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extract genome sequence
by Yan He 25 Sep '12

25 Sep '12

Hi everyone, I have the genome sequence and gene annotation file. Is there a tool on Galaxy to extract the 5,000 bp upstream, 5,000 bp downstream and genome sequences of the genes (including exons and introns) from the genome sequence? Any suggestions are highly appreciated! Thanks! Yan

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public repository for workflows?
by Kenny Billiau 25 Sep '12

25 Sep '12

Hi, I've browsed the archives briefly, but didn't find a lot of talk about publicly available workflows or workflow repositories, except the ones mentioned here: https://main.g2.bx.psu.edu/workflow/list_published If I only google, then I simply find myexperiment.org, which is mostly taverna workflows on there (and a whopping 9 galaxy ones). Any chance anyone can point me to some other resources? wkr, Kenny -- ====================================================================== Ing. Kenny Billiau Bioinformatics Group Scientific Programmer +49 331 567 8626 billiau(a)mpimp-golm.mpg.de Max Planck Institute for Molecular Plant Physiology Am Mühlenberg 1, 14476 Potsdam-Golm, Germany http://bioinformatics.mpimp-golm.mpg.de ======================================================================

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Galaxy September 20, 2012 Distribution & News Brief
by Jennifer Jackson 21 Sep '12

21 Sep '12

*Galaxy September 20, 2012 Distribution & News Brief* http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_20 <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_20> /*Highlights:* http://wiki.g2.bx.psu.edu/News <http://wiki.g2.bx.psu.edu/News>/ * A /*new Galaxy tool*/<http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_20#Galaxy_Tool_Factory> that writes other /*new Galaxy tools*/! The /*Tool Factory*/ is in the Galaxy's Main *Tool Shed* (*/toolfactory/*). Try it now! * Learn how to *display multiple versions of a tool* in the Galaxy tool panel. * *CloudLaunch Overhaul* includes Boto 2.5.2 and simplified instance selection and key generation. * Release also includes more *Tool Shed *updates, *Framework* and *API* updates, plus *Security* and *Bug* fixes. http://getgalaxy.org http://bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist> *new: * $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist* upgrade:* $ hg pull -u -r da9d740fce31 ** *Thanks for using Galaxy!* Jennifer Jackson & Galaxy Team http://galaxyproject.org

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How much FPKM can be take into consideration when compare gene expression
by Du, Jianguang 20 Sep '12

20 Sep '12

Dear All, I am comparing the gene expression between two cell types by examining the Cufflink output file -- gene differential expression testing<javascript:void(0);>. The file lists the FPKM of genes in two cell types and log2 of fold. I want to look for genes that have more than 2-flod of expression in cell type A than in cell type B. What is the minimum FPKM in cell type A so that only the genes that have FPKM highier than this number can be taken into consideration for further analysis? For example, The FPKM of gene X in cell type A is 80, and in cell type B is 20, the fold of difference is 4. The FPKM of gene Y in cell type A is 4, and in cell type B is 1, the fold of difference is also 4. Is there a minimum FPKM in cell type A for genes to be selected for further analysis? Thanks. Jianguang

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How to rotate Galaxy log file
by Lukasz Lacinski 19 Sep '12

19 Sep '12

Dear All, I use an init script that comes with Galaxy in the contrib/ subdirectory to start Galaxy. The log file --log-file /home/galaxy/galaxy.log specified in the script grows really quickly. How to logrotate the file? Thanks, Lukasz

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Cloudman share string not working
by greg 18 Sep '12

18 Sep '12

Hi guys, I entered my share string "cm-808d863548acae7c2328c39a90f52e29/shared/2012-09-17--19-47" on this page "https://biocloudcentral.herokuapp.com/launch" in the field labeled "Shared cluster string" and click the button to create my instance. But then when I log into Cloudman the "Initial Cluster configuration" dialog is still appearing. I ran the same thing yesterday with an older share string and everything worked fine. Any ideas what could be going on? I'm pretty stuck. Thanks, Greg This is all I see in the cluster status log (I entered my share string again on the dialog, the disk status says 0 / 0 and applications and data lights are yellow, and don't seem to progress): 13:34:46 - Master starting 13:34:50 - Retrieved file 'shared/2012-09-17--19-47/shared_instance_file_list.txt' from bucket 'cm-808d863548acae7c2328c39a90f52e29' to 'shared_instance_file_list.txt'. 13:41:29 - Retrieved file 'shared/2012-09-17--19-47/shared_instance_file_list.txt' from bucket 'cm-808d863548acae7c2328c39a90f52e29' to 'shared_instance_file_list.txt'. 13:41:30 - Retrieved file 'persistent_data.yaml' from bucket 'cm-c8c215c4c67525d91b3a2598f9e370f7' to 'shared_p_d.yaml'. 13:41:31 - Created a data volume 'vol-7f2cc105' of size 5GB from shared cluster's snapshot 'snap-cfa775ba' 13:41:31 - Saved file 'persistent_data.yaml' to bucket 'cm-c8c215c4c67525d91b3a2598f9e370f7' 13:41:31 - Retrieved file 'persistent_data.yaml' from bucket 'cm-c8c215c4c67525d91b3a2598f9e370f7' to 'pd.yaml'.

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Error executing tool: Unable to create output dataset: object store is full
by Angela Inácio 18 Sep '12

18 Sep '12

Hi, I tried to convert my tabular data in fastq data, and galaxy did not allowed me: Error executing tool: Unable to create output dataset: object store is full could you please explain me what this mean? Thanks

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Re: [galaxy-user] Galaxy error: can't fine fasta file
by Jennifer Jackson 17 Sep '12

17 Sep '12

Hi Kenneth, It is likely that the path is wrong in the .loc file. It has to point to the actual files, not just the directory. Inside here /9720/genome_references/ncbi/nr-protein-db is where all the nr.* files are? In that case, the path should be /9720/genome_references/ncbi/nr-protein-db/nr You will want to open the .loc file in a text editor that allows you to view the whitespace, too, to double check that the columns are single tab separated and that there are no extra spaces before or after the data in any individual column. The middle column can contain internal spaces, but those should be the only spaces in any row. You also do not want any trailing blank/empty lines in the file. And yes, restart the server. A checklist is at the top of the wiki to help: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Best, Jen Galaxy team On 9/17/12 12:46 PM, Kenneth R. Auerbach wrote: > Hi Jennifer, > > I changed the path of the nr files in the .loc file to the following: > > nr NCBI NR (non -redundant) /9720/genome_references/ncbi/nr-protein-db > > This is the directory that has all those many nr files (index files, > etc....) > > But I still get the same error where the old path is still referenced. > Does the galaxy server need to be restarted for the new .loc file to go > into effect? > > Thank you. > Ken. > > > > On Mon, 2012-09-17 at 10:42 -0700, Jennifer Jackson wrote: >> Hi Kenneth, >> >> Yes, target databases require indexes and *.loc file set-up. Please see >> this wiki for details. For Genbank data such as NR, FTP the pre-built >> indexes and use those (generating them with formatdb is not necessary). >> >> http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup >> >> See the second section, 'Tips for Installing Tools -> 'Megablast >> installation', then down in the wiki again under 'Megablast' for more >> detail. The same indexes can be used for BLAST+ (both now are based on >> BLAST+). The location of the data can be where you have it - it seems >> like Galaxy is looking in the right place for it (it does not go under a >> genome like the other indexes on the wiki). >> >> Also, make sure the data is uncompressed before you use it. And be sure >> to point to the data into the blastdb.loc file (this appears to be done >> already based on your error message, but double check). >> >> Hopefully this helps, >> >> Jen >> Galaxy team >> >> On 9/17/12 10:11 AM, Kenneth R. Auerbach wrote: >>> Hi Jennifer, >>> >>> Thank you for that info. I have another question, when I submit my job I >>> get this error: >>> >>> ----- >>> An error occurred running this job: BLAST Database error: No alias or >>> index file found for protein database >>> [/9720/genome_references/ncbi/nr-protein-db/nr-newstyle/nr] in search >>> path >>> [/9720/galaxyprod/galaxy-dist/database/job_working_directory/1560::] >>> Return error code 2 from command: >>> blast >>> ------ >>> I checked and the 'nr' database file is there in that path and it has >>> read permissions for everyone. It's in a directory called 'nr-newstyle' >>> with only its archive file (.gz). There are no other files. Should there >>> also be 'alias' or 'index' files as well? Are other files needed besides >>> 'nr'? >>> >>> Thank you. >>> >>> On Mon, 2012-09-17 at 09:29 -0700, Jennifer Jackson wrote: >>>> Hello Kenneth, >>>> >>>> Are you using BLAST+ in a local install or cloud instance? The problem >>>> may be that the query dataset needs to have the datatype assigned as >>>> "fasta". To do this, click on the pencil icon for the dataset to reach >>>> the Edit Attributes form. Then either scroll down to (or click on the >>>> tab for) the attribute "Datatype" and change to "fasta" and save. [The >>>> UI is undergoing some changes, so you may or may not have the new tabs >>>> style form in your instance yet). >>>> >>>> The best mailing list going forward for local/cloud support is >>>> galaxy-dev(a)bx.psu.edu. >>>> http://wiki.g2.bx.psu.edu/Mailing%20Lists >>>> >>>> Take care and please let us know if your question has been misunderstood, >>>> >>>> Jen >>>> Galaxy team >>>> >>>> On 9/17/12 8:52 AM, Kenneth R. Auerbach wrote: >>>>> Hello, >>>>> >>>>> I'm new to Galaxy. >>>>> When I read in a fasta file to Galaxy and then try to use it (in a blast >>>>> search) as the query sequence, I get the error message below, although >>>>> the uploaded fasta file is present in the history. Can anyone tell me >>>>> what the problem could be? Is there some other step I need to do? >>>>> >>>>> Thank you. >>>>> >>>>> Error that appears under "nucleotide query sequence": >>>>> ----- >>>>> "History does not include a dataset of the required format / build" >>>>> ----- >>>>> >>>>> ___________________________________________________________ >>>>> 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

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Re: [galaxy-user] Galaxy error: can't fine fasta file
by Jennifer Jackson 17 Sep '12

17 Sep '12

Hi Kenneth, Yes, target databases require indexes and *.loc file set-up. Please see this wiki for details. For Genbank data such as NR, FTP the pre-built indexes and use those (generating them with formatdb is not necessary). http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup See the second section, 'Tips for Installing Tools -> 'Megablast installation', then down in the wiki again under 'Megablast' for more detail. The same indexes can be used for BLAST+ (both now are based on BLAST+). The location of the data can be where you have it - it seems like Galaxy is looking in the right place for it (it does not go under a genome like the other indexes on the wiki). Also, make sure the data is uncompressed before you use it. And be sure to point to the data into the blastdb.loc file (this appears to be done already based on your error message, but double check). Hopefully this helps, Jen Galaxy team On 9/17/12 10:11 AM, Kenneth R. Auerbach wrote: > Hi Jennifer, > > Thank you for that info. I have another question, when I submit my job I > get this error: > > ----- > An error occurred running this job: BLAST Database error: No alias or > index file found for protein database > [/9720/genome_references/ncbi/nr-protein-db/nr-newstyle/nr] in search > path > [/9720/galaxyprod/galaxy-dist/database/job_working_directory/1560::] > Return error code 2 from command: > blast > ------ > I checked and the 'nr' database file is there in that path and it has > read permissions for everyone. It's in a directory called 'nr-newstyle' > with only its archive file (.gz). There are no other files. Should there > also be 'alias' or 'index' files as well? Are other files needed besides > 'nr'? > > Thank you. > > On Mon, 2012-09-17 at 09:29 -0700, Jennifer Jackson wrote: >> Hello Kenneth, >> >> Are you using BLAST+ in a local install or cloud instance? The problem >> may be that the query dataset needs to have the datatype assigned as >> "fasta". To do this, click on the pencil icon for the dataset to reach >> the Edit Attributes form. Then either scroll down to (or click on the >> tab for) the attribute "Datatype" and change to "fasta" and save. [The >> UI is undergoing some changes, so you may or may not have the new tabs >> style form in your instance yet). >> >> The best mailing list going forward for local/cloud support is >> galaxy-dev(a)bx.psu.edu. >> http://wiki.g2.bx.psu.edu/Mailing%20Lists >> >> Take care and please let us know if your question has been misunderstood, >> >> Jen >> Galaxy team >> >> On 9/17/12 8:52 AM, Kenneth R. Auerbach wrote: >>> Hello, >>> >>> I'm new to Galaxy. >>> When I read in a fasta file to Galaxy and then try to use it (in a blast >>> search) as the query sequence, I get the error message below, although >>> the uploaded fasta file is present in the history. Can anyone tell me >>> what the problem could be? Is there some other step I need to do? >>> >>> Thank you. >>> >>> Error that appears under "nucleotide query sequence": >>> ----- >>> "History does not include a dataset of the required format / build" >>> ----- >>> >>> ___________________________________________________________ >>> 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

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FTP upload problem
by Yan He 17 Sep '12

17 Sep '12

Hi everyone, When I tried to upload my files using Filezilla, I got the error message "530 Sorry, the maximum number of clients (3) for this user are already connected." Can anyone give me some suggestions how to solve this problem? I have been stuck here for a whole day. Thanks very much! Yan

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