Re: [galaxy-user] Samtools Mpileup output
On Wed, Nov 6, 2013 at 12:08 PM, Fabrice Besnard wrote: > Would you have any advice to select the output format, or alternatively, > a tool in Galaxy that can convert pileup into .vcf? > Hi Fabrice, I believe you only get the BCF output when "Genotype Likelihood Computation" is set to "Perform genotype likelihood computation". Hope it helps, Carlos ___ 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/
Re: [galaxy-user] Secure file upload gateway for Galaxy
On Tue, Sep 24, 2013 at 7:58 AM, Georgios Magklaras wrote: > Hi, > > Do you have best recipes for SFTP/Aspera upload gateway integration to > Galaxy? We would welcome advise on that matter. > Hi, I haven't implemented yet, but I'm planning on using plain scp(windows user can use WinSCP). I shouldn't have problems doing so by using this option in universe_wsgi.ini: # Add an option to the library upload form which allows authorized # non-administrators to upload a directory of files. The configured directory # must contain sub-directories named the same as the non-admin user's Galaxy # login ( email ). The non-admin user is restricted to uploading files or # sub-directories of files contained in their directory. user_library_import_dir = /local/opt/galaxy/import_dir Hope it helps, Carlos ___ 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/
Re: [galaxy-user] Change format with "edit attributes"
Hi Gema, Quick comment. If you do have the QUAL file to begin with, I would recommend doing the combine first, then barcode splitter(which can do fastq too), then bowtie. This way you have the benefits of mapping using the real quality score. --Carlos On Wed, Apr 3, 2013 at 11:07 AM, Daniel Blankenberg wrote: > Hi Gema, > > For example, see the "Combine FASTA and QUAL into FASTQ" tool for creating a > FASTQ file from FASTA data; when quality data is not provided, fake score > values will be used. > > > Thanks for using Galaxy, > > Dan > > On Apr 3, 2013, at 10:42 AM, Peter Cock wrote: > > > > On Wed, Apr 3, 2013 at 3:40 PM, Gema Sanz Santos wrote: >> >> Hello, >> >> I'm trying to change the format to the output files from Barcode splitter >> from FASTA to FASTAQ so I can use them in Bowtie for Illumina. I've read >> that it can be done through the edit attributes, I go to datatype and select >> fastaq, save and then go to convert format and press convert but the >> resulting file is 0 bytes and is not recognized by Bowtie. >> >> I´ve also tried to upload by copying the link and selecting fastaq as >> format but in this case, I got the file shown in the picture and it is not >> recognized by Bowtie again. >> >> >> >> What can I do?? I don´t know how to continue because I´m not able to >> change the format to fastaq! >> >> Thank you very much for your help in advance >> >> Best, >> Gema >> > > Hi Gema, > > There seem to be several factors confusing you here. > > The screenshot shows FASTA data wrongly labelled as FASTQ. > > The Galaxy "edit attributes" does NOT actually edit the data. There are > separate tools which can convert from one format to another, which gives you > a new entry in the history (another green box on the right). > > You can convert from FASTQ to FASTA, but doing the opposite is not possible > without inventing quality scores (e.g. give everything score 30). > > Does that help? > > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > ___ > 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/ ___ 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/
Re: [galaxy-user] Rscript not found when running shell script in Galaxy
On Tue, Feb 12, 2013 at 5:54 AM, Makis Ladoukakis wrote: > Dear users, > > Has anyone encountered this problem before? I wrote a shell script which > among other things calls some R scripts like this.. > > Rscript rscript_to_use.R > > When I run it via terminal it's fine plus I have verified Rscript works. But > when I upload my tool to Galaxy and try to run it I get the following error: > > /path/to/script/shell_script.sh: line 26: Rscript: command not found > > Are you using a cluster to submit galaxy tasks? If so, you might want to use '-V' in 'default_cluster_job_runner' ( I think this works for SGE and Torque ) or set 'environment_setup_file' and make sure $PATH is correctly set by that method. Also, in the future I would recommend sending these type of questions about local or cloud Galaxy instances to galaxy-dev mailing list. Hope it helps, Carlos ___ 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] Remove "unpaired" reads from quality-filtered pared-end fastq files.
Not the most convenient solution, but what I normally do in this situation is to combine the two files, filter then split again. There are tools for combining and splitting paired fastq files in Galaxy. Hope it helps, Carlos On Jan 8, 2013 12:55 AM, "柴田 弘紀" wrote: > Hi there, > > I obtained two fastq files from GA paired end run. I filtered each file by > quality using fastq tool kit. Then some forward reads may be removed by low > quality whereas the reverse counterparts are OK to be remained on the other > file, or vice versa. > > I want to remove those "unpaired" reads from filtered fastq files so that > the two new fastq files contain the identical sets of the reads. > > Is it possible to do it on galaxy? > > Thank you very much. > > Hiroki > ___ > 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/
Re: [galaxy-user] Installing Galaxy on a Cluster - What to do about Python
On Wed, Nov 7, 2012 at 9:52 AM, Oleksandr Moskalenko wrote: > > On Nov 7, 2012, at 9:47 AM, greg wrote: > >> Thanks, but I'm confused. How will the cluster jobs galaxy submits >> know to use the virtual env? >> >> Or since all jobs are submitted as the galaxy user it will have the correct >> one? >> >> -Greg > > Greg, > > You can configure the environment for batch jobs in the file specified in the > "environment_setup_file =" configuration directive. > You can do this or at least for SGE you can also use '-V' while configuring your job runner URL. drmaa://-V -q all.q/ Hope it helps, Carlos ___ 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] Installing Galaxy on a Cluster - What to do about Python
On Tue, Nov 6, 2012 at 2:27 PM, greg wrote: > Could anyone provide me with some basic directions on how to set it up > with virtualenv? I've never used it before. > I do this by adding this to the ~/.bashrc file of the user running galaxy( in galaxy.fedora-init: RUN_AS="galaxy") source $HOME/env/bin/activate Hope it helps, Carlos ___ 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] Batch jobs...
On Fri, Oct 26, 2012 at 7:46 AM, Björn Grüning wrote: > Hi Neil, > > if you run your workflow, there is small little symbol/icon (looks like > papers). If you click these ... you can select multiple input files at > once. Also you can probably use the Galaxy API for your task [1]. > Well this would only work if one of the 2 input files Neil mentions is fix. Multiple input files selection doesn't work for workflows with more than one input files, unless there is only one input changing in each run and the rest are fix. At least as far as I know. Using the API might be your only option if this is the case. --Carlos ___ 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] Are tools must be installed in local machine?
Hi Sachit, Björn answer is correct. The issue is what is a "tool". There are what Galaxy calls "tools". Some of which are installed by default and some of which you can install from the toolshed. There are in many cases just wrappers to third-party tools that need to be installed and available in the environment PATH of the user running Galaxy. Examples of these are TopHat, Bowtie and BWA. Björn mentions in some cases the third-party tool is automatically installed, but this is new and most third-party tools need to be installed manually still. If you are using Debian, thanks to the "Debian Med Team", many tools are already available in the repositories. Both TopHat and Bowtie are. So apt-getting them should do for you. Just remember to configure the .loc files in Galaxy with the location of the index files. This link will be helpful: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Hope this helps, Carlos On Mon, Oct 8, 2012 at 6:48 AM, Sachit Adhikari wrote: > I don't think you understood my question very well. Tophat and Bowtie are > available by default in Galaxy. Tophat and Bowtie however is not installed > in my operating system. Will it still work in Galaxy? > > > On Mon, Oct 8, 2012 at 3:22 PM, Björn Grüning > wrote: >> >> Hi Sachit, >> >> you need to install such tools by yourself, unless you are using some >> new tools from the toolshed. For example the ncbi-tools or BWA from the >> toolshed are capable of installing all dependency automatically. >> In the future the plan is to move all heavy tools to the toolshed with >> automatic dependency and version handling, afaik. >> >> Regards, >> Bjoern >> >> > Hello. The tools like Tophat, Bowtie etc are pre-installed in Galaxy. >> > Are those tools must be installed in order to work in Galaxy. For >> > example: I am using Debian machine(Don't have tophat and bowtie >> > installed). Will tophat and bowtie work in my local galaxy? Thanks >> > ___ >> > 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/
Re: [galaxy-user] Is there web-based CummeRbund?
Hi Jianguang, I'm the author of cummeRbund wrapper in the test Galaxy Tool Shed. I never got around to quite finish it, that's why I never submitted to main. Also cummeRbund received a big update since the time I was writing this wrapper. I don't think I can recommend using the wrapper in its current state at all. In any case, even if the wrapper could help you, you would need to deploy a local or a cloud instance of Galaxy, as is not clear to me that this wrapper would make its way to Galaxy Main server any time soon. You would probably be better of by dealing with R and cummeRbund, which by the way you should be able to use in Windows. If I find the time to play with the cummeRbund Galaxy wrapper again, I'll make sure to comment about it in this list. Best, Carlos On Sat, Aug 25, 2012 at 8:09 PM, Dave Clements wrote: > Hi Jianguang, > > I went to http://galaxy.psu.edu/search/web/ and searched for cummerbund. > > It looks like there is a cummerbund wrapper in the test Galaxy Tool Shed, > but that is about it. > > Dave C > > On Fri, Aug 24, 2012 at 3:23 PM, Du, Jianguang wrote: >> >> Dear All, >> >> I am going to visualize Cuffdiff outputs. I understand that CummeRbund can >> be used to visualize Cuffdiff outputs. However, I am not good at Linux >> system and feel difficult to understand CummeRbund manual. Is there >> web-based CummeRbund program (like Tophat and Cufflink) available for use? >> >> If web-based CummeRbund does not exist, is there other web-based program >> can be used to visualize Cuffdiff outputs? >> >> Thanks. >> >> Jianguang >> >> >> ___ >> 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/ > > > > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://galaxyproject.org/wiki/ > > > ___ > 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/
Re: [galaxy-user] Installing galaxy with Apache ...
This thread my help you: http://dev.list.galaxyproject.org/Running-Galaxy-behind-apache2-td4624545.html On Thu, Aug 23, 2012 at 5:48 PM, wrote: > Hi Jelle, >I'm still having issues with Apache. I've moved > > RewriteEngine on > RewriteRule ^/galaxy$ /galaxy/ [R] > RewriteRule ^/galaxy/static/style/(.*) > /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] > RewriteRule ^/galaxy/static/scripts/(.*) > /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] > RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] > RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico > [L] > RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] > RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] > > from /var/www/.htaccess to /etc/apache2/httpd.conf > > I still get a "404 Not found" error when trying to access galaxy > (http://140.253.78.44/galaxy ) > > http://140.253.78.44 still gets the "It Works!" Apache default index.html > > and http://140.253.78.44:8080 gets the galaxy page > > /var/log/apache2/error.log states... > > [Fri Aug 24 07:35:27 2012] [error] [client 140.253.78.44] File does not > exist: /var/www/favicon.ico > [Fri Aug 24 07:36:25 2012] [error] [client 140.253.78.44] File does not > exist: /var/www/galaxy > > Now if I change httpd.conf and add the vitrtualHost tags to: > > ServerName localhost > > RewriteEngine on > RewriteRule ^/galaxy$ /galaxy/ [R] > RewriteRule ^/galaxy/static/style/(.*) > /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] > RewriteRule ^/galaxy/static/scripts/(.*) > /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] > RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] > RewriteRule ^/galaxy/favicon.ico > /home/galaxy/galaxy-dist/static/favicon.ico [L] > RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt > [L] > RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] > > > I now get a "403 Forbidden" error when trying to access > (http://140.253.78.44/galaxy ) You don't have permission to access /galaxy/ > on this server, and /var/log/apache2/error.log states.. > > [Fri Aug 24 07:45:33 2012] [error] [client 140.253.78.44] attempt to make > remote request from mod_rewrite without proxy enabled: > proxy:http://localhost:8080/ > [Fri Aug 24 07:45:34 2012] [error] [client 140.253.78.44] File does not > exist: /etc/apache2/htdocs > > Any help much appreciated > > Neil > > From: Jelle Scholtalbers [j.scholtalb...@gmail.com] > Sent: Thursday, August 23, 2012 8:20 PM > To: Burdett, Neil (ICT Centre, Herston - RBWH) > Cc: galaxy-user@lists.bx.psu.edu > Subject: Re: [galaxy-user] Installing galaxy with Apache ... > > Hi Neil, > > with your current apache configuration, you should probably see Galaxy > at http://yourip/galaxy > This is due to your Rewriterule /galaxy and for that you have also set > proxy_prefix = /galaxy in your universe_wsgi.ini > > You should probably remove the empty galaxy directory under /var/www > Furthermore, most of the time you will not need a directory with 777 > in your apache web/documentroot.. > > Cheers, > Jelle > > On Thu, Aug 23, 2012 at 8:34 AM, wrote: >> Hi >>I've installed galaxy with the default settings and it works fine. >> >> On a new Ubuntu machine I am trying to get galaxy running with Apache. But I >> am having problems, I've followed the documentation. >> >> After installing Apache I can put my ip address into a browser and I get >> message saying Apache is working fine. It displays a message from >> /var/www/index.html >> >> Now when I start galaxy I was assuming I would get redirected to the galaxy >> welcome page, but this doesn't happen and it remains at /var/www/index.html. >> To view the welcome page I have to add ":8080" after the ip address. Is this >> still required? I thought that Apache would know to redirect to my >> distributionWhat am I doing wrong? >> >> /etc/apache2/sites-available/default-ssl and >> /etc/apache2/sites-available/default look like this ... >> >> DocumentRoot /var/www >> >> Options FollowSymLinks >> AllowOverride None >> >> >> Options Indexes FollowSymLinks MultiViews >> AllowOverride None >> Order allow,deny >> allow from all >> >> >> etc ... >> >> /var/www/.htaccess >> >> RewriteEngine on >> RewriteRule ^/galaxy$ /galaxy/ [R] >> RewriteRule ^/galaxy/static/style/(.*) >> /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] >> RewriteRule ^/galaxy/static/scripts/(.*) >> /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] >> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] >> RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico >> [L] >> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static
Re: [galaxy-user] Question about Unified genotyper
Hi Mathew, Regarding 1 you might want to read this thread: http://user.list.galaxyproject.org/Problem-with-Depth-of-Coverage-on-BAM-files-GATK-tools-td4654147.html All tools from GATK are limited to hg_g1k_v37 as far as I know. Best, Carlos On Mon, Aug 6, 2012 at 10:30 AM, Mathew Bunj wrote: > I have been trying to use either Unified genotyper or Freebayes on one of > the Bam file. Both are failing. > > 1. With Unified genotyper it give me message saying Sequences are not > currently available for specified build. I have hg19 related data and using > default settings (pick up hg_g1k_v37 no other option). I am not sure why > it is giving me this error. > 2. As an alternative I tried to run Freebayes with default setting and > choosing hg19 - it i snot giving any specific message but undetr bug icon > gives me -killed. > > Now in order to make sure my Bam is OK, I tested out side Galaxy mPile up > and with in Galaxy pile up. Any suggestion why UNified genotyper is not > working. If needed I can share my history. > > Thanks. > > > > > ___ > 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/
Re: [galaxy-user] Getting the installed data to show up in the sample files at run time
On Fri, Jul 6, 2012 at 3:07 AM, Aarti Desai wrote: > These show up in the history with the appropriate size. But when I choose > the “Map with BWA for Illumina” option, the two fastq files do not show up > in the FASTQ file drop down. Hi Aarti, Most tools in galaxy that work with fastq file need specifically fastqsanger input file. Even if your file have the quality values in Sanger format, the auto detect format logic won't be able to determine this. If you know you fastq file are in fact in Sanger format, editing your file metadata and selecting fastqsanger for the format would do the trick. If you aren't sure, you should use Fastq Groomer tool to convert them to Sanger format. I would recommend to watch the several screencast describing mapping analysis in Galaxy. Hope it helps, Carlos ___ 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] Getting reference index files in local galaxy install
Also make sure you are using TABs to separate the fields in the .loc file, this has bitten me several time in the past. My vim config places 4 spaces instead of TAB, to deactivate this option you can do ":set noexpandtab". Hope it helps, Carlos On Thu, Jul 5, 2012 at 4:39 AM, Avik Datta wrote: > Hi Aarti, > > Check the name of your ref file. If it is hg19.fa, then modify loc file as > "hg19 hg19 HG19_BWA /root/Ref_INDEX/HG19BWAIndex/base/hg19.fa" > > Avik Datta > > On Thu, Jul 5, 2012 at 1:42 PM, Aarti Desai > wrote: >> >> Hi, >> >> We have a local install of galaxy and I’m trying to add the reference >> index files for bwa using the information provided in the following link >> >> http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup >> >> >> >> I have modified the bwa_index.loc file present in the ../tool-data >> directory by adding the path to where the index is on our server (Also >> attached). However, even after restarting the server, the reference genome >> does not show when choosing the “use a built-in index option”. I’m not sure >> whether the loc file is correctly created and whether any other >> configuration file needs to be changed/updated. Help in the matter greatly >> appreciated. >> >> >> >> Thanks, >> >> Aarti >> >> >> >> From: galaxy-user-boun...@lists.bx.psu.edu >> [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson >> Sent: Thursday, July 05, 2012 1:23 AM >> To: Lindsey Kelly >> Cc: galaxy-user@lists.bx.psu.edu >> Subject: Re: [galaxy-user] Initial QC and grooming for Illumina HiSeq2000 >> paired end RNAseq data >> >> >> >> Hello Lindsey, >> >> Yes, you have this correct. The general path would be to: >> >> - join forward and reverse data per run >> - run FASTQ Groomer & FastQC >>(note: if your data is already in Sanger FASTQ format with Phred+33 >> quality scaled >>values, the datatype '.fastqsanger' can be directly assigned and the >> FASTQ Groomer >> step skipped. This is likely true if your data is a from the latest >> CASAVA pipeline, but >>please double check.) >> - discard data as needed based on quality >> - split forward and reverse data that passes QC >> - concatenate all forward reads from a sample into one FASTQ file >> - concatenate all reverse reads from a sample into one FASTQ file. >> - for each sample, run TopHat using the two concatenated FASTQ files >> >> To manipulate paired end data, please see the tools -> NGS: QC and >> manipulation: FASTQ splitter & FASTQ joiner. >> >> To combined data files head-to-tail from multiple runs into a single FASTQ >> file please see the tool -> Text Manipulation: Concatenate datasets. >> >> I am not sure of the actual volume of data, but if these start to get >> large or TopHat errors with a memory problem, a local or cluster instance >> would be the recommendation: http://getgalaxy.org >> >> For reference: >> http://tophat.cbcb.umd.edu/manual.html >> http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html >> >> Hopefully this helps. Others are welcome to post comments/suggestions. >> >> Jen >> Galaxy team >> >> On 7/2/12 11:17 AM, Lindsey Kelly wrote: >> >> I am trying to do RNAseq analysis on Paired end data from the Hiseq2000. >> I have about 50 files for each sample (25 forward and 25 reverse - although >> each sample has a different number of files). >> >> I think that I need to: >> >> -convert them into FASTQ sanger format using the FASTSQ groomer tool >> >> -check the quality using the FASTQqc tool >> >> >> >> I don't know how to handle this many files. Do I have to groom and run >> the QC for each file? Should I join the paired files and run both tools on >> each pair, or should I combine all of the data for each sample (which I >> don't know how to do) and then groom and run the QC for all of the reads for >> the sample. >> >> >> Thanks in advance for advice >> >> Lindsey >> >> >> >> >> ___ >> >> 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://galaxyproject.org >> >> >> >> DISCLAIMER == This e-mail may contain privileged and confidential >> information which is the property of Persistent Systems Ltd. It is intended >> only for the use of the individual or entity to which it is addressed. If >> you are not the intended recipient, you are not authorized to read, retain, >> copy, print, distribute or use this message. If you have received this >> commun
Re: [galaxy-user] Problem with Depth of Coverage on BAM files (GATK tools)
Hi Lilach, Sorry for the late response. Jen just confirmed the disadvantages of my approach. I don't know how difficult could be for you to double check the coordinates you have in your interval file are correct for hg_g1k_v37. If you feel confident they will work and want to proceed, you could do something like this outside of galaxy, you could also I'm sure find a way to do it inside galaxy: sed 's/^chr//' interval_file.csv > interval_file_g1k.csv If you have coordinates for the mitochondrial chromosome you might have to do also: sed 's/^MT/M/' interval_file.csv > interval_file_g1k.csv As if I remember correctly UCSC uses chrMT and GATK expects just M. Please double check this as I'm not sure. It would be also nice is there were a confirmation on what exactly hg_g1k_v37 is, and where you could find annotations for it. Annotations from Ensembl would do? Regards, Carlos On Mon, Jun 25, 2012 at 5:22 PM, Jennifer Jackson wrote: > Hello Lilach, > > Currently, the human reference genome indexed for the GATK-beta tools is > 'hg_g1k_v37'. The GATK-beta tools are under active revision by our team, so > we expect there to be little to no change to the beta version on the main > public instance until this is completed. > > Attempting to convert data between different builds is not recommended. > These tools are very sensitive to exact inputs, which extends to naming > conventions, etc. The best practice path is to start and continue an > analysis project with the same exact genome build throughout. > > If you want to use the hg19 indexes provided by the GATK project, a cloud > instance is the current option (using a hg19 genome as a 'custom genome' > will exceed the processing limits available on the public Galaxy instance). > Following the links on the GATK tools can provide more information about > sources, including links on the GATK web site which will note the exact > contents of the both of these genome versions, downloads, and other > resources. > > Hopefully this helps to clear up any confusion, > > Best, > > Jen > Galaxy team > > > On 6/21/12 7:50 AM, Lilach Friedman wrote: > > Hi Jennifer, > Thank you for this reply. > > I made a new BWA file, this time using the hg19(full) genome. > However, when I am trying to use DepthOfCoverage, the reference genomr is > stucked on the hg_g1k_v37 (this is the only option to select), and I cannot > change it to hg19(full). Most probably, because I selected hg_g1k_v37 in the > previous time I tried to use DepthOfCoverage. > It seems as a bug? How can I change it? > > Thanks, > Lilach > > > 2012/6/18 Jennifer Jackson >> >> Hi Lilach, >> >> The problem with this analysis probably has to do with a mismatch between >> the genomes: the intervals obtained from UCSC (hg19) and the BAM from your >> BWA (hg_g1k_v37) run. >> >> UCSC does not contain the genome 'hg_g1k_v37' - the genome available from >> UCSC is 'hg19'. >> >> Even though these are technically the same human release, on a practical >> level, they have a different arrangement for some of the chromosomes. You >> can compare NBCI GRCh37 with UCSC hg19 for an explanation. Reference >> genomes must be exact in order to be used with tools - base for base. When >> they are exact, the identifier will be exact between Galaxy and the source >> (UCSC, Ensembl) or the full Build name will provide enough information to >> make a connection to NCBI or other. >> >> Sometimes genomes are similar enough that a dataset sourced from one can >> be used with another, if the database attribute is changed and the data from >> the regions that differ is removed. This may be possible in your case, only >> trying will let you know how difficult it actually is with your analysis. >> The GATK pipeline is very sensitive to exact inputs. You will need to be >> careful with genome database assignments, etc. Following the links on the >> tool forms to the GATK help pages can provide some more detail about >> expected inputs, if this is something that you are going to try. >> >> Good luck with the re-run! >> >> Jen >> Galaxy team >> >> >> On 6/18/12 4:42 AM, Lilach Friedman wrote: >> >> Hi, >> I am trying to used Depth of Coverage to see the coverages is specific >> intervals. >> The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy >> and the file type was changed to intervals. >> >> I gave to Depth of Coverage two BAM files (resulted from BWA, selection of >> only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM) >> and the intervals file (in advanced GATK options). >> The consensus genome is hg_g1k_v37. >> >> I got the following error message: >> >> An error occurred running this job: Picked up _JAVA_OPTIONS: >> -Djava.io.tmpdir=/space/g2main >> # ERROR >> -- >> # ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): >> # ERROR The invalid argume >> >> >> Is it a bug, or did I do anything wrong? >> >>
Re: [galaxy-user] Problem with Depth of Coverage on BAM files (GATK tools)
On Thu, Jun 21, 2012 at 10:50 AM, Lilach Friedman wrote: > Hi Jennifer, > Thank you for this reply. > > I made a new BWA file, this time using the hg19(full) genome. > However, when I am trying to use DepthOfCoverage, the reference genomr is > stucked on the hg_g1k_v37 (this is the only option to select), and I cannot > change it to hg19(full). Most probably, because I selected hg_g1k_v37 in the > previous time I tried to use DepthOfCoverage. > It seems as a bug? How can I change it? > Hi Lilach, I have been dealing with these issues for some time now. The only genome you can use with Picard and GATK tools in Galaxy is hg_g1k_v37. I think this is why. From GATK Wiki[1]: "If you are using human data, your reads must be aligned to one of the official b3x (e.g. b36, b37) or hg1x (e.g. hg18, hg19) references. The contig ordering in the reference you used must exactly match that of one of the official references canonical orderings. These are defined by historical karotyping of largest to smallest chromosomes, followed by the X, Y, and MT. The order is thus 1, 2, 3, ..., 10, 11, 12, ... 20, 21, 22, X, Y, MT. The GATK will detect misordered contigs (for example, lexicographically sorted) and throw an error. This draconian approach, though unnecessary technically, ensures that all supplementary data provided with the GATK works correctly. You can use ReorderSam to fix a BAM file aligned to a missorted reference sequence." [1]http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK So far what I have done when presented with a BAM file produced with reference with lexicographical chromosomes ordering, is to use Picard's ReorderSam tool, also in Galaxy, selecting hg_g1k_v37 as reference. You might not be able to this, as if a recall correctly hg19 also use chr1, chr2... instead of 1, 2, ... In that case more work needs to be done and at that point is almost easier to just remap with the correct reference for use with GATK. In your case it seems you already have it. What you might need to do is resort your intervals file and probably change the chromosomes identifiers, this I think can be done inside Galaxy. I would love to hear comments about this approach, as sometime I do worry like Hiram's comment hints to, that hg19 and hg_g1k_v37 might not be completely identical beside the chromosome ordering. In that case my resorted BAM or intervals files might be incorrect. Hope it helps, Carlos > Thanks, > Lilach > > > > 2012/6/18 Jennifer Jackson >> >> Hi Lilach, >> >> The problem with this analysis probably has to do with a mismatch between >> the genomes: the intervals obtained from UCSC (hg19) and the BAM from your >> BWA (hg_g1k_v37) run. >> >> UCSC does not contain the genome 'hg_g1k_v37' - the genome available from >> UCSC is 'hg19'. >> >> Even though these are technically the same human release, on a practical >> level, they have a different arrangement for some of the chromosomes. You >> can compare NBCI GRCh37 with UCSC hg19 for an explanation. Reference >> genomes must be exact in order to be used with tools - base for base. When >> they are exact, the identifier will be exact between Galaxy and the source >> (UCSC, Ensembl) or the full Build name will provide enough information to >> make a connection to NCBI or other. >> >> Sometimes genomes are similar enough that a dataset sourced from one can >> be used with another, if the database attribute is changed and the data from >> the regions that differ is removed. This may be possible in your case, only >> trying will let you know how difficult it actually is with your analysis. >> The GATK pipeline is very sensitive to exact inputs. You will need to be >> careful with genome database assignments, etc. Following the links on the >> tool forms to the GATK help pages can provide some more detail about >> expected inputs, if this is something that you are going to try. >> >> Good luck with the re-run! >> >> Jen >> Galaxy team >> >> >> On 6/18/12 4:42 AM, Lilach Friedman wrote: >> >> Hi, >> I am trying to used Depth of Coverage to see the coverages is specific >> intervals. >> The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy >> and the file type was changed to intervals. >> >> I gave to Depth of Coverage two BAM files (resulted from BWA, selection of >> only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM) >> and the intervals file (in advanced GATK options). >> The consensus genome is hg_g1k_v37. >> >> I got the following error message: >> >> An error occurred running this job: Picked up _JAVA_OPTIONS: >> -Djava.io.tmpdir=/space/g2main >> # ERROR >> -- >> # ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): >> # ERROR The invalid argume >> >> >> Is it a bug, or did I do anything wrong? >> >> I will be grateful for any help. >> >> Thanks! >> Lilach >> >> >> __
Re: [galaxy-user] Tophat mapping
On Wed, Apr 18, 2012 at 8:37 AM, Jeremy Goecks wrote: > I am wondering if these "non-coding reads" will be included when cufflinks > calculates transcript/gene expression. > > > Reads will only be included if they map to assembled/known transcripts. Well it depends what transcript annotation file you pass to cuffdiff. If you run cufflinks without using --GTF: "Tells Cufflinks to use the supplied reference annotation (a GFF file) to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript."[1] In Galaxy language, option "Use Reference Annotation:" with "Use reference annotation" selected. Then the two other options, "No" or "Use reference annotation as guide", will allow cufflinks to estimate unknown transcripts. If later you use cuffmerge to produce the transcripts annotation from your cufflinks runs and use it for cuffdiff, the "non-coding reads" will almost for sure pollute your transcript expression estimates. [1]http://cufflinks.cbcb.umd.edu/manual.html Jeremy, do you have a workflow to estimate what percent of the reads are mapping to unknown expressed regions? I would like to be able to produce this estimate before I make a decision on which transcripts annotation I should pass to cuffdiff. I would expect a small percent of reads to map outside of known expressed regions, but is this number is to big, then I would like to check for potential problems with my library. Regards, Carlos ___ 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] Cuffdiff
Hi Ateequr, I don't think there is an easy answer to your question. I would highly recommend you take a look to this recently released paper from Tophat and Cufflinks authors: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. http://www.ncbi.nlm.nih.gov/pubmed/22383036 The somehow short answer to your question is, you should run cuffdiff with the transcript file from cuffmerge, although I don't quite understand what you mean by "and concatenate data sets". You should not concatenate the BAM files, or you won't be able to run cuffdiff correctly. Depending on how you ran cufflinks, by using the transcript file from cuffmerge you will get expression values for possible new transcripts not present in the databases. This is commonly desired. If you aren't interested in possible new transcripts, then you could simply use a GFF file with transcripts definitions for the genome you are using. In this case you will have the advantage of getting the results with IDs compatibles with the database source the GFF came from. If you use the cuffmerge file you might have the results using cufflinks generated IDs. Hope it helps, Carlos On Tue, Apr 17, 2012 at 11:00 AM, Ateequr Rehman wrote: > Dear All > I have simple and question for cuffdiff > should we run cuffdif on merge transcript file (produced by cuffmerge) and > concatenate data sets > or directly on cufflink produced files, in the later case, i have two > transcript files resulting from cufflink on sample 1 and 2 respectively, > result using sample 1 as transcripts are not the same when i am suing sample > 2 as transcript > > i am bit confused what should be the correct way > > any help is very much welcomed > > Best > ateeq > > Ateequr Rehman > House No. 2 ground floor > Blauenstr. 10 > 79115 Freiburg im Breisgau > > ___ > 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/
Re: [galaxy-user] Help!! Tophat paired end reads
Hi Jennifer, This is a subject I'm interested in. I wonder if you could share a workflow to estimate percentage of reads mapping to for example exomes(I can get the coordinates for a GFF dataset). I have a mapping result for RNA-seq data and by looking in the browser, it seems to also have a lot of reads mapping outside of exomes, but I would like to put numbers on it. Thanks, Carlos P.D. I'm trying now to get GATK's 'Depth of Coverage' to work, but I'm having some issues with it. Is there any other options in Galaxy? On Mon, Apr 16, 2012 at 12:27 AM, Jennifer Jackson wrote: > Hi Jiwen, > > The bioinformatics part of your analysis sounds as if it went fine, so that > is good news. This list may not be the best place to get feedback about > library construction methods, but we can see who has help to offer. > > I did a quick search myself and found this recent publication that includes > a comparison of rRNA depletion methods with mapping profiles: > http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0027288 > > Best, > > Jen > Galaxy team > > > On 4/15/12 8:24 AM, 杨继文 wrote: >> >> Hi, >> I am very confused by my mapping. Please help me figure out what's wrong >> with my operation. >> I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to >> map these reads. >> After mapping, I used IGV to have a look at the mapping. >> I can see that some of the reads fall into exons or span exons (splice >> junction). These reads seem to fit very well. However, I can also see a >> lot reads mapped to non-coding region. Are these reads from pre-mRNA? or >> my mapping was wrong? Did anybody have similar experience?? >> Furthermore, I can see huge enrichment of reads in 3' UTR (much much >> more than the coding region). Is this normal? Is this caused by the rRNA >> depletion method ? >> Looking forward to your reply >> Jiwen >> >> >> >> >> ___ >> 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://galaxyproject.org > ___ > 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/
Re: [galaxy-user] Tophat paired end read
Jiwen, I wonder if you are thinking about the situation where you could be discarding reads that are to short after trimming?. In that case you could be getting the two files out of sync. If this is the case, I think you do need to join the files first, do the trimming and then take them apart again. Regards, Carlos On Mon, Apr 9, 2012 at 1:25 PM, Jennifer Jackson wrote: > Hello Jiwen, > > No, you do not need to join the files for the quality processing. > > Hopefully this helps! > > Best, > > Jen > Galaxy team > > > On 4/9/12 9:14 AM, 杨继文 wrote: >> >> Hi all, >> I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate >> files. Before mapping, I need to trim the reads. >> >> My questions is : Do I have to join pair end reads before timming, and >> then split again for Tophat??? >> >> Lookiong forward to your answers. >> >> Thanks >> >> Jiwen >> >> >> >> >> ___ >> 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/
Re: [galaxy-user] CummeRband in Galaxy platform
Hi Bomba, I'm also quite interested on getting cummeRbund into Galaxy. I was able to start developing a tool to use it, but with tough time constraints at work and school, I haven't been able to get it to a point where I'm happy publishing it in the Main Toolshed. It is however in the Test Toolshed[1], you could find it by searching. If you have a local or cloud instance you should be able to install it and start playing with it. I got to the point where you can generate most kind of plots and you can select what kind of feature you want to plot, genes/isoform/TSS/CDS. There is a lot to do still. For example I think it is a most to be able to use a list of genes as input for some of the graphs, like scatterplots and heatmaps, right now you can do this but you have to enter the genes one by one. There is no support for any non-plotting function, like getSig() or getSigTable(). Hopefully I will find the time in the near future to get it in shape for submission to the Main Toolshed. This however doesn't mean it would appear in the Main Galaxy sever, that's a decision only Galaxy developers can make. Lastly, if there is interest in contributing to this effort, please let me know as I'll be happy to collaborate with other interested party developing this tool. [1]http://testtoolshed.g2.bx.psu.edu/ Regards, Carlos On Fri, Mar 30, 2012 at 9:45 AM, Bomba Dam wrote: > Hi Galaxy team, > > Are there any plans to add the CummeRband tool in the Galaxy platform. > > It would be very nice to have it within Galaxy, this will help people like > us (Biologists, without much programming knowledge) to do the complete > RNA-seq analysis and visualize the data in graphical forms > > Cheers. > > Bomba > > -- > > > > > > ___ > 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] How can I sort BAM/SAM file by read names?
Hi, I need to sort a BAM file by read names, I was wondering if this is possible with a tool included in Galaxy? I know any BAM file produced inside Galaxy will be sorted by coordinates, but I couldn't find an option to change this to queryname in any tool. Picard has the tool SortSam[1], perfect for this task, but it doesn't seem to be included at the moment. Is there any other option currently included? Are there any plans to include one? [1]http://picard.sourceforge.net/command-line-overview.shtml#SortSam Thanks, Carlos ___ 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] Tophat "Mean Inner Distance between Mate Pairs"
Hi Jiwen, This is a subject that has me very confused too. This thread at seqanswer didn't help much either: http://seqanswers.com/forums/showthread.php?t=8730 But it does have some good comments on the subject. I did try using the two possible options I can think of: fragment length - pair end read length - adaptor length And: fragment length - pair end read length With the latter I get around 10% increase on properly paired reads. I wonder if Tophat internally takes into account the adapters. Still, it would be nice to get a definitive answer in this subject. Regards, Carlos 2012/3/6 杨继文 : > Hi all, > > When mapping pair end RNA-seq reads using tophat, we need to type in "Mean > Inner Distance between Mate Pairs". In galaxy, we can read the following > information: > > This is the expected (mean) inner distance between mate pairs. For, example, > for paired end runs with fragments > selected at 300bp, where each end is 50bp, you should set -r to be 200. > There is no default, and this parameter > is required for paired end runs. > > I think the size of fragment (here 300bp) includes not only the length of > pair end reads, but also the length of adaptors. so, maybe the Mean Inner > Distance between Mate Pairs should be : fragment length - pair end read > length - adaptor length. Am I right? or did I miss something? > > Is it a must to type in the accurate value? > > Looking forward to your reply > > JIwen > > > > > ___ > 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/
Re: [galaxy-user] ILLumina 1.9 Hiseq
Hi Jen, I have a related question. If Illumina 1.9 is already in Sanger format, is it still necessary to groom the FASTQ files for TopHat? Would it be enough to directly change the data type to Sanger without grooming? Thanks, Carlos On Wed, Feb 29, 2012 at 10:57 AM, Jennifer Jackson wrote: > Hello, > > The input quality score type should be set as "Sanger" for your data. > > Thanks! > > Jen > Galaxy team > > > On 2/29/12 7:39 AM, Ateequr Rehman wrote: >> >> Dear Glaxy users and admin >> >> I ran my sequence data on FASTQC tool, >> output says it is >> Encoding Sanger / Illumina 1.9 >> >> now i want to groom my file, but groomer does not have option for 1.9 in >> "Input FASTQ quality scores type" >> >> any idea which option i should select to grroom my file, >> >> later i want to run Bowtie or Tophat, >> >> Thanks >> ** >> >> >> >> ___ >> 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/wiki/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/
Re: [galaxy-user] Sam filtering and Header/Sorting issues
Hi Denis, In a similar situation I was able to move forward using NGS: Picard (beta) / Replace SAM/BAM Header to copy back the header from the original unfiltered BAM or SAM file. Hope it helps, Carlos On Tue, Feb 28, 2012 at 3:15 PM, denis puthier wrote: > Dear All, > I would like to add some filtering steps in my RNA-Seq pipeline. To do so, I > used the accepted.hits from TopHat and apply a filter using NGS: SAM Tools >> Filter SAM and select reads with bitwise flag 0x0002. This does the job. > However, I am unable to use cufflink after this step and got the following > error message that seems to indicate that the file contains no header and is > unsorted. Is there a workaround ? > Thanks a lot > > http://main.g2.bx.psu.edu/u/dputhier/h/srx011549 > > > Error running cufflinks. > return code = 1 > cufflinks: /lib64/libz.so.1: no version information available (required by > cufflinks) > Command line: > cufflinks -q --no-update-check -s 20 -I 30 -F 0.10 -j 0.15 -p 8 > -m 200 -g /galaxy/main_pool/pool5/files/003/858/dataset_3858145.dat > /galaxy/main_pool/pool1/files/003/858/dataset_3858306.dat > [bam_header_read] EOF marker is absent. > [bam_header_read] invalid BAM binary header (this is not a BAM file). > File /galaxy/main_pool/pool1/files/003/858/dataset_3858306.dat doesn't > appear to be a valid BAM file, trying SAM... > [14:11:28] Loading reference annotation. > [14:11:28] Inspecting reads and determining fragment length distribution. > > Error: this SAM file doesn't appear to be correctly sorted! > current hit is at chr10:181061, last one was at chr1:245006405 > Cufflinks requires that if your file has SQ records in > the SAM header that they appear in the same order as the chromosomes names > in the alignments. > If there are no SQ records in the header, or if the header is missing, > the alignments must be sorted lexicographically by chromsome > name and by position. > > > -- > > Denis Puthier > laboratoire INSERM > TAGC/INSERM U928 > Parc Scientifique de Luminy case 928 > 163, avenue de Luminy > 13288 MARSEILLE cedex 09 > FRANCE > Mail: puth...@tagc.univ-mrs.fr > Tel: (National) 04 91 82 87 11 / (International) 33 4 91 82 87 11 > Fax: (National) 04 91 82 87 01 / (International) 33 4 91 82 87 01 > > Web: > http://tagc.univ-mrs.fr/puthier > http://biologie.univ-mrs.fr/view-data.php?id=245 > http://tagc.univ-mrs.fr/tbrowser > > > ___ > 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] Solution for: Error running cuffdiff. Error: cannot open reference GTF file CONDITION, CONTROL for reading
Hi, I ran into this error running cuffdiff. I had a hard time debugging this user error, so I though it would be nice to share the solution. This was in a local instance, but I don't see why it wouldn't happen in Galaxy Main under the same circumstances. Tool execution generated the following error message: Error running cuffdiff. Error: cannot open reference GTF file CONDITION,CONTROL for reading The tool produced the following additional output: cuffdiff v1.3.0 () cuffdiff --no-update-check -q -p 4 -c 1000 --FDR 0.05 -N -b --labels CONDITION,CONTROL /local/db/genomes/illumina/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf /local/opt/galaxy_central/database/files/001/dataset_1339.dat,/local/opt/galaxy_central/database/files/001/dataset_1391.dat /local/opt/galaxy_central/database/files/001/dataset_1452.dat,/local/opt/galaxy_central/database/files/001/dataset_1478.dat The problem ended being the use of "Perform Bias Correction"(-b) and a GTF file with no "Database/Build" associated. Looking at cuffdiff wrapper I found, if a FASTA reference is not selected from the history, the FASTA reference of the GTF file associated build is used. If there is not build association, your cuffdiff run will fail with this not so helpful error. My feeling is, cuffdiff should check for a non-dashed string after '-b' and complain if is absents, but this doesn't happen currently. Kind regards, Carlos ___ 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] Sort sam or bam
Hi Claire, Your welcome!. If you feel it could be helpful, this is what I have so far as a workflow for GATK: http://test.g2.bx.psu.edu/u/cjav/w/gatk Is not complete, but I think it could be a good starting point. Please if you ended using this workflow as a starting point and find something you think it could be improve, let me know. There are things like which annotations or ROD file I should use, that I haven't been able to quite understand. Regards, Carlos On Mon, Jan 23, 2012 at 7:44 AM, Clare Sloggett wrote: > Hi Carlos, > > Thanks! I didn't realise the conversion was doing that. > > In fact I want bam files (I'm also using GATK) so this is really helpful. > > Cheers, > Clare > > On Thu, Jan 19, 2012 at 2:32 AM, Carlos Borroto > wrote: >> Hi Clare, >> >> I ran into a similar question testing out GATK pipeline on Galaxy. My >> solution was to always convert my SAM files to BAM. The wrapper also >> sorts the final BAM file output and it does this using the known >> 'samtools sort', which sorts chromosomes in the same order of the >> reference genome. The reference genome can be automatically selected >> by the build associated with the dataset or choose from the history. >> >> I haven't confirmed if a conversion from BAM to SAM would do the same thing. >> >> Hope it helps, >> Carlos >> >> On Wed, Jan 18, 2012 at 12:00 AM, Clare Sloggett wrote: >>> Hi Jen, >>> >>> Thanks for this, belatedly! And happy new year! >>> >>> I think this will work for some of my cases but possibly not all, >>> since it looks like chromosomes are being sorted alphabetically. It >>> depends what the reference genome used was and what tools you're >>> planning to use after sorting as to whether this is ok. >>> >>> I was initially just wondering why 'samtools sort' hadn't been wrapped >>> - not as a complaint, but since the various other samtools options >>> mostly seem to be already wrapped, I wondered if there was some >>> particular reason not to have this one. If I were to try to wrap >>> 'samtools sort' myself is there some difficulty I should know about? >>> >>> Thanks again, >>> Clare >>> >>> On Wed, Dec 7, 2011 at 4:24 AM, Jennifer Jackson wrote: >>>> Hello Clare, >>>> >>>> An example of how to sort a SAM file is included in the workflow from #2 on >>>> this FAQ (it can be imported and the sort modified as needed): >>>> http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq >>>> >>>> If you are starting with a BAM file, convert BAM->SAM, then after sorting, >>>> back with SAM->BAM, using tools in the group "NGS: SAM Tools". >>>> >>>> Best regards, >>>> >>>> Jen >>>> Galaxy team >>>> >>>> >>>> On 12/4/11 9:45 PM, Clare Sloggett wrote: >>>>> >>>>> Hi galaxy users, >>>>> >>>>> Am I right in thinking there is no tool for sorting a sam/bam file in >>>>> Galaxy? >>>>> >>>>> I think this has probably been discussed before, sorry. I just want to >>>>> check I haven't missed anything, since sibling tools from e.g. the >>>>> samtools and picard suites are wrapped. >>>>> >>>>> Thanks, >>>>> Clare >>>>> >>>> >>>> -- >>>> Jennifer Jackson >>>> http://usegalaxy.org >>>> http://galaxyproject.org/wiki/Support >>>> >>>> >>> >>> >>> >>> -- >>> E: s...@unimelb.edu.au >>> P: 03 903 53357 >>> M: 0414 854 759 >>> ___ >>> 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/ >> >> > > > > -- > E: s...@unimelb.edu.au > P: 03 903 53357 > M: 0414 854 759 ___ 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] Sort sam or bam
Hi Clare, I ran into a similar question testing out GATK pipeline on Galaxy. My solution was to always convert my SAM files to BAM. The wrapper also sorts the final BAM file output and it does this using the known 'samtools sort', which sorts chromosomes in the same order of the reference genome. The reference genome can be automatically selected by the build associated with the dataset or choose from the history. I haven't confirmed if a conversion from BAM to SAM would do the same thing. Hope it helps, Carlos On Wed, Jan 18, 2012 at 12:00 AM, Clare Sloggett wrote: > Hi Jen, > > Thanks for this, belatedly! And happy new year! > > I think this will work for some of my cases but possibly not all, > since it looks like chromosomes are being sorted alphabetically. It > depends what the reference genome used was and what tools you're > planning to use after sorting as to whether this is ok. > > I was initially just wondering why 'samtools sort' hadn't been wrapped > - not as a complaint, but since the various other samtools options > mostly seem to be already wrapped, I wondered if there was some > particular reason not to have this one. If I were to try to wrap > 'samtools sort' myself is there some difficulty I should know about? > > Thanks again, > Clare > > On Wed, Dec 7, 2011 at 4:24 AM, Jennifer Jackson wrote: >> Hello Clare, >> >> An example of how to sort a SAM file is included in the workflow from #2 on >> this FAQ (it can be imported and the sort modified as needed): >> http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq >> >> If you are starting with a BAM file, convert BAM->SAM, then after sorting, >> back with SAM->BAM, using tools in the group "NGS: SAM Tools". >> >> Best regards, >> >> Jen >> Galaxy team >> >> >> On 12/4/11 9:45 PM, Clare Sloggett wrote: >>> >>> Hi galaxy users, >>> >>> Am I right in thinking there is no tool for sorting a sam/bam file in >>> Galaxy? >>> >>> I think this has probably been discussed before, sorry. I just want to >>> check I haven't missed anything, since sibling tools from e.g. the >>> samtools and picard suites are wrapped. >>> >>> Thanks, >>> Clare >>> >> >> -- >> Jennifer Jackson >> http://usegalaxy.org >> http://galaxyproject.org/wiki/Support >> >> > > > > -- > E: s...@unimelb.edu.au > P: 03 903 53357 > M: 0414 854 759 > ___ > 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/
Re: [galaxy-user] Genomic interval file for GATK
Hi Raj, I've been also testing GATK Beta pipeline on Galaxy. This is the workflow I have so far: http://test.g2.bx.psu.edu/u/cjav/w/gatk There are a few error coming up that I haven't had the time to fix or work around yet, but I think it could be a good starting point. For example an issue with annotations in Variant Recalibrator tool, was recently fixed: https://bitbucket.org/galaxy/galaxy-central/issue/682/variant-recalibrator-error-with I haven't yet used the new manual method to enter annotations in the workflow. Regarding your questions, I don't have one for 1), I would love to hear about a solution. In my case I'm working with RNA-seq data, so I think everything would speed up if I use a good interval file, but is not clear for me at the moment how to use it or when. For 2), every time a tool outputs a BAM file in Galaxy, it is sorted and indexed automatically, in fact even if the downstream tool can use a SAM file, I still convert it to BAM just to make sure it is sorted and indexed. Regards, Carlos On Thu, Dec 8, 2011 at 1:11 AM, Praveen Raj Somarajan < pravee...@ocimumbio.com> wrote: > All, > > ** ** > > I'm using a locally installed galaxy with GATK 1.3 beta (recently > updated). I would be interested in variant calling using GATK on both > Illumina and SOLiD data. My questions are: > > ** ** > > 1) What should be the format that "Genomic Interval" option can accept in > beta version. It produced an error when I provided an (enrichment coords) > bed file? DepthOfCoverage had also produced error when I used bed files. > Would beta release (v1.3) accept bed file as input for genomic intervals?* > *** > > ** ** > > 2) SAMtool index is seem to be missing in Galaxy. Is this true or any > other module (say SAM->BAM) incorporates this functionality? > > ** ** > > Looking forward to your comments. > > ** ** > > Raj > > ** ** > > ** ** > > -- > This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended > solely for the use of the addressee(s). If you are not the intended > recipient, please notify the sender by e-mail and delete the original > message. Further, you are not to copy, disclose, or distribute this e-mail > or its contents to any other person and any such actions that are unlawful. > This e-mail may contain viruses. Ocimum Biosolutions has taken every > reasonable precaution to minimize this risk, but is not liable for any > damage you may sustain as a result of any virus in this e-mail. You should > carry out your own virus checks before opening the e-mail or attachment. > The information contained in this email and any attachments is > confidential and may be subject to copyright or other intellectual property > protection. If you are not the intended recipient, you are not authorized > to use or disclose this information, and we request that you notify us by > reply mail or telephone and delete the original message from your mail > system. > > OCIMUMBIO SOLUTIONS (P) LTD > > ___ > 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/
Re: [galaxy-user] Galaxy test won't run a bwa job
Thanks Mike, that's what I ended doing. On Tue, Nov 22, 2011 at 4:32 PM, Mike Dufault wrote: > Hi Carlos, > > You can always run your BWA on the Main Galaxy and then import the data > directly into the Test Galaxy using the http: address; no need to download > to your local machine. > > The http: address can be found by by selecting properties on the disk > icon. Instead of downloading, you can just copy the http:. > > I hope this helps, > Mike > > --- On *Tue, 11/22/11, Carlos Borroto * wrote: > > > From: Carlos Borroto > Subject: Re: [galaxy-user] Galaxy test won't run a bwa job > To: "Jennifer Jackson" > Cc: galaxy-user@lists.bx.psu.edu > Date: Tuesday, November 22, 2011, 3:12 PM > > > Hi Jen, > > I did as you recommended a rerun my job, but after 2hrs is still waiting. > > This is my history if that helps: > http://test.g2.bx.psu.edu/u/cjav/h/gatk---hg19---example > > Regards, > Carlos > > On Tue, Nov 22, 2011 at 12:30 PM, Jennifer Jackson > http://mc/compose?to=j...@bx.psu.edu>> > wrote: > > Hello Carlos, > > > > The NGS cluster was down yesterday for maintenance. Restarting the BWA > job > > should initiate the run. > > > > Hopefully this helps, > > > > Jen > > Galaxy team > > > > On 11/22/11 7:56 AM, Carlos Borroto wrote: > >> > >> Hi, > >> > >> I'm trying to test a workflow using tools only available on the test > >> server, for this I have uploaded a limited subset of my data that > >> should run fairly quickly. The first step is a BWA mapping, but the > >> job has being in the queue since yesterday. Is it fine to run this > >> kind of test there? > >> > >> Thanks, > >> Carlos > >> ___ > >> 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/wiki/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/
Re: [galaxy-user] Galaxy test won't run a bwa job
Hi Jen, I did as you recommended a rerun my job, but after 2hrs is still waiting. This is my history if that helps: http://test.g2.bx.psu.edu/u/cjav/h/gatk---hg19---example Regards, Carlos On Tue, Nov 22, 2011 at 12:30 PM, Jennifer Jackson wrote: > Hello Carlos, > > The NGS cluster was down yesterday for maintenance. Restarting the BWA job > should initiate the run. > > Hopefully this helps, > > Jen > Galaxy team > > On 11/22/11 7:56 AM, Carlos Borroto wrote: >> >> Hi, >> >> I'm trying to test a workflow using tools only available on the test >> server, for this I have uploaded a limited subset of my data that >> should run fairly quickly. The first step is a BWA mapping, but the >> job has being in the queue since yesterday. Is it fine to run this >> kind of test there? >> >> Thanks, >> Carlos >> ___ >> 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/wiki/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/
[galaxy-user] Galaxy test won't run a bwa job
Hi, I'm trying to test a workflow using tools only available on the test server, for this I have uploaded a limited subset of my data that should run fairly quickly. The first step is a BWA mapping, but the job has being in the queue since yesterday. Is it fine to run this kind of test there? Thanks, Carlos ___ 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] How to use GATK Unified Genotyper with "A list of genomic intervals over which to operate" option
Hi, I would like to run "Unified Genotyper" on a region of a BAM file, I see the advance option "A list of genomic intervals over which to operate" exist and seems to be what I need. The problem is I only get a drop-down menu with the single option "Selection is optional", which I don't understand. Thanks, Carlos ___ 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] Xgrid and Galaxy
Hi Paul, If you manage to get Xgrid working with galaxy, please share your success, as I would love to try it. But know that you can use SGE on Mac OS X. I was able to get it working by following this blog post and screencast: http://www.bioteam.net/2010/02/grid-engine-6-2-on-mac-os-x/ I tried to compile SGE by myself, but couldn't, so I used this binaries: http://biote.am/sge/ --Carlos On Fri, Aug 19, 2011 at 4:14 AM, Roman Valls wrote: > I'm no expert on MacOS but since Xgrid seems to have an opensource DRMAA > implementation, it *might* be possible (with some > integration/programming efforts): > > http://edbaskerville.com/2006/08/22/xgriddrmaa-011-with-examples/ > > This blog author might help you if you run into issues.. > > Hope that helps ! > > On 2011-08-16 22:26, Paul Cantalupo wrote: >> Hello, >> >> I'm trying to determine if Galaxy will work with Xgrid to set up a >> small cluster of Mac's for next-gen sequencing projects. I saw on >> http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server >> that Galaxy supports Torque PBS or Sun Grid. I don't think that Sun >> Grid runs on Snow Leopard and I don't know about Torque. Snow Leopard >> already comes with Xgrid so I was hoping to use it. >> >> Thank you for your help, >> >> >> Paul Cantalupo >> University of Pittsburgh >> ___ >> 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/
Re: [galaxy-user] Unable to queue tophat's job for execution
This problem went away. Thanks. On Tue, Aug 9, 2011 at 10:55 AM, Carlos Borroto wrote: > Hi, > > The main Galaxy server is failing to schedule tophat's jobs. Giving error: > "Unable to queue job for execution. Resubmitting the job may succeed." > > I've been able to run other tools jobs. > > Thanks, > Carlos > ___ 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] Unable to queue tophat's job for execution
Hi, The main Galaxy server is failing to schedule tophat's jobs. Giving error: "Unable to queue job for execution. Resubmitting the job may succeed." I've been able to run other tools jobs. Thanks, Carlos ___ 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/
