- galaxy-user - lists.galaxyproject.org

Re: [galaxy-user] Galaxy Help
by Jennifer Jackson 04 Feb '13

04 Feb '13

Hi John, If you have other sequence types, there are other alignment tool choices on the public Main server. The est2genome tool has a fairly specific use, so I thought that this was your input/goal. For ChIP-seq, RNA-seq, or other NGS datatypes, please see the tools under 'NGS: Mapping' and 'NGS: RNA Analysis'. We have tutorials for these tools - from the top menu bar follow 'Shared Data -> Published Pages". Good places to start are 'Galaxy Exercises', 'Galaxy RNA-seq Analysis Exercise', and 'Using Galaxy' (but review the others as wanted, I am not sure what type of data you are working with). More tutorials are in our wiki here: http://wiki.galaxyproject.org/Learn#Other_Tutorials Other public Galaxy sites offer specialized tools for working with certain data types - the best way to find out what they have to is visit them and review. We keep a list of links in our wiki here: http://wiki.galaxyproject.org/Big%20Picture/Choices -> http://wiki.galaxyproject.org/PublicGalaxyServers Good luck with your project! Next time, or if you have followup, please be sure to leave the mailing list in the cc to help us with tracking. Thanks! Jen Galaxy team On 2/4/13 8:08 AM, John Phillips wrote: > Are you sure that there is no way for me to align multiple sequences? I > apologize if I did not use the correct technical language, but from what > I understand, everyone seems to be citing you guys for sequence alignments. > > Thank you, > -John > > > On Sun, Feb 3, 2013 at 1:34 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hi John, > > The current link is: > > http://wiki.galaxyproject.org/__FTPUpload > <http://wiki.galaxyproject.org/FTPUpload> > > We changed our wiki base and many of the older links do not > redirect. I'll let our wiki admin Dave know about this and see what > can be done. If this comes up again soon, the base always redirects > to "http://galaxyproject.org -> http://wiki.galaxyproject.org"__, > and clicking into "Learn" will likely take to you want to go - the > primary hub page for user documentation - including the links in > tutorials (plus the wiki side navigation bar with a few different > search options). > > And is true that we do not offer large scale EST to genomic > alignment on the public server. Galaxy choices such as > BLAST+/Megablast are for use with a local or cloud Galaxy instance. > > When using a local instance, the tool wrapper can be obtained from > the Tool Shed (http://toolshed.g2.bx.psu.edu__) A cloud ami would > have these tools as part of the package. You can also check the Tool > Shed for other options - more are added all the time. > > Local: http://getgalaxy.org > Cloud: http://usegalaxy.org/cloud > > Hopefully this helps, > > Jen > Galaxy team > > > On 2/2/13 3:17 PM, John Phillips wrote: > > 1. > > > To Whom it May Concern: > > > I am using the Galaxy interface, and according to the tutorial > screencast, I should be able to upload my own reference genome. The > address given in the tutorial > (http://galaxyproject.org/__FTPUpload > <http://galaxyproject.org/FTPUpload>) leads > to a 404 file not found page. I was wondering if there is an > alternative > site that can allow me to do this. > > Also, I tried to use the est2genome tool in order to try and > align my > uploaded sequences. It would only allow me to compare two > sequences at a > time. Is it possible to align a larger number of sequences at > once? I > understand there are other programs that allow for this kind of > procedure (e.g. Sequencher), but I would like to do this in Galaxy. > > Thank you for your time, > > -- > -John G. Phillips > Graduate Research Assistant > University of Tulsa > 231-233-6914 <tel:231-233-6914> > > > _____________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org <http://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 > <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 Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org > > > > > -- > -John G. Phillips > Graduate Research Assistant > University of Tulsa > 231-233-6914 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

1 0

Galaxy Help
by John Phillips 03 Feb '13

03 Feb '13

1. To Whom it May Concern: I am using the Galaxy interface, and according to the tutorial screencast, I should be able to upload my own reference genome. The address given in the tutorial (http://galaxyproject.org/FTPUpload) leads to a 404 file not found page. I was wondering if there is an alternative site that can allow me to do this. Also, I tried to use the est2genome tool in order to try and align my uploaded sequences. It would only allow me to compare two sequences at a time. Is it possible to align a larger number of sequences at once? I understand there are other programs that allow for this kind of procedure (e.g. Sequencher), but I would like to do this in Galaxy. Thank you for your time, -- -John G. Phillips Graduate Research Assistant University of Tulsa 231-233-6914

2 1

Re: [galaxy-user] Fwd: Converting files to gd_snp format
by Cathy Riemer 02 Feb '13

02 Feb '13

Hello Mike, The tutorial you were looking at was made using one of our local Galaxy instances, in advance of updating the main public server. The main server already includes most of the tools used in the examples, but two of the format conversion tools ("MasterVar to gd_snp" and "pgSnp to gd_snp") are not posted there yet. I apologize for the delay. We are in the process of moving some of the tools from the Phenotype Association section of the toolbox to the Convert Formats section, while simultaneously migrating those and the rest of the Phenotype Association tools from their current, manually configured installation method to the new Galaxy Tool Shed paradigm. We have encountered some technical difficulties with that, but we hope to have the update accomplished within the next few weeks. If you need it sooner, let me know and I'll send you the underlying Perl script for the "pgSnp to gd_snp" tool, so you can run that locally to convert your file and then upload the output to your Galaxy history. Thanks for your patience! -Cathy Riemer > ---------- Forwarded message ---------- > From: Sheehan, Michael - (michaelsheehan) <michaelsheehan(a)email.arizona.edu> > Date: Wed, Jan 30, 2013 at 1:30 AM > Subject: [galaxy-user] Converting files to gd_snp format > To: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> > > > I would like to convert VCF files to gd_snp format to be used in some > population genomic analyses. A tutorial online makes it seem like this > is the correct path to follow to conduct such analyses: > > http://www.bx.psu.edu/~giardine/tutorials/example2/part1/snpTable.html > > I have been using Galaxy on the free public server and this tools does > not appear to be present anywhere. Does anyone know where the tool has > gone or is there a way to add the needed tools back? > > Thanks > Mike >

1 0

can't download big files
by Allan Sun 01 Feb '13

01 Feb '13

Hello everyone, We have galaxy-dist-17d57db9a7c0 installed on our Mandriva 2009 64bit. There are 2 big fasta files, file A is 4.4G and file B is 3.3G which I tried to download without success. I've used browser download,including mozilla,IE and Chrome,also from suggestion by Jennifer: linux command: wget and curl -O.None of them work. For file A,the downloaded file size is always 450M(9% of total size),no matter which way ( mentionedabove )I use, For file B,the downloaded file size is 0 byte. Following is the error report by :curl -O curl: (18) transfer closed with 4294967296 bytes remaining to read Any help will be very appreciated. Allan

2 2

Error using Trackster
by Kilaru, Varun 01 Feb '13

01 Feb '13

Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error: hashMustFindVal: 'chr11' not found grep: writing output: Broken pipe This is followed by a number of lines of the same error code. I am not sure what is happening. Can you please elaborate? Thanks, Varun ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

2 5

Error using trackster
by Kilaru, Varun 01 Feb '13

01 Feb '13

Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error: ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

1 0

February 2013 Galaxy Update
by Dave Clements 01 Feb '13

01 Feb '13

1 0

error message running Cufflinks on local galaxy
by Davide Degli Esposti 01 Feb '13

01 Feb '13

Dear Jen, I have downloaded Galaxy on my computer. When trying to run cufflinks locally I have this error message: 8: Cufflinks on data 3 and data 2: gene expression error An error occurred running this job:Could not determine Cufflinks version cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.150000 -p 4 -G /Users/davidedegliesposti/galaxy-dist/database/files/000/dataset_2.dat -N Error running cufflinks. return code = 127 /bin/sh: cufflinks: command May this be due to an error of installation? Thank you for your help Davide --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------

2 1

error running cufflinks
by Davide Degli Esposti 01 Feb '13

01 Feb '13

Dear Jen, after a couple of days of running cufflinks on a sam file (data 9) with an annotated reference in gtf (data 28), I have this message in return that I am not able to decode: 32: Cufflinks on data 9 and data 28: total map mass error An error occurred running this job:cufflinks v2.0.2 cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.150000 -p 8 -G /galaxy/main_pool/pool6/files/005/663/dataset_5663874.dat -u -N -b /galaxy/data/hg19/sam_index/hg19.fa Error running cufflinks. return code = 1 cufflinks: /lib64/lib Thank you for you help Best regards Davide --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------

2 1

gather results from multiple histories
by mark.rose＠syngenta.com 01 Feb '13

01 Feb '13

Hi All Let's say that I have results produced from a step in multiple different histories and that I now want to gather these results into a new history so that they can be joined. Is there a way to do this without exporting results to my desktop and then uploading? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

2 1