWA alignment of solid data. I keep getting the following error: [bam_sort_core] merging from 40 files... freebayes: invalid option -- Y did you mean --bam ? I'm not sure where this is set in the code to try to debug things. I'm wondering if anyones had this error, and how to fix it? Just to note, I'm running Brad Chapmans branch of galaxy for the LIMS functionality. But it appears to be an issue with either galaxy-dist or this one. Thanks in advance for any advice. Juan Perin___ 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/
Re: [galaxy-dev] Freebayes
Juan, What version of freebayes are you running? The freebayes configuration in the galaxy repository was written with the .4 series in mind, and it appears that the options have changed with the .6 series. We'll update the tool config, but in the meanwhile you could probably get it working again for your local use by editing the tools/human_genome_variation/freebayes.xml file to comment out the no-longer-valid parameter in line 34: -Y $params.postIntegBanddepth Let me know if this doesn't get things moving again for you, Dannon On Apr 1, 2011, at 1:17 PM, Juan Carlos Perin wrote: I'm trying to run Freebayes SNP calling on a bam file from a BWA alignment of solid data. I keep getting the following error: [bam_sort_core] merging from 40 files... freebayes: invalid option -- Y did you mean --bam ? I'm not sure where this is set in the code to try to debug things. I'm wondering if anyones had this error, and how to fix it? Just to note, I'm running Brad Chapmans branch of galaxy for the LIMS functionality. But it appears to be an issue with either galaxy-dist or this one. Thanks in advance for any advice. Juan Perin ___ 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/ ___ 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/
[galaxy-dev] suggestions for the SAM-to-BAM tool
Hi, Couple of things that can be slightly improved in the SAM-to-BAM tool: 1. Reference list is not informative (it's the technical way to say: list of chromosomes and their sizes based on a FASTA file). Users do not generally know what reference list is. 2. The Locally Cached option is not informative (I had to look in the source code to understand what it means). What it should say is something like: Get list of chromosomes/sizes based on the dataset's organism/database (could be shorter, but should be friendly enough). 3. There's no option of having the chromosome list in the SAM file header. Some SAM files will contain the header (can even be done in the standard bowtie tool wrapper) - saves the need to specify where to get the reference list from. 4. Autodetection in the set-metadata step will go a long way here: if the SAM file already have a header, then no need to even ask about it. If it doesn't have a header but have a DBKEY, then we're still OK. If no DBKEY and no header, then complain or ask for a FASTA file from current history. (I realize the implementing this feature is hard and annoying, I don't imply that it's easy to do, just that it's needed). 5. Inside the python script (sam_to_bam.py) there's a comment that says: for some reason the samtools view command gzips the resulting bam file without warning . Not sure why one cares about that, but samtools view -u will output an uncompressed BAM file. 6. samtools support piping, so a lot of I/O (and some time) can be spared by piping the two commands together: samtools view -u -b -S INPUT.SAM | samtools sort - OUTPUT Instead of running two commands and generating a temporary unsorted BAM file. -gordon ___ 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/
[galaxy-dev] Community server bug and request
Tiny bug: When viewing a file inside a tarball, the content-type is forced to text/plain. Works for most files, but not with image files (example: the Sequence Logo tool has a jpg image in the tarball, the browser will display it as text/plain with binary characters). This is done in ./lib/galaxy/webapps/community/controllers/tool.py, function view_tool_file, line 206: trans.response.set_content_type( 'text/plain' ) regardless of the file type. The complicated solution would be to use the mimetype library (http://docs.python.org/library/mimetypes.html) or python-magic (https://github.com/ahupp/python-magic), but a simpler workaround would be to just check the file name for jpg/png/gif extensions and change the content-type appropriately. Feature request: A way to easily link to tools, so I can send to them to other people or point them in the right direction. Example: Ross's Web logo tool (great tool, BTW), If I want to tell where it is, the link is: http://community.g2.bx.psu.edu/tool/browse_tools?sort=namef-state=approvedwebapp=communityoperation=view_toolid=c2f60f4c1895f3ac or direct downloading the tarball is: http://community.g2.bx.psu.edu/common/download_tool?cntrller=toolid=c2f60f4c1895f3ac Both are probably not stable links (if a new version is uploaded). -gordon ___ 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/
Re: [galaxy-dev] Anyone has tools for NCBI Lite-SRA format ?
anton wrote, On 04/01/2011 09:02 PM: We are getting multiple requests for this but did not have the bandwidth to do it. So if you are planning to implement - share through the toolshed and we will roll it to main. To start, this patch adds SRA binary type with sniffing and upload support: http://cancan.cshl.edu/labmembers/gordon/files/sra_binary_data_type.patch It only adds the datatype to datatypes_conf.xml.sample, so existing installations must manually add the following lines to their datatypes_conf.xml: datatype extension=sra type=galaxy.datatypes.binary:Sra mimetype=application/octet-stream display_in_upload=true/ and sniffer type=galaxy.datatypes.binary:Sra/ A question to people who are using fastq-dump on the command line: What are the most common parameters you're using ? I've heard about using Illumina or Sanger quality scale (-Q 64 / -Q 33), Minimal read length (-M), Clipping (-W), quality filtering (-E). Suggestions are very welcomed. -gordon ___ 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/
