Re: [galaxy-user] Quality report
On Wed, Nov 6, 2013 at 12:54 PM, Benjamin Osei-agyeman benjy_o...@yahoo.co.uk wrote: The report was obtained after running fastqc on my data. However after looking at the report statistics, the Quality is not good in the Per Base Sequence Quality and there is a difference between the mean and median at each cycle. How can the quality be improved? Is the quality poor across the entire read, or just at one end? You can improve overall quality in two ways. By filtering out lower quality reads (the Filter by Quality tool or Filter FASTQ tool) or by trimming a portion of the reads (the FASTQ trimmer tool). It is important to understand that these tools work by throwing away data, you can't improve the overall quality of reads you already have. The FASTQC tool is telling you about the quality of your sequencing experiment. The only way to improve the overall quality is to do the experiment again. And why is there a difference between the mean and median in the fastqc report at each cycle? It means your quality score distribution is skewed. This is not necessarily a concern. -- James Taylor, Associate Professor, Biology/CS, Emory University ___ 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] Need your helps about Galaxy
As I said before, there is no easy way to do this. You just need to dump the old database and load into the new database. I would suggest making a copy of the old database with a current version of Galaxy. The migration scripts will then bring it up to date so you will have identical schemas. You should then be able to dump and load easily enough, you will just need to move the dump file between servers. -- James Taylor, Associate Professor, Biology/CS, Emory University On Mon, Sep 23, 2013 at 3:36 PM, Lei Yan leiyan2...@gmail.com wrote: Dear Dannon, I built a new cloud Galaxy instance today. Would you please tell me how to transfer given accounts from an old Galaxy to this new one? This is old Galaxy: http://galaxylocal.genenetwork.org:8080/ This is new Galaxy: http://galaxyclass.genenetwork.org/ Thanks a lot. Lei Yan Center for Integrative and Translational Genomics UTHSC ___ 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] Secure file upload gateway for Galaxy
Galaxy's FTP support uses ProFTPD, which has modules for both TLS (FTPS) and SFTP. -- James Taylor, Associate Professor, Biology/CS, Emory University On Tue, Sep 24, 2013 at 7:58 AM, Georgios Magklaras georg...@biotek.uio.no wrote: Hi, Our team at the University of Oslo is building a Life Science Portal based on Galaxy. We operate several standalone instances and we have the necessary sysadmin experience, but we really need to implement a more secure file upload mechanism than FTP (we do not like to send cleartext password credentials in the open ), and we understand that Galaxy does not integrate an upload method other than FTP with reference to this screencast: http://screencast.g2.bx.psu.edu/quickie_17_ftp_upload/flow.html One possible solution for this is to setup an SFTP upload server with a huge scratch space, that runs the SFTP upload gateway on one end and an IP restricted FTP server on the other, so that users can then upload/index the SFTP uploaded data into their Galaxy session via the URL upload field. This two step process might be a bit cumbersome for some of our users and we are looking for ways to simplify it. Do you have best recipes for SFTP/Aspera upload gateway integration to Galaxy? We would welcome advise on that matter. GM Best regards, -- -- George Magklaras PhD RHCE no: 805008309135525 Head of IT/Senior Systems Engineer Biotechnology Center of Oslo and the Norwegian Center for Molecular Medicine/ Vitenskapelig Databehandling (VD) - Research Computing Services - USIT EMBnet TMPC Chair http://folk.uio.no/georgios http://www.uio.no/english/services/it/research/hpc/abel/ Tel: +47 22840535 ___ 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] How do I add Ray to Galaxy Central in the tool shed ?
I want to add Ray (a scalable de novo assembler for genomes and metagenomes) to Galaxy. And I really want you to do this! I will also have to write a wrapper for Ray to prepare the command line from the options provided by the Galaxy API. But where is stored the executable (in my case, where is sdtored Ray) ? Does Galaxy include the specs to build all the tools available in Galaxy-Central ? No, we are gradually moving all the tools out of galaxy-central into the Tool Shed. You probably want to look at this page: http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories Which describes how you can add a recipe to the toolshed that will install the Ray binaries. ___ 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] How to share an history with a SPECIFIC user ?
Sarah, when you share with a specfic user, it will not show up under the Shared Data section since that is only for published items. The person you share it with should see it under Histories Shared with me which is in the History options menu: -- James Taylor, Assistant Professor, Biology/CS, Emory University On Mon, Jun 3, 2013 at 11:22 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote: Hello Jennifer, I would like to share only with a specific user but when I use the meth 3 with the email address into last section, my history is not shared. I need to publish AND share with a mail , in order to see my history in shared data . It seems to be a bug ? Thanks in advance, Sarah Jennifer Jackson a écrit : Hello Sarah, On the history menu's share or publish page, there are three ways to share, one section per method: 1 - generate a share link. this can be share with one or more users, account holders or not 2 - publish the history - this places it in the list of all Shared Histories where everyone using that server can see it 3 - share with just a user by entering in their email address into last section Hopefully this helps, Jen Galaxy team On 6/3/13 6:58 AM, Sarah Maman wrote: Hello, My question is about sharing histories with a specific user. The share is not effective for a specific one but for all users logged in our local instance. Could you please help me ? Thank you in advance, Sarah -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ 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/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ 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/ attachment: tmp.png___ 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] Unable to use FASTQ tool on Main over several days
Hi, could you be more specific. Name one or two specific tools that are not working. Also, when does the error occur, after submitting the job or before loading the tool? -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, May 24, 2013 at 10:31 AM, Eduardo Fox ofoxo...@gmail.com wrote: Please, I have been unable to use any of the tools under FASTQ Tools for the last 4 days. I keep getting an error message with codes, for instance GURU MEDITATION: #376b73ae417d41f3a7c2088770e13b8f. Is this part of the platform down for some reason? Best wishes and thanks, E. Fox ___ 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] problem uploading txt data
Are the first four lines of your file deliberately whitespace? This will definitely cause problems for file type detection (it is not a valid TSV file as is). -- James Taylor, Assistant Professor, Biology/CS, Emory University On Sun, May 12, 2013 at 10:52 AM, Chunyu Liu liuc...@gmail.com wrote: hi, I had an odd problem today, seems not a problem before: I am trying to upload a simple tab-delimited text file into galaxy, but it kept telling me: empty format: txt, database: hg19 The uploaded binary file contains inappropriate content Also, showed filesize as 0 bytes. I tried Unix format, DOS format. It is a very small data, only 348 bytes. 4 rows, as attached. What is WRONG? Thanks! Chunyu ___ 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] ImportError: Unable to run arch-specific checks
Since you have isolated the problem to running on ceph, I'm not sure there is much help we can offer. My understanding is that the posix filesystem part of ceph (as opposed to the object store) is still in development and could have bugs. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Apr 25, 2013 at 7:35 AM, Shun Liang shun.li...@cruk.cam.ac.uk wrote: Dear Galaxy Developers, Here is some more information about the environment I am trying to install Galaxy on. I am using Ubuntu 12.10 on armv7l architecture. I encountered the Import Error problem when I was running Galaxy on the Ceph file system. This is how the Ceph file system is mounted on the machine: galaxy@arm01-25:~$ mount | grep ceph 10.20.232.4,10.20.232.8,10.20.232.12,10.20.232.16,10.20.232.20:/ on /mnt/ceph type ceph (name=admin,key=client.admin) I have later tried to install and run Galaxy on the same machine but on a different directory which is within the EXT4 file system mounted on the hard drive. Galaxy runs on that directory without any problem. I hope this gives some clue to you to solve the problem. Many thanks, Shun From: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] on behalf of Shun Liang [shun.li...@cruk.cam.ac.uk] Sent: 24 April 2013 14:56 To: galaxy-u...@bx.psu.edu Subject: [galaxy-user] ImportError: Unable to run arch-specific checks Dear Galaxy Developers, I am trying to run Galaxy on ARM architecture. I am able to scramble the eggs locally. However, I am unable to run Galaxy on my machine as run.sh gives an error after some initialization steps: galaxy@arm01-48:/mnt/ceph/galaxy/galaxy-dist$ ./run.sh Initializing datatypes_conf.xml from datatypes_conf.xml.sample Initializing external_service_types_conf.xml from external_service_types_conf.xml.sample Initializing migrated_tools_conf.xml from migrated_tools_conf.xml.sample Initializing reports_wsgi.ini from reports_wsgi.ini.sample Initializing shed_tool_conf.xml from shed_tool_conf.xml.sample Initializing tool_conf.xml from tool_conf.xml.sample Initializing shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample Initializing tool_data_table_conf.xml from tool_data_table_conf.xml.sample Initializing tool_sheds_conf.xml from tool_sheds_conf.xml.sample Initializing data_manager_conf.xml from data_manager_conf.xml.sample Initializing shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample Initializing openid_conf.xml from openid_conf.xml.sample Initializing tool-data/shared/ncbi/builds.txt from builds.txt.sample Initializing tool-data/shared/ensembl/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/publicbuilds.txt from publicbuilds.txt.sample Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample Initializing tool-data/add_scores.loc from add_scores.loc.sample Initializing tool-data/alignseq.loc from alignseq.loc.sample Initializing tool-data/all_fasta.loc from all_fasta.loc.sample Initializing tool-data/annotation_profiler_options.xml from annotation_profiler_options.xml.sample Initializing tool-data/annotation_profiler_valid_builds.txt from annotation_profiler_valid_builds.txt.sample Initializing tool-data/bfast_indexes.loc from bfast_indexes.loc.sample Initializing tool-data/binned_scores.loc from binned_scores.loc.sample Initializing tool-data/blastdb.loc from blastdb.loc.sample Initializing tool-data/blastdb_p.loc from blastdb_p.loc.sample Initializing tool-data/bowtie2_indices.loc from bowtie2_indices.loc.sample Initializing tool-data/ccat_configurations.loc from ccat_configurations.loc.sample Initializing tool-data/codingSnps.loc from codingSnps.loc.sample Initializing tool-data/encode_datasets.loc from encode_datasets.loc.sample Initializing tool-data/faseq.loc from faseq.loc.sample Initializing tool-data/funDo.loc from funDo.loc.sample Initializing tool-data/gatk_annotations.txt from gatk_annotations.txt.sample Initializing tool-data/gatk_sorted_picard_index.loc from gatk_sorted_picard_index.loc.sample Initializing tool-data/liftOver.loc from liftOver.loc.sample Initializing tool-data/maf_index.loc from maf_index.loc.sample Initializing tool-data/maf_pairwise.loc from maf_pairwise.loc.sample Initializing tool-data/microbial_data.loc from microbial_data.loc.sample Initializing tool-data/mosaik_index.loc from mosaik_index.loc.sample Initializing tool-data/ngs_sim_fasta.loc from ngs_sim_fasta.loc.sample Initializing tool-data/perm_base_index.loc from perm_base_index.loc.sample Initializing tool-data/perm_color_index.loc from perm_color_index.loc.sample Initializing tool-data/phastOdds.loc from phastOdds.loc.sample Initializing tool-data/picard_index.loc
Re: [galaxy-user] glitch in .wig visualization in trackster?
Hi Michael, sorry it took a while but we've figured out the root cause of this issue and will be deploying a fix shortly. Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Mar 22, 2013 at 4:20 PM, Michael Axtell mj...@psu.edu wrote: Hi everyone. I'm having an issue with a wiggle file. I'm using Trackster on the public-main instance of Galaxy, with a custom genome build. My wiggle file fails to be shown. When added to the visualization using the 'add tracks' dialog, I see the usual hatched gray lines with the message processing data, this may take some time. But then after a few minutes the track just goes to hatched gray lines with no messages, and the intensities are never displayed, nor is any error message (or any message at all, just stuck with the hatched gray lines). The .wig file has been extensively validated to conform to UCSC spec. In addition, the same file displays data just fine when loaded into Broad's IGV. So I'm confident it is formatted correctly. The custom genome is not a great one .. scaffolds not pseudomolecules, and there are many thousands of scaffolds in the assembly (scaffold N50 is 1.3M at scaffold 111 out of ~2,100 scaffolds; total length ~480M). If I slice my problematic wiggle file to only keep sub-sections of the data, sometimes it works. I tested a number of such sub-slices, and some worked and some didn't, as below (the numbers refer to scaffold numbers in my custom genome): 1-50 : worked 1-100 : worked 1-200 : worked 1-300 : failed 1-400 : failed 1-500 : failed 100-250 : worked 200-300 : worked 300-400 : worked 500-600 : worked From the above, it seems possible the error is that Trackster just doesn't like wig files that exceed a certain number of chromosomes/scaffolds? Or some sort of data overload issue? Some other information: This custom genome build works fine on trackster to visualize several other datasets in gff, gff3, and bed format. In addition, the problem wiggle file is not so large .. the full file is only ~48M. It is a fixedStep file with span and step both equal to 100, and the data are relatively sparse. If anyone has a clue, let me know .. thanks! -- Michael J. Axtell, Ph.D. Associate Professor Dept. of Biology Penn State University http://axtell-lab-psu.weebly.com ___ 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] How to connect to private instance of galaxy from another computer
Yes, you will need to edit universe_wsgi.ini and change the entry for host = (exactly what you need to do is documented in that file). -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Mar 13, 2013 at 3:40 AM, Michael Milevskiy m.milevs...@uq.edu.auwrote: Dear Galaxy, ** ** I am running an instance of Galaxy on my computer through localhost:8080/ and am wondering if I can use this on my laptop? I basically don’t want to be at the computer at the same time and don’t want to upload files to and from my laptop but just use the galaxy interface to work with my data. ** ** Regards, ** ** Michael J.G. Milevskiy | BBiomedSc PhD Student School of Chemical and Molecular Biosciences Prof. Melissa Brown - Group Leader Molecular Biosciences Building 76-432 The University of Queensland | (07) 3365 4635 ** ** ___ 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 ARM Architecture
You are definitely in uncharted territory with an arm server. Can you try building just bx-python itself and let us know what the errors are? -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Feb 21, 2013 at 11:03 AM, Shun Liang shun.li...@cruk.cam.ac.uk wrote: Hi, I am trying to install Galaxy on an ARMV7 architecture Linux server. I ran run.sh and failed because some of the python eggs could not be fetched. I then have a look at http://eggs.galaxyproject.org/; and I have realized there aren't any armv7 builds for those eggs. I then decided to build (or scramble) the eggs on my own. I ran scripts/scramble.py and this also failed with the following message (after building a lot of things): scramble(): Copied egg to: /nfs/users/galaxy_dist/eggs/twill-0.9-py2.7.egg Traceback (most recent call last): File scripts/scramble.py, line 26, in module eggs = c.scramble() File /nfs/users/galaxy_dist/lib/galaxy/eggs/scramble.py, line 242, in scramble raise last_exc # only 1 failure out of the crate, be more informative galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for bx_python 0.7.1 May I ask what may cause this problem? Have I done anything wrong? Or, is it even possible to install Galaxy on ARM architecture Linux? Many thanks, Shun ___ 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] Error using Trackster
What is the type of the file from GEO? Any additional information you provide will help debug this. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Feb 1, 2013 at 1:53 PM, Kilaru, Varun vkil...@emory.edu wrote: 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). ___ 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-dev] Workflows
Neil, .../api/workflows is not a path in the galaxy directory, but a URL that you should access over HTTP. For example, if you login to Galaxy Test, and then access https://test.g2.bx.psu.edu/api/workflows you will get a json dict of all of your workflows, including the workflow id that you are looking for. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 15, 2013 at 8:52 PM, neil.burd...@csiro.au wrote: Hi Sorry if these questions are obvious but I just don’t know how to find the answers. I’m trying to get one of the API examples to work in http://wiki.galaxyproject.org/Learn/API/Examples . I’ve got my API key but how do I get/find the workflow id (f2db41e1fa331b3e in the examples). I’ve created workflow but don’t know how to access this key. Also in the first example it states galaxy_url/api/workflows However I don’t have the “api/workflows” directory structure in my galaxy-dist, do I need to create this? Thanks Neil ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ 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 dataset listing
You are probably seeing the mtDNA re-sequencing datasets associated with this paper: http://genomebiology.com/2011/12/6/R59 -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Jan 4, 2013 at 10:46 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Hello, It is good to see there are some testing dataset in fastq format from galaxy s3. Is there any brief information about the test data? For example, RNAseq or Chipseq, etc? Many thanks, Kathryn ___ 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 CloudMan - Nodes can't make their own qsub calls?
You probably need to sudo to sgeadmin (cloudman guys correct me if you have this setup differently). I don't see any reason not to make worker nodes submit hosts by default in a future cloudman release. -- jt On Thu, Sep 13, 2012 at 4:17 PM, greg margeem...@gmail.com wrote: As a follow up I found a command that should add the new nodes as submit hosts and I tried to run it but I got this error: $ qconf -as ip-10-28-164-178.ec2.internal denied: ubuntu must be manager for this operation What does it mean by manager? How would I run this command? I guess my preference is for Cloudman to do this automatically though so I'll be distributing this program to 3rd party users using the built-in cloudman sharing. I can't rightly ask users to be running qconf. Thanks again, Greg On Thu, Sep 13, 2012 at 3:59 PM, greg margeem...@gmail.com wrote: Hi guys, I created a new Galaxy instance web launcher (https://biocloudcentral.herokuapp.com/launch) and then I ssh'd into the master node. I'm trying to run a Perl script that makes several qsub calls to other perl scripts. Now the catch is that one of those perl scripts makes its own qsub calls. And I'm getting this error when it tries to do that: Unable to run job: denied: host ip-10-29-176-111.ec2.internal is no submit host. Somehow this works fine on other clusters I've run this code on. Any idea what could be going on? Do I need to make all of the nodes submit hosts? Thanks a bunch! -Greg ___ 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] [Genome] Problems with MAF blocks from Galaxy
Excerpts from ele.ga...@tiscali.it's message of Wed Jan 12 15:19:36 + 2011: I have a problem with MAF blocks using Galaxy. Hi Elena, I'm copying the galaxy-user list since this is a Galaxy related question. 1) the starting position of the MAF block extracted from Galaxy is shifted of one position downstream; If you enter a region into the position box in the genome browser, it will interpret it as one-based. However, when working with bed files in Galaxy (and the genome browser) the intervals are zero-based. This is likely the problem. 2) the number of species displayed is not 28 in both Maf (from Galaxy) and Genome Browser. This is entirely expected. If the alignment procedure does not identify putatively orthologous sequence in the other species, no sequence will be shown in the MAF output for that species. There are several reasons this could happen, including: no significant pairwise local alignment found by lastz, or a signifigant alignment found, but eliminated by the chaining/netting procedure. 3) the alignment seems to be different (for example, species that have aligned sequences in the Genome Browser, are not in the MAF block retrieve from Galaxy). Can you point out an example of this? In particular, are you sure you are using the same original alignments in Galaxy and the Genome Browser? Thanks, James -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
