June 2011 - galaxy-dev - lists.galaxyproject.org

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

23 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-dev] Installation problems on osx
by Ira Cooke 23 Jun '11

23 Jun '11

Good to know that I'm not the only one. Also, I didn't put the rescramble commands in my original email ( In case there are other mac users googling this thread). cd galaxy-dist/scripts/ rm -r ../eggs/numpy-1.3.0-py2.6-macosx-10.6-universal-ucs2.egg rm -r ../eggs/bx_python-0.7.0_494c2d1d68b3-py2.6-macosx-10.6-universal-ucs2.egg python scramble.py numpy python scramble.py bx_python Of course, you also need developer tools installed. Ira On 23/06/2011, at 2:16 AM, Michael Steder wrote: > Hi Ira, > > I had the same problem and scrambling the eggs myself seemed to be the workaround. > > I'm not sure why we're having problems. It does seem to be specific to mac though, as I can run this same checkout on linux without any workarounds. > > ~Mike > > On Jun 21, 2011, at 11:47 PM, Ira Cooke wrote: > >> Hi, >> >> I recently downloaded galaxy and had some problems installing it on my machine (running Mac OSX 10.6.7 ). I've found a workaround to my problem, but I thought I should post here in case it is useful. >> >> I obtained the standard galaxy distribution using >> >> hg clone https://bitbucket.org/galaxy/galaxy-dist/ >> >> I then tried running sh run.sh but got; >> >> Traceback (most recent call last): >> File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory >> from galaxy.app import UniverseApplication >> File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/app.py", line 11, in <module> >> from galaxy.tools.imp_exp import load_history_imp_exp_tools >> File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> >> from galaxy.web.base.controller import UsesHistory >> File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> >> from galaxy.visualization.tracks.data_providers import get_data_provider >> File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> >> from bx.arrays.array_tree import FileArrayTreeDict >> File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) >> ValueError: numpy.dtype does not appear to be the correct type object >> >> >> I googled this error and found a post suggesting that I try virtualenv ... I tried that but it made no difference. >> >> Python --version returns >> 2.6.1 >> >> After some digging I tried rescrambling the numpy and then the bx_python egg. After rescrambling the latter sh run.sh worked. >> >> Anyway I'm not sure if other mac users have had similar problems. In my case I'm pretty sure I had installed things with easy_install in the past ...but I assume using virtualenv would have solved that problem. >> >> Ira >> >> >> ___________________________________________________________ >> 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/ >

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error when using exec_before_job
by Leandro Hermida 23 Jun '11

23 Jun '11

Hi, I've tried to do a simple test where I change the output dataset name programmatically before it appears in the history using exec_before_job(). I just copied some example code: def exec_before_job(inp_data, out_data, param_dict, tool): for name, data in out_data.items(): data.name = 'New name' I get the following error: Traceback (most recent call last): File "/gpfshpc/home/lhermida/soft/galaxy/galaxy_dist/lib/galaxy/jobs/runners/drmaa.py", line 124, in queue_job job_wrapper.prepare() File "/gpfshpc/home/lhermida/soft/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 364, in prepare out_data=out_data, tool=self.tool, param_dict=incoming) File "/gpfshpc/home/lhermida/soft/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1664, in call_hook return code( *args, **kwargs ) TypeError: ('E', 'r', 'r', 'o', 'r', ' ', 'i', 'n', ' ', "'", 'T', 'e', 's', 't', 'i', 'n', 'g', "'", ' ', 'h', 'o', 'o', 'k', ' ', "'", 'e', 'x', 'e', 'c', '_', 'b', 'e', 'f', 'o', 'r', 'e', '_', 'j', 'o', 'b', "'", ',', ' ', 'o', 'r', 'i', 'g', 'i', 'n', 'a', 'l', ' ', 'm', 'e', 's', 's', 'a', 'g', 'e', ':', ' ', 'e', 'x', 'e', 'c', '_', 'b', 'e', 'f', 'o', 'r', 'e', '_', 'j', 'o', 'b', '(', ')', ' ', 'g', 'o', 't', ' ', 'm', 'u', 'l', 't', 'i', 'p', 'l', 'e', ' ', 'v', 'a', 'l', 'u', 'e', 's', ' ', 'f', 'o', 'r', ' ', 'k', 'e', 'y', 'w', 'o', 'r', 'd', ' ', 'a', 'r', 'g', 'u', 'm', 'e', 'n', 't', ' ', "'", 'i', 'n', 'p', '_', 'd', 'a', 't', 'a', "'") Any ideas? Leandro

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user_library_import_dir configuration
by Shantanu Pavgi 23 Jun '11

23 Jun '11

Hi, I have setup 'user_library_import_dir' to allow non-admin users to import data libraries. The configured directory contains subdirectories with galaxy-login (email) name. I couldn't figure out how to view these files in galaxy web interface though. Any help? Also, what filesystem permissions are needed for user_library_import_dir and library_import_dir (admin accessible)? -- Thanks, Shantanu.

2 4

number of dataset files within 000
by Shantanu Pavgi 23 Jun '11

23 Jun '11

Hi, The galaxy dataset files (file_path) are arranged within a subdirectory '000' (database/files/000). Will galaxy create a new subdirectory for storing datasets files after certain file count value is reached(say ~ 1000)? It may not be a problem while using web interface, but I am wondering if this could be a problem if user tries filesystem info commands from shell - e.g regular ls command output. Also, curious to know if subdirectory name '000' signifies something here? -- Thanks, Shantanu

2 2

Installation problems on osx
by Ira Cooke 22 Jun '11

22 Jun '11

Hi, I recently downloaded galaxy and had some problems installing it on my machine (running Mac OSX 10.6.7 ). I've found a workaround to my problem, but I thought I should post here in case it is useful. I obtained the standard galaxy distribution using hg clone https://bitbucket.org/galaxy/galaxy-dist/ I then tried running sh run.sh but got; Traceback (most recent call last): File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object I googled this error and found a post suggesting that I try virtualenv ... I tried that but it made no difference. Python --version returns 2.6.1 After some digging I tried rescrambling the numpy and then the bx_python egg. After rescrambling the latter sh run.sh worked. Anyway I'm not sure if other mac users have had similar problems. In my case I'm pretty sure I had installed things with easy_install in the past ...but I assume using virtualenv would have solved that problem. Ira

2 1

rpy and R
by Ryan Davis 22 Jun '11

22 Jun '11

Hi all, I'm currently working on setting up a Galaxy on our local server. I'm going through the tool dependencies list and install everything on it. I installed the latest R version (2.12.2) and now I'm trying to install rpy 1.0.3. I have installed R with --enable-R-shlib and also done this step: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/R/lib/ However I get the following error with the install of rpy 1.0.3. Thanks for the help, Ryan [cgtepper@hobbes rpy-1.0.3]$ python setup.py install RHOMES= [] DEBUG= True Setting RHOMES to ['/usr/lib64/R'] ### Using R verion 2.12.2 installed at /usr/lib64/R ### RHOME= /usr/lib64/R copying src/rpymodule.c -> src/rpymodule2122.c copying src/R_eval.c -> src/R_eval2122.c copying src/io.c -> src/io2122.c running install running build running build_py running build_ext building '_rpy2122' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DRPY_SHNAME=_rpy2122 -DINIT_RPY=init_rpy2122 -UPRE_2_2 -UWITH_NUMERIC -I/usr/lib64/R/include -Isrc -I/usr/share/R/include -I/usr/local/include/python2.6 -c src/rpymodule2122.c -o build/temp.linux-x86_64-2.6/src/rpymodule2122.o -shared src/rpymodule2122.c:42:23: error: Rversion.h: No such file or directory src/rpymodule2122.c:43:28: error: missing binary operator before token "(" In file included from src/rpymodule2122.c:51: src/RPy.h:51:15: error: R.h: No such file or directory src/RPy.h:52:22: error: Rdefines.h: No such file or directory src/RPy.h:53:24: error: Rinternals.h: No such file or directory src/RPy.h:57:28: error: R_ext/Rdynload.h: No such file or directory src/RPy.h:58:29: error: R_ext/eventloop.h: No such file or directory In file included from src/RPy.h:71, from src/rpymodule2122.c:51: src/rpy_Rinterface.h:51:27: error: R_ext/Boolean.h: No such file or directory In file included from src/rpy_Rinterface.h:61, from src/RPy.h:71, from src/rpymodule2122.c:51: src/rpy_Startup.h:70: error: expected specifier-qualifier-list before Rboolean In file included from src/RPy.h:71, from src/rpymodule2122.c:51: src/rpy_Rinterface.h:70: error: expected =, ,, ;, asm or __attribute__ before R_Interactive src/rpy_Rinterface.h:71: error: expected =, ,, ;, asm or __attribute__ before R_Quiet src/rpy_Rinterface.h:72: error: expected =, ,, ;, asm or __attribute__ before R_Slave src/rpy_Rinterface.h:73: error: expected =, ,, ;, asm or __attribute__ before R_Verbose src/rpy_Rinterface.h:76: error: expected declaration specifiers or ... before Rboolean src/rpy_Rinterface.h:85: warning: function declaration isnt a prototype src/rpy_Rinterface.h:96: warning: function declaration isnt a prototype src/rpy_Rinterface.h:101: warning: function declaration isnt a prototype src/rpy_Rinterface.h:102: warning: function declaration isnt a prototype src/rpy_Rinterface.h:103: warning: function declaration isnt a prototype src/rpy_Rinterface.h:112: warning: parameter names (without types) in function declaration In file included from src/rpymodule2122.c:51: src/RPy.h:77:51: error: Rdevices.h: No such file or directory In file included from src/RPy.h:108, from src/rpymodule2122.c:51: src/robjobject.h:47: error: expected specifier-qualifier-list before SEXP src/robjobject.h:62: error: expected ) before int In file included from src/rpymodule2122.c:51: src/RPy.h:115: error: expected =, ,, ;, asm or __attribute__ before to_Robj src/RPy.h:116: warning: parameter names (without types) in function declaration src/RPy.h:117: warning: parameter names (without types) in function declaration src/RPy.h:118: error: expected ) before int src/RPy.h:129: error: expected =, ,, ;, asm or __attribute__ before do_eval_expr src/RPy.h:130: error: expected =, ,, ;, asm or __attribute__ before do_eval_fun src/RPy.h:131: error: expected =, ,, ;, asm or __attribute__ before get_fun_from_name src/RPy.h:208: error: expected ) before robj src/RPy.h:209: error: expected ) before robj src/RPy.h:210: error: expected ) before robj src/RPy.h:211: error: expected ) before robj src/rpymodule2122.c:77: error: expected =, ,, ;, asm or __attribute__ before get_item src/rpymodule2122.c:78: error: expected =, ,, ;, asm or __attribute__ before set_item src/rpymodule2122.c:79: error: expected =, ,, ;, asm or __attribute__ before length src/rpymodule2122.c:80: error: expected =, ,, ;, asm or __attribute__ before aperm src/rpymodule2122.c:113: error: expected =, ,, ;, asm or __attribute__ before R_References src/rpymodule2122.c:116: error: expected =, ,, ;, asm or __attribute__ before RecursiveRelease src/rpymodule2122.c: In function Robj_dealloc: src/rpymodule2122.c:133: error: R_References undeclared (first use in this function) src/rpymodule2122.c:133: error: (Each undeclared identifier is reported only once src/rpymodule2122.c:133: error: for each function it appears in.) src/rpymodule2122.c:133: warning: implicit declaration of function RecursiveRelease src/rpymodule2122.c:133: error: RobjObject has no member named R_obj src/rpymodule2122.c:134: warning: implicit declaration of function SET_SYMVALUE src/rpymodule2122.c:134: warning: implicit declaration of function install src/rpymodule2122.c: At top level: src/rpymodule2122.c:140: error: expected ) before robj src/rpymodule2122.c:207: error: expected =, ,, ;, asm or __attribute__ before seq_to_R src/rpymodule2122.c:292: error: expected =, ,, ;, asm or __attribute__ before dict_to_R src/rpymodule2122.c:510: error: expected =, ,, ;, asm or __attribute__ before to_Robj src/rpymodule2122.c:627: error: expected declaration specifiers or ... before SEXP src/rpymodule2122.c: In function to_PyDict: src/rpymodule2122.c:641: warning: implicit declaration of function CHAR src/rpymodule2122.c:641: warning: implicit declaration of function STRING_ELT src/rpymodule2122.c:641: error: names undeclared (first use in this function) src/rpymodule2122.c:641: warning: assignment makes pointer from integer without a cast src/rpymodule2122.c: At top level: src/rpymodule2122.c:751: error: expected ) before robj src/rpymodule2122.c:774: error: expected ) before robj src/rpymodule2122.c:901: error: expected ) before robj src/rpymodule2122.c:939: error: expected ) before robj src/rpymodule2122.c:977: error: expected ) before robj src/rpymodule2122.c:999: error: expected ) before robj src/rpymodule2122.c:1016: error: expected ) before robj src/rpymodule2122.c:1048: error: expected declaration specifiers or ... before SEXP src/rpymodule2122.c: In function make_args: src/rpymodule2122.c:1050: error: SEXP undeclared (first use in this function) src/rpymodule2122.c:1050: error: expected ; before r src/rpymodule2122.c:1054: error: r undeclared (first use in this function) src/rpymodule2122.c:1054: warning: implicit declaration of function to_Robj src/rpymodule2122.c:1057: warning: implicit declaration of function SETCAR src/rpymodule2122.c:1057: error: e undeclared (first use in this function) src/rpymodule2122.c:1058: warning: implicit declaration of function CDR src/rpymodule2122.c: At top level: src/rpymodule2122.c:1092: error: expected declaration specifiers or ... before SEXP src/rpymodule2122.c: In function make_kwds: src/rpymodule2122.c:1094: error: SEXP undeclared (first use in this function) src/rpymodule2122.c:1094: error: expected ; before r src/rpymodule2122.c:1108: error: r undeclared (first use in this function) src/rpymodule2122.c:1113: error: e undeclared (first use in this function) src/rpymodule2122.c:1125: warning: implicit declaration of function SET_TAG src/rpymodule2122.c:1125: warning: implicit declaration of function Rf_install src/rpymodule2122.c: In function Robj_call: src/rpymodule2122.c:1142: error: SEXP undeclared (first use in this function) src/rpymodule2122.c:1142: error: expected ; before exp src/rpymodule2122.c:1155: warning: implicit declaration of function PROTECT src/rpymodule2122.c:1155: warning: implicit declaration of function allocVector src/rpymodule2122.c:1155: error: LANGSXP undeclared (first use in this function) src/rpymodule2122.c:1155: error: invalid lvalue in assignment src/rpymodule2122.c:1156: error: e undeclared (first use in this function) src/rpymodule2122.c:1157: error: RobjObject has no member named R_obj src/rpymodule2122.c:1160: error: too many arguments to function make_args src/rpymodule2122.c:1161: warning: implicit declaration of function UNPROTECT src/rpymodule2122.c:1164: error: too many arguments to function make_kwds src/rpymodule2122.c:1169: error: res undeclared (first use in this function) src/rpymodule2122.c:1169: warning: implicit declaration of function do_eval_expr src/rpymodule2122.c:1176: error: RobjObject has no member named conversion src/rpymodule2122.c:1180: warning: implicit declaration of function to_Pyobj_with_mode src/rpymodule2122.c:1180: warning: assignment makes pointer from integer without a cast src/rpymodule2122.c: At top level: src/rpymodule2122.c:1191: error: expected declaration specifiers or ... before SEXP src/rpymodule2122.c: In function make_argl: src/rpymodule2122.c:1193: error: SEXP undeclared (first use in this function) src/rpymodule2122.c:1193: error: expected ; before rvalue src/rpymodule2122.c:1239: error: rvalue undeclared (first use in this function) src/rpymodule2122.c:1247: error: e undeclared (first use in this function) src/rpymodule2122.c: In function Robj_lcall: src/rpymodule2122.c:1279: error: SEXP undeclared (first use in this function) src/rpymodule2122.c:1279: error: expected ; before exp src/rpymodule2122.c:1308: error: LANGSXP undeclared (first use in this function) src/rpymodule2122.c:1308: error: invalid lvalue in assignment src/rpymodule2122.c:1309: error: e undeclared (first use in this function) src/rpymodule2122.c:1310: error: RobjObject has no member named R_obj src/rpymodule2122.c:1314: error: too many arguments to function make_argl src/rpymodule2122.c:1320: error: res undeclared (first use in this function) src/rpymodule2122.c:1328: error: RobjObject has no member named conversion src/rpymodule2122.c:1332: warning: assignment makes pointer from integer without a cast src/rpymodule2122.c: In function Robj_autoconvert: src/rpymodule2122.c:1359: error: RobjObject has no member named conversion src/rpymodule2122.c:1361: error: RobjObject has no member named conversion src/rpymodule2122.c: In function Robj_as_py: src/rpymodule2122.c:1388: error: RobjObject has no member named R_obj src/rpymodule2122.c:1388: warning: assignment makes pointer from integer without a cast src/rpymodule2122.c: In function Robj_len: src/rpymodule2122.c:1406: error: SEXP undeclared (first use in this function) src/rpymodule2122.c:1406: error: expected ; before e src/rpymodule2122.c:1408: error: e undeclared (first use in this function) src/rpymodule2122.c:1408: error: LANGSXP undeclared (first use in this function) src/rpymodule2122.c:1409: error: length undeclared (first use in this function) src/rpymodule2122.c:1410: error: RobjObject has no member named R_obj src/rpymodule2122.c:1412: error: robj undeclared (first use in this function) src/rpymodule2122.c:1418: warning: implicit declaration of function INTEGER_DATA src/rpymodule2122.c:1418: error: subscripted value is neither array nor pointer src/rpymodule2122.c: In function Robj_ass_item: src/rpymodule2122.c:1425: error: SEXP undeclared (first use in this function) src/rpymodule2122.c:1425: error: expected ; before e src/rpymodule2122.c:1427: error: e undeclared (first use in this function) src/rpymodule2122.c:1427: error: LANGSXP undeclared (first use in this function) src/rpymodule2122.c:1428: error: ri undeclared (first use in this function) src/rpymodule2122.c:1428: warning: implicit declaration of function NEW_INTEGER src/rpymodule2122.c:1429: error: subscripted value is neither array nor pointer src/rpymodule2122.c:1430: error: set_item undeclared (first use in this function) src/rpymodule2122.c:1431: error: RobjObject has no member named R_obj src/rpymodule2122.c:1438: error: robj undeclared (first use in this function) src/rpymodule2122.c:1443: error: RobjObject has no member named R_obj src/rpymodule2122.c: In function Robj_item: src/rpymodule2122.c:1452: error: SEXP undeclared (first use in this function) src/rpymodule2122.c:1452: error: expected ; before ri src/rpymodule2122.c:1463: error: ri undeclared (first use in this function) src/rpymodule2122.c:1464: error: subscripted value is neither array nor pointer src/rpymodule2122.c:1465: error: e undeclared (first use in this function) src/rpymodule2122.c:1465: error: LANGSXP undeclared (first use in this function) src/rpymodule2122.c:1466: error: get_item undeclared (first use in this function) src/rpymodule2122.c:1467: error: RobjObject has no member named R_obj src/rpymodule2122.c:1470: error: robj undeclared (first use in this function) src/rpymodule2122.c:1482: warning: assignment makes pointer from integer without a cast src/rpymodule2122.c: In function Robj_slice: src/rpymodule2122.c:1493: error: SEXP undeclared (first use in this function) src/rpymodule2122.c:1493: error: expected ; before robj src/rpymodule2122.c:1532: error: INTSXP undeclared (first use in this function) src/rpymodule2122.c:1532: error: invalid lvalue in assignment src/rpymodule2122.c:1535: warning: implicit declaration of function INTEGER_POINTER src/rpymodule2122.c:1535: error: subscripted value is neither array nor pointer src/rpymodule2122.c:1538: error: e undeclared (first use in this function) src/rpymodule2122.c:1538: error: LANGSXP undeclared (first use in this function) src/rpymodule2122.c:1539: error: get_item undeclared (first use in this function) src/rpymodule2122.c:1540: error: RobjObject has no member named R_obj src/rpymodule2122.c:1543: error: robj undeclared (first use in this function) src/rpymodule2122.c:1555: warning: assignment makes pointer from integer without a cast src/rpymodule2122.c: At top level: src/rpymodule2122.c:1565: warning: initialization from incompatible pointer type src/rpymodule2122.c:1568: warning: intargfunc is deprecated src/rpymodule2122.c:1568: warning: initialization from incompatible pointer type src/rpymodule2122.c:1569: warning: intintargfunc is deprecated src/rpymodule2122.c:1569: warning: initialization from incompatible pointer type src/rpymodule2122.c:1570: warning: initialization from incompatible pointer type src/rpymodule2122.c: In function get_fun: src/rpymodule2122.c:1668: error: SEXP undeclared (first use in this function) src/rpymodule2122.c:1668: error: expected ; before robj src/rpymodule2122.c:1675: error: robj undeclared (first use in this function) src/rpymodule2122.c:1675: warning: implicit declaration of function get_fun_from_name src/rpymodule2122.c:1679: warning: implicit declaration of function Robj_new src/rpymodule2122.c:1679: warning: cast to pointer from integer of different size src/rpymodule2122.c: In function r_events: src/rpymodule2122.c:1727: warning: implicit declaration of function R_checkActivity src/rpymodule2122.c:1727: warning: assignment makes pointer from integer without a cast src/rpymodule2122.c:1728: warning: implicit declaration of function R_runHandlers src/rpymodule2122.c:1728: error: R_InputHandlers undeclared (first use in this function) src/rpymodule2122.c: In function r_finalize: src/rpymodule2122.c:1778: warning: implicit declaration of function R_dot_Last src/rpymodule2122.c:1779: warning: implicit declaration of function R_RunExitFinalizers src/rpymodule2122.c:1781:28: error: missing binary operator before token "(" src/rpymodule2122.c:1784: warning: implicit declaration of function KillAllDevices src/rpymodule2122.c:1787:28: error: missing binary operator before token "(" src/rpymodule2122.c:1798: warning: implicit declaration of function R_system src/rpymodule2122.c:1803: warning: implicit declaration of function R_gc src/rpymodule2122.c: In function init_rpy2122: src/rpymodule2122.c:1980: error: SEXP undeclared (first use in this function) src/rpymodule2122.c:1980: error: expected ; before interact src/rpymodule2122.c:2070: error: get_item undeclared (first use in this function) src/rpymodule2122.c:2071: error: set_item undeclared (first use in this function) src/rpymodule2122.c:2072: error: length undeclared (first use in this function) src/rpymodule2122.c:2075: error: aperm undeclared (first use in this function) src/rpymodule2122.c:2078: error: R_References undeclared (first use in this function) src/rpymodule2122.c:2078: error: R_NilValue undeclared (first use in this function) src/rpymodule2122.c:2085: error: interact undeclared (first use in this function) src/rpymodule2122.c:2085: warning: implicit declaration of function do_eval_fun src/rpymodule2122.c:2086: warning: implicit declaration of function INTEGER src/rpymodule2122.c:2086: error: subscripted value is neither array nor pointer error: command 'gcc' failed with exit status 1

3 3

Sharing authentication between Galaxy and other WSGI apps on the same web server (with custom UI)?
by Duddy, John 20 Jun '11

20 Jun '11

I'd like to have Galaxy and another application installed on the same Apache server and have the user authenticate only once. I think I understand how to do that by deferring authentication to Apache (instead of using Galaxy's built-in database). So far, so good, I think. What I'm wondering is if it is possible (in external user mode) to control the user experience of authentication versus being stuck with the one where the browser pops up the authentication dialog. Is it possible to implement a shared authentication mechanism that uses web pages for the UI? Or would we have to give up Apache-based security and snoop the Galaxy session cookie instead? Many thanks - John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

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Re: [galaxy-dev] problems previewing certain files, downloading files and with login
by Matthew Conte 20 Jun '11

20 Jun '11

Hi Nate, I was able to finally track down the login issue. It had to do with the following setting in my universe_wsgi.ini: * * *cookie_path = /galaxy* Removing this out fixed the problem and I should be fine leaving it out out since I don't need to run more than one instance of Galaxy. I probably shouldn't have had this setting in the first place, though I'm not exactly sure what this caused the problem. Anyways, thanks for all the help tracking these issues down. -Matt On Mon, May 16, 2011 at 5:26 PM, Matthew Conte <mconte(a)umd.edu> wrote: > Yep. > On May 16, 2011 7:14 AM, "Nate Coraor" <nate(a)bx.psu.edu> wrote: > > Matthew Conte wrote: > >> On Fri, May 13, 2011 at 11:18 AM, Nate Coraor <nate(a)bx.psu.edu> wrote: > >> > >> > That's correct, although it should've been fixed. Can you remove the > >> > contents of galaxy-dist/database/compiled_templates, clear cache, > >> > reload, and see if you still get the same results? > >> > > >> > Thanks, > >> > --nate > >> > > >> > >> I've removed the contents of that folder, cleared the browser cache, > >> reloaded and still get the same results (nothing different in the log > >> either). > >> > >> I'm not sure if this will help, but maybe I should mention that when I > try > >> to log in I do get the following screen to flash for a brief second > before > >> automatically taking me back to the welcome screen: > >> > >> [image: Screen shot 2011-05-13 at 1.44.25 PM.png] > > > > I'm going to try to set up a test environment to replicate this shortly. > > Does this happen with both Apache and nginx? > > > > --nate >

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Re: [galaxy-dev] [galaxy-bugs] tool updates for local installation
by Greg Von Kuster 20 Jun '11

20 Jun '11

Helo Ravi, please send all questions to one of the Galaxy mail lists as sending to personal emails will usually not generate responses. I've forwarded your question to the dev list since I am not involved in the Galaxy cloud development efforts. On Jun 17, 2011, at 5:47 PM, Sanka, Ravi wrote: > Hello Greg, > > Thank you for your quick response. I have another, related question. > > I understand that there is an Amazon-Cloud version of Galaxy called CloudMan, where tool updates are taken care of for the users. > > Does CloudMan take care of its own updates? If so, how often do the tools get updated? > > ----------------------------------------------- > Ravi Sanka > ICS - Bioinformatics Engineer > J. Craig Venter Institute > 301-795-7743 > ----------------------------------------------- > > From: Greg Von Kuster [mailto:greg@bx.psu.edu] > Sent: Friday, June 17, 2011 3:24 PM > To: Sanka, Ravi > Cc: galaxy-bugs(a)bx.psu.edu > Subject: Re: [galaxy-bugs] tool updates for local installation > > Hello Ravi, > > At the current time, it is up to the owner of the Galaxy instance to look at the Galaxy tool shed for updates, and pull them to their local instance. Regarding 3rd party dependencies, it is again the responsibility of the owner of the Galaxy instance to handle the dependencies. This will change at some point in the future, at which point we'll let you know of the changes. > > Thanks for your interest! > > Greg Von Kuster > > On Jun 17, 2011, at 3:02 PM, Sanka, Ravi wrote: > > > Greetings, > > My name is Ravi Sanka. I have a question for maintaining tools on a local installation of Galaxy. > > What happens one or more updates are available for the tools that are part of the Galaxy community? Is it the client’s responsibility to search for updates of each tool on his install? Or do update alerts get sent by Galaxy to keep the tools at the most recent version? > > And what about those tools that are part of the Galaxy community but use third-party software (i.e. NCBI Blast+)? Is it the same for them, or does a different procedure apply? > > Thanks, > - Ravi Sanka > > > > > Greg Von Kuster > Galaxy Development Team > greg(a)bx.psu.edu > > > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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