April 2014 - galaxy-dev - lists.galaxyproject.org

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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Galaxy stable not working on MAC OSX, but default is OK
by Bernardo Bello 14 Apr '14

14 Apr '14

Hi, Seems I have some problems to run Galaxy stable. Here is the output I receive when running run.sh. Thanks for your help, Bernardo ------------------------------------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------------------------------------ Bernardos-MacBook-Pro:galaxy-central bernardo$ hg update stable 622 files updated, 0 files merged, 158 files removed, 0 files unresolved Bernardos-MacBook-Pro:galaxy-central bernardo$ sh run.sh Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/Users/bernardo/galaxy-central/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/Users/bernardo/galaxy-central/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/Users/bernardo/galaxy-central/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "/Users/bernardo/galaxy-central/lib/galaxy/util/pastescript/serve.py", line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/Users/bernardo/galaxy-central/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/Users/bernardo/galaxy-central/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj global_conf=global_conf) File "/Users/bernardo/galaxy-central/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext global_conf=global_conf) File "/Users/bernardo/galaxy-central/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/Users/bernardo/galaxy-central/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context section) File "/Users/bernardo/galaxy-central/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit value = import_string(found_expr) File "/Users/bernardo/galaxy-central/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/Users/bernardo/galaxy-central/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/bernardo/galaxy-central/lib/galaxy/web/__init__.py", line 4, in <module> from framework import expose File "/Users/bernardo/galaxy-central/lib/galaxy/web/framework/__init__.py", line 41, in <module> from babel.support import Translations File "/Users/bernardo/galaxy-central/eggs/Babel-0.9.4-py2.7.egg/babel/support.py", line 29, in <module> from babel.dates import format_date, format_datetime, format_time, LC_TIME File "/Users/bernardo/galaxy-central/eggs/Babel-0.9.4-py2.7.egg/babel/dates.py", line 34, in <module> LC_TIME = default_locale('LC_TIME') File "/Users/bernardo/galaxy-central/eggs/Babel-0.9.4-py2.7.egg/babel/core.py", line 642, in default_locale return '_'.join(filter(None, parse_locale(locale))) File "/Users/bernardo/galaxy-central/eggs/Babel-0.9.4-py2.7.egg/babel/core.py", line 763, in parse_locale raise ValueError('expected only letters, got %r' % lang) ValueError: expected only letters, got 'utf-8' -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona, Spain) Tel.: 647 42 52 63 *www.cresa.es <http://www.cresa.es> *

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Manually installing a Data Manager & running its tests
by Peter Cock 14 Apr '14

14 Apr '14

Hi all, I'm currently trying to manually install Dan's example Data Manager for the NCBI BLAST databases - but without using the Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_bla… To be precise, I'm currently using a slightly modified version which we've moved into the Galaxy BLAST+ wrapper repository (thus far, only slight changes to folder names have been made from Dan's original): https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blas… https://github.com/peterjc/galaxy_blast/commit/21d7cff3e8dca13c4bd0f716a79a… My goal is to be able to run the functional tests, $ ./run_functional_tests.sh -id data_manager_blast_db As with any other manually installed tool, I have added this data-manager to my tool_conf.xml.sample file (and for local testing via the GUI, the tool_conf.xml file as well): <tool file="ncbi_blastdb/blastdb.xml" /> Specific to data-managers, I have manually incorporated the additions to the central data_manager_conf.xml file (this would normally be merged at runtime if installed from the ToolShed): $ more data_manager_conf.xml <?xml version="1.0"?> <data_managers> <data_manager tool_file="ncbi_blastdb/blastdb.xml" id="data_manager_blast_db"> <data_table name="blastdb"> <output> <column name="value" /> <column name="name" /> <column name="path" output_ref="out_file" > <move type="directory"> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">blastdb/${path}</target> </move> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/blastdb/${path}/${nucleotide_alias_name}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> </data_table> </data_manager> </data_managers> Note the tool_file setting points correctly at the relative path within the tools folder, and the tool does define a test: $ more tools/ncbi_blastdb/blastdb.xml <tool id="data_manager_blast_db" name="Blast DB" version="0.0.2" tool_type="manage_data"> <description>Downloader</description> ... <tests> <test> <param name="blastdb_name" value="est"/> <param name="advanced_selector" value="basic"/> <output name="out_file" file="est_out.json"/> </test> </tests> ... $ ./run_functional_tests.sh -list | grep manager data_manager_blast_db Blast DB $ ./run_functional_tests.sh -id data_manager_blast_db ... galaxy.tools DEBUG 2014-04-11 15:59:00,780 Loaded tool id: data_manager_blast_db, version: 0.0.2 into tool panel. ... galaxy.tools.data_manager.manager DEBUG 2014-04-11 15:59:00,864 Loaded Data Manager: data_manager_blast_db ... Failure: ValueError (No such test TestForTool_data_manager_blast_db) ... ERROR ====================================================================== ERROR: Failure: ValueError (No such test TestForTool_data_manager_blast_db) ---------------------------------------------------------------------- Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/eggs/nose-0.11.1-py2.6.egg/nose/failure.py", line 39, in runTest raise self.exc_class(self.exc_val) ValueError: No such test TestForTool_data_manager_blast_db ---------------------------------------------------------------------- I get the same error via TravisCI, e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/22782979 (This suggests using Twill vs the API does not matter) Am I missing something simple here? Thanks, Peter

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Add a private genome in database/build , only visible for a specific user connected on a local instance.
by Sarah Maman 14 Apr '14

14 Apr '14

Hello, I would like to know if it's possible to limit the access to a private reference genome, for a specific user, in database/build field ? In fact, I would like that the reference genome is visible/shown only for a specific user connected to your local Galaxy instance, and hidden for others users. Should I specify something in galaxy-dist/tool-data/shared/ucsc/builds.txt file ? Thanks in advance, Sarah Maman -- --*-- Sarah Maman INRA - GenPhySE - 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 --*--

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