galaxy-user June 2011

galaxy-user@lists.galaxyproject.org

81 participants
79 discussions

June 23, 2011 Galaxy Development News Brief
by Jennifer Jackson 24 Jun '11

24 Jun '11

June 23, 2011 Galaxy Development News Brief http://galaxyproject.org/wiki/Features/DevNewsBrief/2011_06_23 ---- == Source Distribution == http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 720455407d1c ---- == GCC 2011 == We had ~ 140 attendees at the 2011 Galaxy Community Conference, held May 25-26, in the Netherlands! * Please see [[http://wiki.g2.bx.psu.edu/GCC2011]] for links to slides and to videos of the talks. * Feedback has been very positive with 100% of respondents saying they would recommend future Galaxy meetings to others. * Many thanks to the Netherlands Bioinformatics Centre (NBIC) for co-sponsoring and hosting this event. http://www.nbic.nl Note: "#NNN" notation refers to fixed/resolved bitbucket issues at http://galaxyproject.org/issues == What's New == === Python Support === Python 2.7 is now supported in beta. Functional tests with 2.7 are a pass. This also includes an upgrade to Numpy 1.6.0. === Cloudman Admin Functions === Galaxy's Cloudman now has an admin interface that allows you to gain insight and control many of the services underlying your cloud instance. Namely, you can: * Add Galaxy admin users through the web interface. * Update Galaxy source (even from a custom repository). * View logs and configurations for individual services. ** e.g., Galaxy, Postgres, SGE, as well as control some of the system-level services To get to the admin interface, just click the 'Admin' link at the top right corner on the main Cloudman UI. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… === New Galaxy Tool Shed === Rather than rigidly structured tool archives, the foundational component of Galaxy's Tool Shed is now an hg (Mercurial) repository. * The Test/Sandbox Tool Shed available at http://testtoolshed.g2.bx.psu.edu * The Production Tool Shed is available at http://toolshed.g2.bx.psu.edu A new select list was added to the upload form in Galaxy's Tool Shed with the following label: "Remove files in the repository (relative to the upload point) that are not in the uploaded archive?" The selection pertains only to uploaded tar archives, not to single file uploads. If 'Yes' is selected, files that exist in the repository (relative to the selected upload point) but that are not in the uploaded archive will be removed from the repository. Otherwise, all existing repository files will remain and the uploaded archive will be added to the repository. Resolves #585 == Updated & Improved == === Tools === * RNA-seq tools: ** Rename and reorder Cuffdiff outputs for clarity. ** Make Cuffcompare wrapper compatible with v1.0.3. * 2bit/twobit datatypes now supported. (thanks Peter van Heusden!) * New tools for FASTA de(interlacing) added. Resolves #447 === Histories === * Add the download/save icon to datasets in an error state, but that contain data. Fixes #207 and #583 * Disk space usage accounting: ** Users can see how much disk a history is consuming. ** Disk used is also a column on the history grid. ** Users can also forcibly purge a dataset from their history. * Admin notes: ** New script (scripts/set_dataset_sizes.py) which will set the value of the new total_size column on the dataset table (includes the contents of the extra_files_path and metadata files). ** The ability for users to purge their own data is conditional on a config variable. Due to limitations in the grid framework, the button can't be removed from the history grid, but clicking it just does the same thing as delete but adds a message explaining that the purge operation wasn't performed. ** For users who were pulling from galaxy-central and that already upgraded to database version 78 prior to this distribution, the following SQL query should be run to set the default value of the 'HistoryDatasetAssociation' purged column: UPDATE history_dataset_association SET purged=false WHERE purged IS NULL === Trackster === * Can run filters on entire dataset. * When adding tracks to Trackster, add them in the order that they appear in the dataset listing. * Use error padding only when needed by placing error messages in div above tiles rather than in tiles. * Add bookmarking to Trackster. Also group Trackster options into a single menu button. * Add trackster_conf tag to tool definition; this tag indicates that tool is compatible with trackster. * Enable importing of visualizations via a shallow copy. === Workflows === * Include tool annotation and tags when cloning workflows. * The workflow editor is now aware of the format_source tag, and updates the output datatype of tools using it accordingly. Patch from Jim Johnson enhancing format="input" handling in workflows. Resolves #582 === Data Libraries === * Library datasets can now be job inputs. This is needed to be able to use the deferred job runner and transfer manager with set_metadata_externally = True. * Fix for importing library datasets into a new named history. Library datasets will no longer be imported into both the current history and the new named history ( only the latter ) in this scenario. * Determining if an accessible dataset exists somewhere in the data library hierarchy now works all the time. It used to work most of the time, but under corner conditions, it would break. * When importing a dataset from a history into a data library, the dataset permissions are now correctly applied to the library dataset. The DATASET_MANAGE_PERMISSIONS permission is a spoecial case in that if it exists on the dataset, the LIBRARY_MANAGE permission must be applied to the library dataset. * Fix for message display and db flushing when importing a library dataset into a history. * No longer render the folder pop-up menu option for selecting a library dataset to import into histories if the folder does not contain any accessible library datasets. === Source === * Move duplicate data type checker methods from sniff and upload into a new ~/datatypes/checkers.py. * No longer allow Datasets to have DatasetPermissions set such that no roles are associated with the DATASET_MANAGE_PERMISSION. Include the automatic creation of a new DatasetPermission for an hda where the DATASET_MANAGE_PERMISSION permission is associated with the hda.history.user's private role if the hda has no roles associated with the DATASET_MANAGE_PERMISSION permission. The creation of the DatasetPermission occurs when the user clicks the pencil icon for the hda. * SMTP Authentication support for all places where Galaxy sends mail. Use STARTTLS where available, too. Fixes #277 === Bug Fixes === * Fix solid2fastq tool to correctly handle cases when csfasta and QUAL filed are out of sync. Fixes #406 * Applied patch from Peter Cock for 'Cut' tool to ignore commented lines. Resolves #534 * Fix to sam2interval. The bug was causing sam2interval to successfully parse unmapped sam entries, which have no valid coordinate. * Enable Cufflinks to work when setting metadata externally. * Remove obsolete test values for Cufflinks and Cuffdiff tests. * In Trackster, have child track inherit mode from parent track. * Trackster bug fixes when (a) running tools in a shared visualization and (b) when drawing a track created by a tool. * Enable tags and annotations to work for new datasets in history. Fixes #550 * Fix bugs in reading and visualizing GFF3 datasets. * Remove unspecified build validators from Cufflinks/compare/diff tools as these cause trouble when running tools on custom genomes. * Disable update check in cuffdiff wrapper. * Unicode fixes and refactoring. * Disable grid controls and content when new content is being fetched. Fixes #272 * Include post-job actions when importing and exporting workflows. Fixes #518 * Improve filtering tool's stdout reporting of lines filtered. Fixes #536 * Show tool search by default. Fixes #575 * Fixes for editing role name, description, and renaming groups. Resolves #539 * Add baseline support for translating special chars to html escape codes for correct html display in the Galaxy Tool Shed. Fixes #564 * Commit versions of tools from the last_gen Tool Shed in order of oldest -> newest in the next-gen tool shed. Fixes #578 * Fix sample tracking to correctly import samples from a csv file. Add the ability to include field values (in addition to field names) when defining sample form rows by importing from a csv file. Fixes #398 ** The csv file must be in the following format: the [:FieldValue] is optional, the named form field will contain the value after the ':' if included. "SampleName,DataLibraryName,FolderName,HistoryName,WorkflowName,Field1Name:Field1Value,Field2Name:Field2Value..." * Change the Galaxy tool shed search feature on the Categories grid to search Repository names and descriptions rather than Category names and descriptions. The ability to search Category names and descriptions has been eliminated. Fixes #480 * Add support for uncompressing a gz or bz2 compressed file upon upload to a galaxy tool shed repository. Fixes #586 * Add the ability to select files for deletion from a tool shed repository using the built-in file browser. Any number of selected files will be deleted. Selecting a folder will delete all of it's contents. Fixes #584 * Required fields for extra sample form data now enforced. Some minor cleanup included. Fixes #301 * Workflow Parameter bug fix for the case when a parameter isn't used in any workflow step, but should still be available for PJAs. * Proper inheritance in model for APIItem. Fixes #527 * Fix broken user create/login links in the FTP upload form. * Set a catchall content-type (application/octet-stream) on metadata file downloads so Safari doesn't consider them to be HTML. * Fix for library upload when there is no current history. * 'fields' is apparently reserved in MySQL 4, fix migration scripts that use it unaliased. (thanks John Eppley!) * Fix the race condition of the upload tool's outputs not being created before the output size check occurs. (thanks Tao Liu!) * Remove hardcoding of universe_wsgi.ini (except for the sample cleanup scripts which, as samples, are expected to be modified by the site anyway). Fixes #358 * Don't provde the output filename to the upload tool if it's outside Galaxy's files_path, since this means we're only linking data and the output paths are not used (and may contain non-shell-safe characters). Fixes #533 * Uploading a compressed library dataset using either the server directory or path paste methods was previously overwriting the input file, which should never happen. Grouped with this change, it is now possible to upload compressed files that remain compressed (by choosing to "link files only"). However, Galaxy does not yet open the compressed file to properly set metadata on its contents. * Cope with white space at start of command after processing template. Fixes #159 * Support optional integer/float arguments. Resolves #403 * Copying datasets now keeps item order. * Hidden parameters no longer take up space in tool form. Fixes #397 * Sniffers are now properly loaded again from datatypes.conf.xml. === About Galaxy === The Galaxy team is a part of BX at Penn State and the Biology and Mathematics and Computer Science departments at Emory University. http://www.psu.edu http://www.bx.psu.edu http://www.emory.edu http://www.biology.emory.edu http://www.mathcs.emory.edu Galaxy is supported in part by NSF, NHGRI, the Huck Institutes of the Life Sciences, The Institute for CyberScience at Penn State, and Emory University. http://www.emory.edu http://www.huck.psu.edu http://www.nsf.gov http://www.genome.gov http://www.ics.psu.edu Galaxy Team http://galaxyproject.org/wiki/GalaxyTeam Galaxy Home http://galaxyproject.org Use Galaxy! http://usegalaxy.org Join us at Twitter! #usegalaxy http://twitter.com/#!/search/galaxyproject -- Want to learn more or have questions? * Visit our wiki: http://galaxyproject.org/wiki * View our Screencasts: http://usegalaxy.org/screencast * Learn from our Tutorials and Examples: http://usegalaxy.org/page/list_published * Subscribe to or email one of our mailing lists: http://lists.bx.psu.edu Subscribe, view archives, join the community! mailto:galaxy-user@bx.psu.edu Using Galaxy: science, data, and tools mailto:galaxy-dev@bx.psu.edu Galaxy Developers: installation, programming, and technical mailto:galaxy-bugs@bx.psu.edu Bug Reports: email us or even better, click the UI's "green bug" -- Thanks for using Galaxy!!

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Re: [galaxy-user] newbies
by Jennifer Jackson 22 Jun '11

22 Jun '11

Hello Curtis, Please see under "Shared Data" in the public Galaxy for examples that cover a range of analysis. For RNA-seq, this tutorial will likely be helpful (under "Shared Data -> Published Pages -> Galaxy RNA-seq Analysis Exercise"): http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Thanks! Jen Galaxy team On 6/22/11 12:48 PM, Robert Curtis Hendrickson wrote: > Jen, > > Are there any pages that give standard workflows for RNAseq, specifically analysis of alternate splicing? > I'm not finding any examples, and it would be quite helpful. > > Regards, > Curtis > > Research Associate > Center for Clinical and Translational Science > University of Alabama at Birmingham -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/

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GenBank Submission - How to Generate Fasta (not fastq) files
by John David Osborne 22 Jun '11

22 Jun '11

I still haven't found an easy solution to this problem and I am afraid I'm going to have to write one my own - which makes little sense as I bet this has been solved thousands of times! Can anybody point me to a script/software to convert a samtools pileup file into a fasta consensus file? It would be nice to set coverage thresholds, etc... but I'll take anything I can work with. The best google could do for me was this: http://biostar.stackexchange.com/questions/1389/how-to-generate-a-consensus… Not that helpful, -John P.S. If there is a better way of doing this (something other than samtools) I'm all ears.

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Extract Genomic DNA Problem
by Stephen Taylor 22 Jun '11

22 Jun '11

Hi, I was trying to extract FASTA sequences using the following tab separated data for Chicken on the Galaxy Main server: chr5 47258168 47259240 chr18 1938527 1939965 chr2 101973625 101974007 chr4 75653898 75674045 chr19 4258837 4263299 chr4 39330049 39372715 chr4 9606881 9610083 chr15 7264937 7265599 chr21 6659189 6667015 chr2 351239 352821 I got the following galaxy output: ==================================== 7: Extract Genomic DNA on data 6 empty format: fasta, database: galGal3 Info: 10 warnings, 1st is: Unable to fetch the sequence from '47258168' to '1072' for build 'galGal3'. Skipped 10 invalid lines, 1st is #1, "chr5 47258168 47259240" Any ideas what I am doing wrong? Thanks, Steve

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Configuring Galaxy Server
by gaurav thareja 22 Jun '11

22 Jun '11

Hi All, Thank you for last reply and links about galaxy structure. The links were helpful. But still I am uncertain about many files and their uses. To previous question, I will require further help on following issues: 1. Where all users information is stored in file structure so that i can add custom users for my galaxy server? 2. Is it possible to customize left purple panel? My real aim is to customize the galaxy browser instance as per my needs and use for internal development, which i think is possible?. So, if you guys have any development documents which can be shared to provide further insights about file and directory structure will be really helpful. Regards Gaurav Thareja

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aspera install on cloud install
by Joseph Hargitai 22 Jun '11

22 Jun '11

Hi, anyone tried to install an aspera server for a galaxy cloud instance? The goal would be to feed some local data faster to the instance. best, joe

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Re: [galaxy-user] cuffcompare error in galaxy (Carlos Javier Borroto)
by 吳正華 22 Jun '11

22 Jun '11

Hi Carlos: After I replaced cuffcompare_wrapper.py & cuffcompare_wrapper.xml with code provided by Jeremy, now I can execute cuffcompare on my local galaxy. You can check following link: https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389 hope this helps. Best John Wu 1. Re: cuffcompare error in galaxy (Carlos Javier Borroto) ---------------------------------------------------------------------- Message: 1 Date: Mon, 20 Jun 2011 14:01:15 -0400 From: Carlos Javier Borroto <carlos.borroto(a)gmail.com> To: ??? <johnwu(a)ibms.sinica.edu.tw> Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] cuffcompare error in galaxy Message-ID: <BANLkTi=jtR88L_X5-SZpgnU4=oVqao=epQ(a)mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi John, I'm finding the exact same error while going through Jeremy's tutorial in a local instance of galaxy-dist. I was wonder if you found the solution. I see cuffcompare wrapper outputs these files: cc_output.combined.gtf cc_output.input1.refmap cc_output.input1.tmap cc_output.loci cc_output.stats cc_output.tracking and in the logs I'm seing this: galaxy.jobs DEBUG 2011-06-20 13:34:49,902 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output to /home/galaxy/galaxy_dist/database/files/000/dataset_68.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,917 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.tmap to /home/galaxy/galaxy_dist/database/files/000/dataset_69.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,932 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.refmap to /home/galaxy/galaxy_dist/database/files/000/dataset_70.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,948 finish(): Moved /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output.combine d.gtf to /home/galaxy/galaxy_dist/database/files/000/dataset_71.dat as directed by from_work_dir Only cc_output.combined.gtf is correctly being moved, the rest aren't being call by the correct filenames. Thanks, -- Carlos Borroto Baltimore, MD 2011/6/10 ??? <johnwu(a)ibms.sinica.edu.tw>: > Dear galaxy team: > > > > I was testing local galaxy of our lab by analyzing RNA-seq data in > Jeremy?s RNA-seq tutorial. > > > > http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise > > > > I could run TopHat, cufflinks, and cuffdiff and got results correctly, > > but when I executed cuffcompare through galaxy, the following error > occurred: > > > > Tool execution generated the following error message: > > Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' > > The tool produced the following additional output: > > cuffcompare v1.0.3 (2403) > > cuffcompare -o cc_output? -s > /home/galaxy/data/galaxy_data/sam_index/hg19.fasta ./input1 > > > > and error messages in log file (galaxy.log) are: > > > > galaxy.jobs INFO 2011-06-10 14:02:15,161 job 130 dispatched > > galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:15,466 executing: > python > /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py > ????????????????????????????-s ????????????????????--ref_file="None" > ????????????????--dbkey=hg19 > --index_dir=/home/galaxy/software/galaxy_dist/tool-data > /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat > > > > galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:27,834 execution finished: > python > /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py > -s???????????????????? --ref_file="None" > ??--dbkey=hg19 > --index_dir=/home/galaxy/software/galaxy_dist/tool-data > /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat > > > > galaxy.jobs DEBUG 2011-06-10 14:02:27,943 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/c > c_output to > /home/galaxy/software/galaxy_dist/database/files/000/dataset_399.dat > as directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:27,971 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/i > nput1.tmap to > /home/galaxy/software/galaxy_dist/database/files/000/dataset_400.dat > as directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:27,999 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/i > nput1.refmap to > /home/galaxy/software/galaxy_dist/database/files/000/dataset_401.dat > as directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:28,027 finish(): Moved > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/c > c_output.combined.gtf to > /home/galaxy/software/galaxy_dist/database/files/000/dataset_402.dat > as directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:28,174 > > > > job 130 ended > > > > > > I?ve tried to manually execute cuffcompare to analyze dataset_398.dat > (which is the output of tophat) and I could get correct cuffcompare output. > > > > $ cuffcompare -o cc_output? -s > /home/galaxy/data/galaxy_data/sam_index/hg19.fasta dataset_398.dat > > > > It seems that the coffcompare_wrapper might have something to do with > this error? > > > > Thanks in advance for your help! > > > > > > Best > > John Wu _______________________________________________ galaxy-user mailing list galaxy-user(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user End of galaxy-user Digest, Vol 60, Issue 21 *******************************************

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Displaying MACS Peaks at UCSC
by Steven Okino 21 Jun '11

21 Jun '11

Hello, I am new to Galaxy and am trying to analyze some ChIP-Seq data. I groomed illumina FASTQ data and used Bowtie to map it to hg18. I then used MACS to call ChIP-Seq peaks; over 13,000 were identified. Analysis of individual peaks shows good consistency with ENCODE data sets on UCSC, so I know the ChIP-Seq worked. However, when I try to display the results at UCSC main I get the following error message on the UCSC browser: What am I doing wrong? Please advise. Thank you, Steven Okino

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Re: [galaxy-user] cuffcompare error in galaxy
by Carlos Javier Borroto 20 Jun '11

20 Jun '11

Hi John, I'm finding the exact same error while going through Jeremy's tutorial in a local instance of galaxy-dist. I was wonder if you found the solution. I see cuffcompare wrapper outputs these files: cc_output.combined.gtf cc_output.input1.refmap cc_output.input1.tmap cc_output.loci cc_output.stats cc_output.tracking and in the logs I'm seing this: galaxy.jobs DEBUG 2011-06-20 13:34:49,902 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output to /home/galaxy/galaxy_dist/database/files/000/dataset_68.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,917 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.tmap to /home/galaxy/galaxy_dist/database/files/000/dataset_69.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,932 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.refmap to /home/galaxy/galaxy_dist/database/files/000/dataset_70.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,948 finish(): Moved /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output.combined.gtf to /home/galaxy/galaxy_dist/database/files/000/dataset_71.dat as directed by from_work_dir Only cc_output.combined.gtf is correctly being moved, the rest aren't being call by the correct filenames. Thanks, -- Carlos Borroto Baltimore, MD 2011/6/10 吳正華 <johnwu(a)ibms.sinica.edu.tw>: > Dear galaxy team: > > > > I was testing local galaxy of our lab by analyzing RNA-seq data in Jeremy’s > RNA-seq tutorial. > > > > http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise > > > > I could run TopHat, cufflinks, and cuffdiff and got results correctly, > > but when I executed cuffcompare through galaxy, the following error > occurred: > > > > Tool execution generated the following error message: > > Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' > > The tool produced the following additional output: > > cuffcompare v1.0.3 (2403) > > cuffcompare -o cc_output -s > /home/galaxy/data/galaxy_data/sam_index/hg19.fasta ./input1 > > > > and error messages in log file (galaxy.log) are: > > > > galaxy.jobs INFO 2011-06-10 14:02:15,161 job 130 dispatched > > galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:15,466 executing: python > /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py > -s --ref_file="None" > --dbkey=hg19 > --index_dir=/home/galaxy/software/galaxy_dist/tool-data > /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat > > > > galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:27,834 execution finished: > python > /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py > -s --ref_file="None" > --dbkey=hg19 > --index_dir=/home/galaxy/software/galaxy_dist/tool-data > /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat > > > > galaxy.jobs DEBUG 2011-06-10 14:02:27,943 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_output > to /home/galaxy/software/galaxy_dist/database/files/000/dataset_399.dat as > directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:27,971 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.tmap > to /home/galaxy/software/galaxy_dist/database/files/000/dataset_400.dat as > directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:27,999 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.refmap > to /home/galaxy/software/galaxy_dist/database/files/000/dataset_401.dat as > directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:28,027 finish(): Moved > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_output.combined.gtf > to /home/galaxy/software/galaxy_dist/database/files/000/dataset_402.dat as > directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:28,174 > > > > job 130 ended > > > > > > I’ve tried to manually execute cuffcompare to analyze dataset_398.dat (which > is the output of tophat) and I could get correct cuffcompare output. > > > > $ cuffcompare -o cc_output -s > /home/galaxy/data/galaxy_data/sam_index/hg19.fasta dataset_398.dat > > > > It seems that the coffcompare_wrapper might have something to do with this > error… > > > > Thanks in advance for your help! > > > > > > Best > > John Wu > > > > > > > > > > ___________________________________________________________ > 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/ >

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Fwd: uploading error
by Assaf Gordon 20 Jun '11

20 Jun '11

Hello Rubina, I've forwarding your email to the galaxy public mailing list, where the Galaxy team can further help you with your upload. Generally speaking, uploading big FASTQ using the web interface is prone to errors. The Galaxy team added a new upload method, using FTP, which is more reliable. Detailed instructions are available here: https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP Regards, -gordon -------- Original Message -------- Subject: uploading error Date: Mon, 20 Jun 2011 18:10:57 +0000 From: <rdalvi01(a)students.poly.edu> To: <gordon(a)cshl.edu> Hi, My name is Rubina. I am using Galaxy to convert fastq files to fasta format. I tried to upload fastq file on the following link. http://main.g2.bx.psu.edu/ However I am not able to upload. Its been a week, but it still shows uploading. Thank You, Rubina

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galaxy-user June 2011