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Problem upgrading bx-python to fix trackster error.
by William Holtz 16 Apr '14

16 Apr '14

I have a set of galaxy generated bam and bigwig files containing over 600 contigs. When I attempt to view any of these files with trackster (on a local server running current galaxy-dist) I get the following in my log file: galaxy.webapps.galaxy.api.datasets ERROR 2014-04-09 17:41:16,063 Error in dataset API at listing contents: 'BinaryFileReader' object has no attribute 'read_bits64': 'BinaryFileReader' object has no attribute 'read_bits64' Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 44, in show is_true( kwd.get( 'retry', False ) ) ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 106, in _converted_datasets_state if not data_provider.has_data( chrom ): File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 1078, in has_data all_dat = bbi.query( chrom, 0, 2147483647, 1 ) or \ File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) File "bbi_file.pyx", line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' Two people have previously reported similar errors to this list. I don't know how to reply to messages that predate me joining the list, so here are links to the threads: http://dev.list.galaxyproject.org/read-bits64-error-when-loading-large-geno… http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-… Following the suggestion of Jeremy Goecks in one of those old threads, I checked my bx-python version. The directory name bx-python is installed in indicates that I have version 0.7.1. Version 0.7.1 is from 2011 and pre-dates the the bug Jeremy mentioned (https://bitbucket.org/james_taylor/bx-python/commits/24893a84ce13a18815e300…) Additionally, I ran: strings ./galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bpt_file.so | grep read_bits64 and found a match, thus confirming the installed version pre-dates the bug fix, as all references to read_bits64 were removed in that commit. Additionally I cloned and compiled the current version of bx-python and found that the above command did not find any matches. The offending installation of bx-python is part of the base installation of galaxy and not an item I added from the toolshed. I am unsure of how to go about replacing this egg with the newer version of bx-python. If someone can update the bx-python egg on http://eggs.g2.bx.psu.edu/ or give me instructions on how to replace my copy of the egg, I would greatly appreciate it! Additionally, I found that all three of the versions of bx-python in the galaxy-main toolshed still contain this bug. Of the three versions of bx-python int the galaxy-test toolshed, only 3:5457e32b427c (2013-12-14) contains the bug fix. Thank you in advance for your assistance! -Will

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Test ToolShed functional test failures
by Peter Cock 16 Apr '14

16 Apr '14

Hi guys, Multiple repositories are showing failing tests, e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr Tests that failed Tool id: blastxml_to_top_descr Tool version: blastxml_to_top_descr Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterj…) Stderr: Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool self.do_it( td ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 27, in do_it test_history = galaxy_interactor.new_history() File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 405, in new_history self.twill_test_case.new_history() File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 469, in new_history self.check_history_for_string('Your history is empty') File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 310, in check_history_for_string raise AssertionError( errmsg ) AssertionError: no match to 'Your' page content written to '/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmp7xhGGg/twilltestcase-eBqu05.html' This looks like a framework regression... Peter

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Re: [galaxy-dev] Can a tool upload a .loc file that is then ... RENAME: custom galaxy tool python modules
by Dooley, Damion 16 Apr '14

16 Apr '14

Sorry about miss-named message. I found a solution which makes me realize this might have been a bit of a python newbie 'duh' issue. For those who might need something similar, solution is to add a .pth file to site-packages folder of python version that galaxy is running under, e.g. /usr/lib/python2.6/site-packages/galaxy-custom-modules.pth contains 1 line of text: /usr/local/galaxy/shared/python2.6_galaxy_custom_modules And now if your code imports say: HTMLReportModule = __import__('custom_templates.html_report') It will look in the python2.6_galaxy_custom_modules folder as well as the tool's folder. Now is this the best solution? I haven't seen any folder reserved for custom client python method code within a galaxy install, right? I believe this approach lets any number of updates happen to the tool or to galaxy while preserving the customized code module(s). Thanks for any input, Damion P.s If anyone wants an extra helpful detail on this dynamic replacement of a standard tool module with a custom one - this tip lets one work with any module folder depth "a.b.c.d.my_module". If you skip the "fromlist" part then you have to bother with mentioning b.c.d.my_module expressly. E.g. for the HTMLReport class defined in html_report.py, # See http://stackoverflow.com/questions/769534 HTMLReportModule = __import__('custom_templates.foo.bar.html_report', fromlist=['does not in fact matter what goes here!']) lets one then simply say: htmlManager = HTMLReportModule.HTMLReport(...) > Message: 2 > ... > Subject: Re: [galaxy-dev] Can a tool upload a .loc file that is then ... > Python code in galaxy tools can import all sorts of modules. Is there a way to add an extra path to the sys.path so that I can include some other python modules that way? I.e. in some galaxy python config file? > > I'd like to say in my tool code > > HTMLReportModule = __import__(html_template) > ... > htmlManager = HTMLReportModule.HTMLReport(tagGroup, options, query_stats) > htmlManager.render(out_tabular_file, out_html_file) > > and in this way provide a switch from a standard report template that my galaxy tool has in its folder, to a custom one that a client has fiddled with and is comfortably outside galaxy's codespace. The html_template variable would have 'templates.html_report' for the stock template, but 'custom_templates.html_report' would pull it from wherever was set in the path. Seems like a secure approach. (I don't want to pass the paths via the browser).

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Enabling an HTML report to prime a tool form
by Dooley, Damion 15 Apr '14

15 Apr '14

Hi Galaxians, I've got a nice html report of blast results by query, and tabular subject result listing a handful of columns. It was set up so that checkboxes by each row and a submit button for each subject sent form data to another tool we have. I'd tricked the other tool's form into thinking it had all the right input for a refresh, including the tool_state string, borrowed from a previous view of that tool. It worked great - it automatically submitted and generated a resulting dataset when the html report/form submitted to it - UNTIL ALAS it seems a change in history or session caused the tool form's tool_state string to fail and trigger an error on load (I guess it encodes some stuff that references the history panel?). Looking at http://dev.list.galaxyproject.org/Feature-suggestion-quot-Re-Run-quot-butto… it seemed like there might be a chance to encode a dummy tool_state? So, its a long shot, but is there a bare-bones tool_state code that doesn't care what's in the history for any given galaxy tool? Since this code is entirely in the html report rendering tool itself python doesn't seem to have access to galaxy system code. Regards, Damion P.s. this is what the form html template looks like (borrowed mostly from the tool's html form itself): <form id="tool_form" name="tool_form" action="../../../tool_runner/index" target="galaxy_main" method="post" enctype="application/x-www-form-urlencoded"> <input type="hidden" name="refresh" value="refresh" /> <input type="hidden" name="tool_id" value="bccdcSelectSubset" /> <input type="hidden" name="tool_state" value="800255f96366643436383763656132396561343433 ... 6471002e" /> <input type="hidden" name="input" value="%(dataset_selection_id)s" /> <input type="hidden" name="incl_excl" value="1" /> <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute stuff" /> <input type="hidden" name="select" value="%(select_row)s" /> ... <tr><td><input type="checkbox" name="select" value="2" />gi|158343637|gb|EU057648.1|</td> <td class="numeric">99.55</td> <td class="numeric">442</td> <td class="numeric">2</td> <td class="numeric">0</td> ...</tr> etc. </form>

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how to delete datasets or save space on local galaxy
by Wang, Xiaofei 15 Apr '14

15 Apr '14

Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. [cid:d28891d2-9d20-4688-8e3e-3bf75caa662e] Thank you so much! Best, Xiaofei

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Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7
by Liisa Koski 15 Apr '14

15 Apr '14

Hello, I just updated to Feb.10 and also noticed that Trackster is not working. I too get the blank screen. Could you please tell me how to manually update the vis packed files? I do not know what these are. Thanks in advance, Liisa

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April 14, 2014 Galaxy Distribution News Brief
by Jennifer Jackson 15 Apr '14

15 Apr '14

*April 14, 2013 Galaxy Distribution News Brief* Distribution Summary 2014_04_14 <https://wiki.galaxyproject.org/News/2014_04_14_Galaxy_Distribution> * Highlights:* * Visualization framework updates and Trackster updates * Tool Shed updates to repos, test frameworks, and documentation * Over 100 genomes with updated content on our rsync server * UI Dataset action controls expanded and overall unification of design * API functionality additions and new job control/admin abilities * Administrator, Configuration, Job control, and Egg features and updates * 18 new community contributions added Get Galaxy getgalaxy <http://getgalaxy.org/> *getgalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy>* *galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/>* *bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* *new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update release_2014.04.14 Upgrades * *Review instructions for core build:Getting the Stable Distribution <http://getgalaxy.org/>* * *Review reset for Tool Shed repos:Resetting Metadata For Installed Repositories <http://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories>* Data 1. New and updated reference genomes added toRsych <https://wiki.galaxyproject.org/Admin/UseGalaxyRsync>server that mirrors contents of the public Mainhttp://usegalaxy.org <http://usegalaxy.org/>instance * New/updated genomes: 115 o includes hg38 o note: all available in tool "Extract Genomic DNA" * New bowtie indexes: 60 * New bowtie2 indexes: 115 * New BWA indexes: 54 * New lastz indexes: 54 * New sam indexes: 64 * New picard (srma) indexes: 59 * New liftOver mappings: 163 2. MAF hg19 100waymultiz conservation alignment sourced fromUCSC <http://genome.ucsc.edu/> 3. Replaced: The sam index for hg_g1k_b37 was updated to use "samtools faidx" with version 0.1.18 (original from GATK 1.4 bundle used 0.1.13). The older index lead to some issues with BAM<->SAM conversion using the newer SAMTools version. Visualizations 1. Framework tuninghttps://trello.com/c/kdhJ1Dit 2. /Trackster/: * Sow complete read/feature across tile boundaries, in all tileshttps://trello.com/c/Q03dC1QC * Better handling of deep coverage regions in read trackshttps://trello.com/c/TxxzqWNx Workflows 1. Prep for dataset collections: Refactor out common logic for running workflows across controllershttps://trello.com/c/pdGNjllH UI 1. New/Updated Dataset Action Controls: * Located at the top of the history pane * Ability to select: all, none, or check individual datasets * Actions: Hide, Unhide, Delete, Undelete, Permanently delete (Purge) * https://wiki.galaxyproject.org/Learn/Managing%20Datasets#Searching_Datasets * Additional actions pending review/implementation * https://trello.com/c/8gLGPzxV,https://trello.com/c/mq1m6X5M, 2. When multiple tool versions installed, default to the latest versionhttps://trello.com/c/zRBZ9nvD 3. Better handling when one of many versions of a tool repo is uninstalledhttps://trello.com/c/BmdG2201 4. Unify the places where histories are shown and used: UI view and in core codehttps://trello.com/c/7cN0nmKH 5. Configure workflow menu, improve buttons and stylinghttps://trello.com/c/xFzp3lt6 6. Handle disabled sessionStorage/localStorage more gracefully in the history panehttps://trello.com/c/V2VCxzmx 7. RemoveBaseViewfrom base-mvchttps://trello.com/c/xUV4qvIc 8. Do not serve non-HTML content that may containJavaScriptin such a way that web browsers execute ithttps://trello.com/c/G67ELiMI 9. There are now 2 interfaces to data libraries (the original and new Beta) and feedback is welcomedhttps://trello.com/c/d3muKvqr 10. Wiki page on how to compile the css.https://wiki.galaxyproject.org/Develop/CSShttps://trello.com/c/gLI6hUjN API 1. New functions: * Make histories importable and/or published via the API is now implimented (sharing with individual users a pending feature update)https://trello.com/c/Bcsadi1q * History export/importhttps://trello.com/c/qhu1KdWU * Ability to extract workflow from a history to workflowshttps://trello.com/c/ZTehdMZH 2. Improved history payload and returned error consistencyhttps://trello.com/c/fWC7WgQf 3. Checkftypeattribute (if defined) on test output datasetshttps://trello.com/c/hFFlM4gY 4. Published histories contents now fully accessible (no permissions issue)https://trello.com/c/KME3ZRRY 5. Correct exception formats used in history & HDAhttps://trello.com/c/bS9wY4Ri Core 1. Admin: History view, allow importing purged datasetshttps://trello.com/c/tbhpQdMF 2. Admin: User list, show 'activated' and 'create_time' columnshttps://trello.com/c/C6MhEHWo 3. Admin: Setting user quota at zero is now permitted (noZeroDivisionError <http://moinmo.in/ZeroDivisionError>)https://trello.com/c/38NoBtlL 4. Admin: Admin user now has permissions to copy datasets from any history to a libraryhttps://trello.com/c/Ed91qIUC 5. Admin: Improvements to 'Impersonate User' implementationhttps://trello.com/c/lny2me4u 6. Config: Renametool-data/shared/ucsc/ucsc_build_sites.txttoucsc_build_sites.txt.sample 7. Jobs: Prevent 'unicode' strings being sent to pbs library as hostnamehttps://trello.com/c/NlFXYDta 8. Jobs: Fix Torque CLI runner to recognize complete ('C') state as 'ok'https://trello.com/c/vSO52k17 9. Jobs: Are now cancelled if a running history item is deleted (via API).https://trello.com/c/PDmUdtbw 10. LWR: Several updates including communication via message queue, more plannedhttps://trello.com/c/6DcXqXNt 11. LWR: Introduce and extend along withComputeEnvironment, to eliminate string based path rewritinghttps://trello.com/c/dL0poowc 12. Egg Update: Guppy 0.1.9+https://trello.com/c/zeSnHEav 13. Egg Update: Boto 2.25 to facilitate launching into VPChttps://trello.com/c/QXfJQhlS 14. Egg Addition: PyYAML 3.10 to be used initially withCloudlaunchfor parsingpersistent_data yamlhttps://trello.com/c/JMZkqBtH 15. Lib: package_libpng_1_6_7 deprecated, replaced with package_libpng_1_6_8https://trello.com/c/Wr5U8laVhttps://trello.com/c/65DOL… Pull Requests Merged Thanks to our Galaxy community contributors! 1. 309 - Job module for API (list and inspect jobs). Kyle Ellrott.https://trello.com/c/s2Gk6QlH 2. 312 - Remove unused imports and unused variables. Fix spacing. Nicola Soranzo.https://trello.com/c/iWaf1ak4 3. 316 - Fixing non-string parameter selection for job searches. Kyle Ellrott.https://trello.com/c/ZXZ9lEkN 4. 317 - Web API: safer and cleaner workflow parameter passing. Simone Leo.https://trello.com/c/JaC2EBM8 5. 318 - Adding deleted field to 'to_dict' and search selection of Workflows. Kyle Ellrott.https://trello.com/c/lv9q67nF 6. 315 - Allow jobs to be filtered by tool_id and history_id as well as by state. The tool_id is compared with the like operator. James Johnsonhttps://trello.com/c/dvLvPUmK 7. 322 - Added "ignore lines starting with specific characters" to group tool. Clayton Turner.https://trello.com/c/j6TP6M7m 8. 323 - API methods to access Workflow Usage. Kyle Ellrott.https://trello.com/c/UetzHj64 9. 325 - Useplaceholderinstead ofvaluein html5 - editor.mako. Trevor Wennblom.https://trello.com/c/PIZAXsOS 10. 326 - Specify third-party cookies must not be blocked - repository.py. Trevor Wennblom.https://trello.com/c/XsAUr6wl 11. 331 - Code housekeeping: standardize whitespace in various locations. Trevor Wennblom.https://trello.com/c/WtWdxP2n 12. 341 - Workflows API enhancements (pull request #337 corrected). Nicola Soranzo and Simone Leo.https://trello.com/c/zizGdqy1 13. 338 - Patch to expose the actual dataset id in the LDDA and HDA to_dict calls (in addition to the instance id). Kyle Ellrotthttps://trello.com/c/BrOscqTJ 14. 339 - Strip trailing slashes in tool IDs. Björn Grüning.https://trello.com/c/bpKNn66u 15. 334 - Optional Input Datasets Not Compatible with Parallelism Tag. Michael Lihttps://trello.com/c/WMgr8Xx0https://trello.com/c/Muw6fd8h 16. 346 - Tool panel label bug correction. Nicola Soranzo.https://trello.com/c/8NpgYM3U 17. 353 - Add BCF datatype sniffing, so BCF files are not uncompressed during upload. Nicola Soranzo.https://trello.com/c/FVKZhlsU 18. 355 - Workflow API: show also workflow owner, so a user can check it before importing. Nicola Soranzo.https://trello.com/c/cMiaYcCI Fixes 1. Fix issue with tool panel display when the tool_conf.xml has only a single entryhttps://trello.com/c/6nJIhOdJ 2. Fix issue when multiple versions of the same tool installed results in separate entries in the tool panelhttps://trello.com/c/SlNI79mR 3. Fix Published Page's JS errorhttps://trello.com/c/yGw1DwwM 4. Fix error in Babel egg utf-8, OSX 10.7https://trello.com/c/PUdh6SWw 5. Fix failures when using unicode in History name editable_text fieldshttps://trello.com/c/MTdotrHR 6. Fix tool form image display for toolshed installed toolshttps://trello.com/c/5G6jlB4B 7. Fix to improve link format in user activation emailshttps://trello.com/c/JALX9DL3 8. Fix problem with rerun of tools havingDataToolParameter <http://moinmo.in/DataToolParameter>set as optionalhttps://trello.com/c/pzHcSGzK 9. Fix bug in Tool Panel when installing repositorieshttps://trello.com/c/AiUefffC Tool Shed Documentation 1. Reorganization of the Tool Shed wiki is underway! See current changeshttps://wiki.galaxyproject.org/ToolShedand what is next uphttps://trello.com/c/Gg0jnll7 2. Data Manager documentation specific to toolshedhttp://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool… Repositories 1. New Tool Shed categorieshttps://trello.com/c/niCdaARH * Genome-Wide Association Study * Imaging * RNA 2. Eliminate the use of fabric as the installation process for repositorieshttps://trello.com/c/zJoRROvv 3. Enhancements for updating a repositoryhttps://trello.com/c/c4Y9t7db * Will now trigger the install of new dependencies * Handles newly defined repository dependencies included in updates to installed repositories 4. Add support for the new repository type: Repository suite definitionhttps://trello.com/c/sxXMmfLs 5. Defined a base set of utilities that can be expected to be on systems into which tool dependencies are being installedhttps://trello.com/c/gYlRdqwr, related to project-in-planninghttps://trello.com/c/7VTlX9rD 6. Dependency ez_setup.py added to keep package_pysam_0_7_7 from failing on tool shedhttps://trello.com/c/AkACDWix 7. Update Main Tool Shed Picard repo that contained invalid toolshttps://trello.com/c/mxxHWxLY 8. UpdateFreeBayesrepo so that it specifies precompiled binaries in dependency definitionhttps://trello.com/c/zYoVHKoV 9. Update EMBOSS repo so that it downloads a precompiled platform-specific binaryhttps://trello.com/c/iW3Amhl5 Install and Test Framework 1. Tool shed install and test framework now works with API driven tool testshttps://trello.com/c/vfr7b0VK 2. Test script to provide coverage for recently discovered scenario that produced a white ghost upon Galaxy installhttps://trello.com/c/JICmJueB 3. Test script to provide coverage for recently introduced repository administration featurehttps://trello.com/c/vjTrhIST 4. Test script to check toolshed dependency files for broken/invalid download URLshttps://trello.com/c/i4GVgZwS Tool Shed Fixes 1. Fix setup_r_environment broken in central repohttps://trello.com/c/zyCzlgzo 2. Fix scenario where by uninstalling and reinstalling a repository that has been updated creates database entries for repositories that are persistently in the New statehttps://trello.com/c/iUDUM4Ut 3. Fixes in automated test frameworkhttps://trello.com/c/QWgsgll8 4. Fix bug in install and test framework related to samtools migrationhttps://trello.com/c/sN2iLCCn Project Updates 1. News <http://wiki.galaxyproject.org/News> 2. Events <http://wiki.galaxyproject.org/Events> 3. Videos on Vimeo <https://vimeo.com/galaxyproject> 4. /April 2014 Galaxy Update <http://wiki.galaxyproject.org/GalaxyUpdates/2014_04>/ 5. /March 2014 Galaxy Update <http://wiki.galaxyproject.org/GalaxyUpdates/2014_03>/ ------------------------------------------------------------------------ About *GalaxyProject.org <http://galaxyproject.org/>* The*Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam>*is a part of the*Center for Comparative Genomics and Bioinformatics <http://www.bx.psu.edu/>*at*Penn State <http://www.psu.edu/>*, and the*Department of Biology <http://www.bio.jhu.edu/>*at*Johns Hopkinis University <http://www.jhu.edu/>*. *Galaxy <http://usegalaxy.org/>*is supported in part by*NSF <http://www.nsf.gov/>*,*NHGRI <http://www.genome.gov/>*, the*Huck Institutes of the Life Sciences <http://www.huck.psu.edu/>*, and*The Institute for CyberScience at Penn State <http://www.ics.psu.edu/>*, and*Johns Hopkins University <http://www.jhu.edu/>*. The/public Main instance <https://wiki.galaxyproject.org/Main>/of*Galaxy*at*http://usegalaxy.org <http://usegalaxy.org/>*utilizes infrastructure generously provided by the*iPlant Collaborative <http://www.iplantcollaborative.org/>*at the*Texas Advanced Computing Center <https://www.tacc.utexas.edu/>*, with support from the*National Science Foundation <http://www.nsf.gov/>*. Follow us on*Twitter@galaxyproject <http://twitter.com/galaxyproject>*or read our tweets at*Galaxy on Twitter <https://wiki.galaxyproject.org/GalaxyOnTwitter>* Have a suggestion? Please see*Using the Galaxy Issue Board <http://wiki.galaxyproject.org/Issues>*, and be sure to up vote the issues important to YOU. -- Jennifer Hillman-Jackson http://galaxyproject.org

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Migrate user data to a new server
by Simon Gladman 15 Apr '14

15 Apr '14

Hi all, I've tried looking in the mailing list for this to no avail. (Maybe my search terms were no good..) I administer a server with about 15 users. The server is failing and so I have set up a new server (with an updated OS, Galaxy version etc (galaxy versions: old - nov 2013, new - Feb 2014). Is there a method for migrating my users and their data across to the new server, without getting them to tell me their passwords.... Cheers, Simon.

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Cufflinks creates invalid output with duplicate GFF IDs
by Ganote, Carrie L 14 Apr '14

14 Apr '14

Hi List, I have a user running a Tuxedo pipeline on our local Galaxy but it has been fraught with errors. The first issue was with running cufflinks with an annotation file which had duplicate IDs - fixed by me running the following: awk '($3 == "exon" || $3 == "CDS")' dataset_8640.dat >> newref Just tossing out the transcript and gene lines seemed to help. Second issue was Error: sequence lines in a FASTA record must have the same length! Converting to and from tabular fixed that. Now the issue is with cuffmerge. The user has run Tophat on a pair of fastq files and a fasta genome. They then ran cufflinks on the Tophat assembly with an annotation file (not the previously mentioned one). This worked. But using the gtf file produced by cufflinks in a cuffmerge step results in: Error running cuffmerge. [Sat Mar 22 14:00:10 2014] Beginning transcriptome assembly merge ------------------------------------------- [Sat Mar 22 14:00:10 2014] Preparing output location cm_output/ [Sat Mar 22 14:02:37 2014] Converting GTF files to SAM [14:02:38] Loading reference annotation. Error: duplicate GFF ID 'CDS:GBG_brugia_K07A12.4b' encountered! [FAILED] Error: could not execute gtf_to_sam I took out the sequence and annotation file in the cuffmerge step with no change in result. I ran gffread on the cufflinks output and sure enough, it explodes. But why would Cufflinks create an invalid file? The file itself has these entries: Bmal_v3_scaffold1 Cufflinks transcript 280476 280630 1 + . gene_id ""; transcript_id "CDS:GBG_brugia_K07A12.4b"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; Bmal_v3_scaffold1 Cufflinks exon 280476 280630 1 + . gene_id ""; transcript_id "CDS:GBG_brugia_K07A12.4b"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; Bmal_v3_scaffold1 Cufflinks transcript 281149 281207 1 + . gene_id ""; transcript_id "CDS:GBG_brugia_K07A12.4b"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; Bmal_v3_scaffold1 Cufflinks exon 281149 281207 1 + . gene_id ""; transcript_id "CDS:GBG_brugia_K07A12.4b"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; # Shortening for brevity: Bmal_v3_scaffold1 Cufflinks transcript 281521 281622 1 ... Bmal_v3_scaffold1 Cufflinks exon 281521 281622 1 ... Bmal_v3_scaffold1 Cufflinks transcript 281743 281863 1 ... Bmal_v3_scaffold1 Cufflinks exon 281743 281863 1 ... Bmal_v3_scaffold1 Cufflinks transcript 282355 282537 1 .. Bmal_v3_scaffold1 Cufflinks exon 282355 282537 1 ... Bmal_v3_scaffold1 Cufflinks transcript 283063 283190 1 ... Bmal_v3_scaffold1 Cufflinks exon 283063 283190 1 ... Bmal_v3_scaffold1 Cufflinks transcript 283879 284035 1 ... Bmal_v3_scaffold1 Cufflinks exon 283879 284035 1 ... Bmal_v3_scaffold1 Cufflinks transcript 280652 280683 1 ... Bmal_v3_scaffold1 Cufflinks exon 280652 280683 1 ... Here's my setup: Galaxy changeset: dc067a95261d was my last pull $ cuffmerge --version merge_cuff_asms v1.0.0 $ cufflinks cufflinks v2.2.0 linked against Boost version 104700 $ tophat --version TopHat v1.3.3 Using tools: Cuffdiff devteam revision: 604fa75232a2 Cufflinks devteam revision: 9aab29e159a7 Cuffmerge devteam revision: 424d49834830 Tophat devteam revision: 1030acbecce6 Has anyone else seen this? I'm re-running the workflow from scratch but I don't really have any leads. Sincerely, Carrie Ganote

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an error to SnpEff (CloudMap)
by Wang, Xiaofei 14 Apr '14

14 Apr '14

Dear there, I got this error as below when I run CloudMap workflow in local galaxy instance. What is it the meaning of this error? Is it a general error or specific one for my data? Thanks a lot! Xiaofei error An error occurred with this dataset: WARNINGS: Some warning were detected Warning type Number of warnings WARNING_TRANSCRIPT_INCOMPLETE 36 WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS 18 WARNING_TRANSCRIPT_NO_START_CODON 100

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