[galaxy-user] Galaxy July 20, 2012 Distribution & News Brief
Galaxy July 20, 2012 Distribution & News Brief *Complete News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_07_20* *Highlights: http://wiki.g2.bx.psu.edu/News/Jul202012%20Distribution%20News%20Brief* * *Freebayes *has moved from the /Galaxy distribution to the Galaxy's Main Tool Shed/ * *EMBOSS* version 5.0.0 tool dependencies in the emboss_5 repository of the Galaxy Main Tool Shed updated to include information for automatically installing. * *Tool Shed* now also supports specifying the third party tool dependencies to be automatically installed in new repositories * *Admin Genome Indexing* is now in /BETA/. Download, index, and track progress right from the admin UI! * *Improved Error Handling* that captures EXIT codes, STDOUT, and STDERR from tools in XML. Be sure to read full details. * *TopHat2/Bowtie2* latest support includes option to 'report discordant pairs', updated tests, and more preset options. * *Trackster* new parameter space visualization. /Includes BRAND NEW Features!!/ More details coming soon, but give a test drive now. *http://getgalaxy.org* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r ec29ce8e27a1 *Thanks for using Galaxy!* We hope to see everyone in /Chicago/ @ *GCC2012*!! The Galaxy Team ___ 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] flaking regions across TSS
Hello Kanwar, On 7/20/12 3:31 PM, shamsher jagat wrote: I am interested in getting regions flanking TSS, I am using Glaxaxy and have downloaded TSS sites using this post steps https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026175.html Now what I would like to do is to get 5000 bp upstream an downstream using flank tool in galaxy, but i realize it only gave me option for gene start or whole gene. The "Region:" options are: 1 - around start - meaning interval start coordinate 2 - around end - meaning interval end coordinate 3 - whole gene - meaning entire intervals Pick option #1. Is it possible to extract 5000 bp upstream and downstream regions across tss start site . The "Location of the flanking region/s:" options are: 4 - Upstream 5 - Downstream 6 - Both Pick option #6 with "Length of the flanking region(s):" set to 5000. Once I have that then I want to find non overlaping genes in my regions from chipseq data. Do you want to identify/label known genes or discover novel genes? This part of your question is not clear. Could you explain in more detail the end goal? It is likely some for of the tool "Operate on Genomic Intervals - > Merge will do what you want", but it is difficult to recommend the correct option. Going forward, sending question to a single public list, as Brooke also suggests, is best. It is generally considered a good idea to not post to two or more, at the same time, with the same email to start threads. Thanks! jen Galaxy team Thanks Kanwar ___ 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/
Re: [galaxy-user] [Genome] flaking regions across TSS
Hi Kanwar, We are unable to provide support for the tools at Galaxy. I see you have copied them on your email, so you will probably hear from them soon. If you have further questions regarding the Genome Browser, please contact us again at gen...@soe.ucsc.edu. -- Brooke Rhead UCSC Genome Bioinformatics Group On 7/20/12 3:31 PM, shamsher jagat wrote: I am interested in getting regions flanking TSS, I am using Glaxaxy and have downloaded TSS sites using this post steps https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026175.html Now what I would like to do is to get 5000 bp upstream an downstream using flank tool in galaxy, but i realize it only gave me option for gene start or whole gene. Is it possible to extract 5000 bp upstream and downstream regions across tss start site . Once I have that then I want to find non overlaping genes in my regions from chipseq data. Thanks Kanwar ___ Genome maillist - gen...@soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome ___ 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] Cuffconfusion
There is an excellent article on how to do differential gene/transcript expression with Tophat and Cufflinks here: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html This article will answer the questions you've posed below and provides numerous figures that will help you create a workflow to meet your needs. Best, J. On Jul 20, 2012, at 6:39 PM, i b wrote: > ok, im really confused now about cufflinks and its tools. > > All I wanted was to look for differentially expressed genes between > two samples: treated (2 replicates) and control (one replicate). > > can anyone give me a workflow for a similar analysis with the various > options chosen? > > I have read a lot of different posts where for cuffdiff they have > used cufflinks, cuffcompare, cuffmerge or any gtf file as imput > together with the bam file. > There must be a difference in using all these different file right??? > > Also: > what is the advantage in using cuffcompare and how we compare them: we > give all cufflinks or we separate control from treated? > Why do we need cuffmerge?isn't it as well combining the cufflinks? > when we use cuffcompare or cuffmerge do we mix all cufflinks no matter > is they are control or treated ones? > > > Please don't send me back to the cufflink page > (http://cufflinks.cbcb.umd.edu/index.html)...I need more simpler > words! > > Thanks, > ib > ___ > 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] Cuffconfusion
ok, im really confused now about cufflinks and its tools. All I wanted was to look for differentially expressed genes between two samples: treated (2 replicates) and control (one replicate). can anyone give me a workflow for a similar analysis with the various options chosen? I have read a lot of different posts where for cuffdiff they have used cufflinks, cuffcompare, cuffmerge or any gtf file as imput together with the bam file. There must be a difference in using all these different file right??? Also: what is the advantage in using cuffcompare and how we compare them: we give all cufflinks or we separate control from treated? Why do we need cuffmerge?isn't it as well combining the cufflinks? when we use cuffcompare or cuffmerge do we mix all cufflinks no matter is they are control or treated ones? Please don't send me back to the cufflink page (http://cufflinks.cbcb.umd.edu/index.html)...I need more simpler words! Thanks, ib ___ 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] flaking regions across TSS
I am interested in getting regions flanking TSS, I am using Glaxaxy and have downloaded TSS sites using this post steps https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026175.html Now what I would like to do is to get 5000 bp upstream an downstream using flank tool in galaxy, but i realize it only gave me option for gene start or whole gene. Is it possible to extract 5000 bp upstream and downstream regions across tss start site . Once I have that then I want to find non overlaping genes in my regions from chipseq data. Thanks Kanwar ___ 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] Problem setting up admin in Galaxy local instance!
Hi Di, You need to remove the starting comment/hash from the admin_users line: admin_users = dkngu...@uw.edu Thanks for using Galaxy, Dan On Jul 20, 2012, at 5:13 PM, Di Nguyen wrote: > Dear all, > > Please help me figure out what went wrong to set up ADMIN in my local > instance using the new retinaMBP! This is what I did > > 1. I changed universe_wsgi.ini.sample file into universe_wsgi.ini (using Mac > TextEdit) > > 2. Then, I edited universe_wsgi.ini as followed: > > # Administrative users - set this to a comma-separated list of valid Galaxy > # users (email addresses). These users will have access to the Admin section > # of the server, and will have access to create users, groups, roles, > # libraries, and more. For more information, see: > # http://wiki.g2.bx.psu.edu/Admin/Interface > #admin_users = dkngu...@uw.edu > > 3. I shutdown Galaxy, rerun sh run.sh, log back in Galaxy but still no Admin > function. > > 4. The reason that I wanted to ad Admin function is to import my NGS files > (bigger than 2Gb fer sure) into Galaxy database. Please give me some tips on > this as well. > > Thank you very much, > > Di Nguyen, postdoc > U of Washington, Seattle, WA > > > ___ > 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] Problem setting up admin in Galaxy local instance!
Dear all, Please help me figure out what went wrong to set up ADMIN in my local instance using the new retinaMBP! This is what I did 1. I changed universe_wsgi.ini.sample file into universe_wsgi.ini (using Mac TextEdit) 2. Then, I edited universe_wsgi.ini as followed: # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = *dkngu...@uw.edu* 3. I shutdown Galaxy, rerun sh run.sh, log back in Galaxy but still no Admin function. 4. The reason that I wanted to ad Admin function is to import my NGS files (bigger than 2Gb fer sure) into Galaxy database. Please give me some tips on this as well. Thank you very much, Di Nguyen, postdoc U of Washington, Seattle, WA ___ 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 failed
Hello Irene, There appears to be a problem with the information entered into the tool form for the labels (e.g. "Group name"). The command string only shows one group label value when there are two group data sets. You submitted a bug report for this same issue, so I will take a look there at the exact error (usually is very specific about problem) and at the exact settings entered into tool form and provide feedback there. Thanks, Jen Galaxy team On 7/20/12 9:19 AM, i b wrote: Hi, I had 3 samples (2replicates treated (A-B) and one untreated (C) ). I did cufflnks and cuffmerge (all 3 cufflinks) I run cuffdiff with the following options: cuffmerge + tophats from A, B, C (2 groups: gr.one with A, B), gropu2: C. I had the following message: 0 bytes An error occurred running this job: cuffdiff v1.3.0 (3022) cuffdiff --no-update-check -q -p 8 -c 10 --FDR 0.05 -N -b /galaxy/data/hg19/sam_index/hg19.fa --labels + /galaxy/main_pool/pool4/files/004/645/dataset_4645857.dat /galaxy/main_pool/pool3/files/004/623/dataset_4623286.dat,/galaxy Where did I do wrong? What does it mean? Cheers, ib ___ 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/
[galaxy-user] cuffdiff failed
Hi, I had 3 samples (2replicates treated (A-B) and one untreated (C) ). I did cufflnks and cuffmerge (all 3 cufflinks) I run cuffdiff with the following options: cuffmerge + tophats from A, B, C (2 groups: gr.one with A, B), gropu2: C. I had the following message: 0 bytes An error occurred running this job: cuffdiff v1.3.0 (3022) cuffdiff --no-update-check -q -p 8 -c 10 --FDR 0.05 -N -b /galaxy/data/hg19/sam_index/hg19.fa --labels + /galaxy/main_pool/pool4/files/004/645/dataset_4645857.dat /galaxy/main_pool/pool3/files/004/623/dataset_4623286.dat,/galaxy Where did I do wrong? What does it mean? Cheers, ib ___ 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] Attempting to use parallelism in BWA
Hi Kevin, I'm not able to reproduce this with python 2.7. Can you confirm that galaxy is indeed using the installed python 2.7 and not, perhaps, 2.4? The structure of python's try/except/finally clause changed with python 2.5 and if you were unintentionally running 2.4 that would explain this error. And lastly, regarding the parallelization of BWA, there's nothing else you need to do; setting use_tasked_jobs = True should handle it. -Dannon On Jul 17, 2012, at 12:27 PM, Kevin C. Dorff wrote: > Hi, > > I am using Python 2.7. I am running with an hg checked out, up to date > version of "https://bitbucket.org/galaxy/galaxy-dist/";. > > I am very new to Galaxy. I have an instance setup and running locally. I am > able to perform routine actions such as uploading files, processing with > Picard, and aligning with BWA. I have been able to make the jobs execute out > our SGE cluster. > > In order to better utilize my cluster, I attempted to enable parallelism of > the tasks that support it (such as BWA) by configuring the universe_wsgi.ini > file with the parameter > >use_tasked_jobs = True > > When I do this and attempt execute a BWA alignment on a 4.1Gb fastq file, I > am given the error > > Result 256 from mv > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_1/dataset_21.dat > > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/files/000/dataset_21.dat > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_0: > Traceback (most recent call last): > File "./scripts/extract_dataset_part.py", line 25, in ? > import galaxy.model.mapping #need to load this before we unpickle, in > order to setup properties assigned by the mappers > File > "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/model/__init__.py", > line 13, in ? > import galaxy.datatypes.registry > File > "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/datatypes/registry.py", > line 146 > finally: > ^ > SyntaxError: invalid syntax > The alignment failed. > > If you need the complete error message, contact me and I can supply you with > it. It's too large to paste in-line and attachments aren't allowed. > > Is there more I need to do to enable parallel jobs (splitting of input, > align, then merge)? > > Any suggestions are greatly appreciated. > > Kevin > ___ > 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] tophat output spice junction output
Hi, where can I find an explanation of the columns in the splice junctions output? From 7 to12 they are only numbered thanks, ib ___ 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] extracting, stitching, converting MAF files: interval_maf_to_merged_fasta.py: command line usage?
Dear Galaxy team / user mailing list, my question is with respect to command line usage, not about interactive / web-based Galaxy usage. Regarding the publication [1], section "2.3 Stitchers". I want to use the stitcher to extract a given region from MAF files, stitch it together and convert it to FASTA. I downloaded and installed Galaxy according to the instructions from http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy I believe the actual stitcher is "interval_maf_to_merged_fasta.py" in the /tools/maf directory (not clear from the paper or docs but I belive this is the tool that implements this functionality). How can I actually extract, stitch, convert with interval_maf_to_merged_fasta.py? I have difficulties figuring all necessary command line parameters out by reading the source code. F.e. here I tried to get the stiched FASTA conversion for a region defined in "foo.bed" out of "chr1.maf": $ python ./tools/maf/interval_maf_to_merged_fasta.py -G -i ../foo.bed -m ../chr1.maf -d hg18 -o stdout Traceback (most recent call last): File "./tools/maf/interval_maf_to_merged_fasta.py", line 196, in if __name__ == "__main__": __main__() File "./tools/maf/interval_maf_to_merged_fasta.py", line 107, in __main__ if options.mafSourceType.lower() in ["cached"]: AttributeError: 'NoneType' object has no attribute 'lower' Is it necessary to index the MAF files first somehow? Do I have to set the type of MAF file, and to what? Would be great if someone could give a short overview how to stitch MAF files command-line based. Thank you! Anton References [1] Blankenberg, D., Taylor, J., Nekrutenko, A. & Galaxy Team. Making whole genome multiple alignments usable for biologists. *Bioinformatics (Oxford, England)* *27*, 2426-2428 (2011) ___ 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/
