- galaxy-dev - lists.galaxyproject.org

jobid exception
by Rémy Dernat 23 Oct '13

23 Oct '13

Hi, After a big upgrade, I have an error when I submit job to SGE through drmaa Here is the error I get: galaxy.jobs.runners.drmaa WARNING 2013-10-14 11:26:08,075 (15615/68154) job check resulted in InvalidJobException: code 18: The job specified by the 'jobid' does not exist. The job is launch to sge because I see it with "qstat" SGE command. On the galaxy Web interface, the job is stuck in yellow (running state), although it is finished. When I submit job by using "local" destination it works fine. Here is my job_conf.xml file : <?xml version="1.0"?>  <job_conf> <plugins> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="sge_default">  <destination id="sge_default" runner="drmaa"> <param id="nativeSpecification">-q all.q -V</param> </destination> <destination id="local" runner="local"/> </destinations> </job_conf> Any help would be usefull. Regards, Rem

2 6

Empty or 'no peek' output.
by Luobin Yang 22 Oct '13

22 Oct '13

This is strange: when I submit a job through the computers on campus to my locally installed Galaxy, the job finishes without no problem, but when I submit the same job through a computer off-campus, the job generates empty or 'no peek' output. What's causing the problem? Luobin

1 0

Associate jobs to a Project ID
by Jean-Francois Payotte 22 Oct '13

22 Oct '13

Dear Galaxy Gurus, I have been requested to find a way to tag each job (created when running a workflow) with a "Project ID". The user would have the possibility to enter a "Project ID" (maybe as a workflow parameter) and then, some mechanism would link all of these jobs with the "Project ID". Ultimately, the goal would be to create reports on our computer resources utilisation (total CPU time each project consumed). This would be really helpful in understanding the costs associated with the projects analyses. I know I can use the "job_runner_external_id" to retrieve the actual CPU usages but I still need to find a way to associate the jobs with the "Project ID". As of now, I don't see any *clean* way to do this. Anyone would have an idea on how I could implement this feature? Or tell me if it's not possible at all? Many thanks for your help. Galaxy is just incredible! Jean-François Payotte

2 1

No "Upload files to repository" button
by Stewart, Andrew 22 Oct '13

22 Oct '13

No "Upload files to repository" button after creating repository in self-hosted toolshed. screenshot: http://imgur.com/AlQB1jL Any ideas what could be wrong?

1 1

Test Tool Shed - tests failing in subprocess / sniff
by Peter Cock 22 Oct '13

22 Oct '13

Hi Dave, Greg, Based on my tool's overnight test results from the Test Tool Shed, something seems to have been broken to do with sniffing datatypes on upload. e.g. using blastxml format, http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr Tool test results Automated test environment 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-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1327, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1276, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'blastxml_file' to value '['blastp_four_human_vs_rhodopsin.xml']' in form 'tool_form' threw exception: cannot find value/label "blastp_four_human..odopsin.xml" in list control control: <SelectControl(blastxml_file=[])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set. Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/runners/local.py", line 83, in queue_job preexec_fn = os.setpgrp ) File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1205, in _execute_child self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: e.g. just fasta and tabular, Tool test results Automated test environment Tests that failed Tool id: seq_primer_clip Tool version: seq_primer_clip 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-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1327, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1276, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'primer_fasta' to value '['dop_primers.fasta']' in form 'tool_form' threw exception: cannot find value/label "dop_primers.fasta" in list control control: <SelectControl(primer_fasta=[])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set. Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/runners/local.py", line 83, in queue_job preexec_fn = os.setpgrp ) File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1205, in _execute_child self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 381 galaxy.jobs: DEBUG: (381) Working directory for job is: /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/database/job_working_directory/000/381 galaxy.jobs.handler: DEBUG: (381) Dispatching to local runner galaxy.jobs: DEBUG: (381) Persisting job destination (destination id: local) galaxy.jobs.handler: INFO: (381) Job dispatched galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools' galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.local: DEBUG: (381) executing: export GALAXY_SLOTS="1"; python /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/tools/data_source/upload.py /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpDEZCBr/tmpG8dIQ8 /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpDEZCBr/tmpMD8cHQ 404:/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/database/job_working_directory/000/381/dataset_404_files:/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpALDdhE/database/files/000/dataset_404.dat galaxy.datatypes.metadata: DEBUG: Cleaning up external metadata files galaxy.jobs.runners.local: ERROR: failure running job 381 Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/runners/local.py", line 83, in queue_job preexec_fn = os.setpgrp ) File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1205, in _execute_child self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: (snip - first test only, rest do the same). Peter

2 1

tool_dependencies.xml <action type="download_by_url"> regression?
by Peter Cock 22 Oct '13

22 Oct '13

This tools has been passing its nightly tests fine, http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus However, there now appears to be a silent installation failure (the install hasn't worked but there was no install error): Automated tool test results Tool test results Automated test environment Tests that failed Tool id: nlstradamus Tool version: nlstradamus Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterj…) Stderr: Fatal error: Exit code 127 () /bin/sh: 1: NLStradamus: not found Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 782, in verify_dataset_correctness self._assert_dataset_state( elem, 'ok' ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 606, in _assert_dataset_state raise AssertionError( errmsg ) AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error On the other hand, over on the main Tool Shed, with what should be the same tool configuration, the install works (although there is a new sniffer bug on the Galaxy side, see separate email): http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus Here's the tool_dependencies.xml file, <?xml version="1.0"?> <tool_dependency> <package name="NLStradamus" version="1.8"> <install version="1.0"> <actions> <action type="download_by_url">http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/NLStradamus.1.8…</action>  <action type="shell_command">g++ NLStradamus.cpp -o NLStradamus -O3</action> <action type="move_file"><source>NLStradamus</source><destination>$INSTALL_DIR/</destination></action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> This downloads NLStradamus v1.8 from this folder, http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/ The C++ tool is compiled as described in the README_C.txt file, using g++, and included in the $PATH. The older slower Perl implementation is not installed. </readme> </package> </tool_dependency> My hunch is a subtle regression in the <action type="download_by_url"> (note in this case the tarball does not contain a sub-folder). Peter

2 1

database I/O error
by Nikhil Joshi 22 Oct '13

22 Oct '13

Hi all, I have a client who is trying to run velvet on a small bacterial assembly in Galaxy. She is using our Core's custom Galaxy in the Amazon Cloud. It has had very few problems and we have been updating it and using it for years. However, after her assembly ran for a while, Galaxy crashed and now gives this error whenever you try to access it: Error Traceback: ⇝ OperationalError: (OperationalError) disk I/O error u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2013-10-17 18:22:49.991937', 0, 110] URL: http://ec2-54-219-128-159.us-west-1.compute.amazonaws.com/user/logout Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request view >> body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.user:509 in logout view >> trans.handle_user_logout( logout_all=logout_all ) Module galaxy.web.framework:713 in handle_user_logout view >> self.sa_session.flush() Module sqlalchemy.orm.scoping:127 in do view >> return getattr(self.registry(), name)(*args, **kwargs) Module sqlalchemy.orm.session:1356 in flush view >> self._flush(objects) Module sqlalchemy.orm.session:1434 in _flush view >> flush_context.execute() Module sqlalchemy.orm.unitofwork:261 in execute view >> UOWExecutor().execute(self, tasks) Module sqlalchemy.orm.unitofwork:753 in execute view >> self.execute_save_steps(trans, task) Module sqlalchemy.orm.unitofwork:768 in execute_save_steps view >> self.save_objects(trans, task) Module sqlalchemy.orm.unitofwork:759 in save_objects view >> task.mapper._save_obj(task.polymorphic_tosave_objects, trans) Module sqlalchemy.orm.mapper:1413 in _save_obj view >> c = connection.execute(statement.values(value_params), params) Module sqlalchemy.engine.base:824 in execute view >> return Connection.executors[c](self, object, multiparams, params) Module sqlalchemy.engine.base:874 in _execute_clauseelement view >> return self.__execute_context(context) Module sqlalchemy.engine.base:896 in __execute_context view >> self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) Module sqlalchemy.engine.base:950 in _cursor_execute view >> self._handle_dbapi_exception(e, statement, parameters, cursor, context) Module sqlalchemy.engine.base:931 in _handle_dbapi_exception view >> raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) disk I/O error u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2013-10-17 18:22:49.991937', 0, 110] I will be getting more information from her soon, but I just wanted to post this to see if anybody had any suggestions about what might be going on and perhaps how to fix it? Any help would be highly appreciated. Thanks! - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

2 1

Uploads stalling on local Galaxy installation
by Tim Booth 22 Oct '13

22 Oct '13

Hi All, Some of the developers will know me already but it's my first time being properly on this list as I'm now working concertedly on Galaxy. I'm responsible for Bio-Linux which currently ships with an out-of-date and slightly flakey galaxy, but I'm working to fix that. I've hit a problem. This may or may not be the same as the issue seen by Luobin Yang. When uploading a file, no job appears in the right-hand panel. If I click refresh I might see a job but it stays in the blue "Dataset is uploading" state forever. I'm working on packaging Galaxy for Debian/Ubuntu/Bio-Linux, specifically Ubuntu 12.04 LTS (python 2.7.3). To rearrange Galaxy into something that resembles a Debian package takes a lot of tinkering and I've patched a few bits of the code, so when uploads started freezing like this I assumed it was something I'd done and started reverting patches. But it turns out I can trigger this problem on a pristine download of the latest server release (20130926 from Bitbucket). All I do is: grab and unpack latest version python ./scripts/fetch_eggs.py -c universe_wsgi.ini.sample python ./scripts/fetch_eggs.py -c universe_wsgi.ini.sample -e psycopg2 (note - I'm not actually using Posgres in this case and I'm assuming this is irrelevant but reporting for completenes) mkdir eggs-cache ; export PYTHON_EGG_CACHE=`pwd`/eggs-cache ./run.sh (wait for SQLite DB to build) Ctrl-C, ./run.sh, test, Ctrl-C, ./run.sh, test, etc... After a few restarts the problem occurs. Failing that, it seems I can make failure more likely by tarring up the whole directory and untarring it again. I suspect all this is doing is affecting the disk cache timing and thus triggering some underlying race condition. Once the server is started, behaviour is apparently consistent - ie. all uploads either fail or all work. Other tasks seem to work, so long as they don't depend on the stalled uploads, but I've only tried a couple of these (just a basic "select first lines"). I'm now convinced there is some sort of race condition on start-up that is responsible. On my DEB package it fails like this all the time, but an issue is clearly there in the unmolested code, just rarer. I don't mind getting into the code to try and debug this but I don't know where to start, even with the source code docs and my rapidly increasing Python-fu. Trying to fathom the interactions between the threads and the browser and the SQLAlchemy layer I either need a good outline document or a developer to hold my hand for a bit. Can someone help me out with this one? Thanks in advance, TIM -- Tim Booth <tbooth(a)ceh.ac.uk> NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705

5 9

Test Toolshed Biopython package dependency & NumPy
by Peter Cock 22 Oct '13

22 Oct '13

On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning wrote: > I updated R, numpy, scipy, scikit and removed the atlas dependency. It > seems to work fine for the ChemicalToolBox. I do not remove the lapack > dependency, because I did not get any complains until now. I'm seeing problems on the Test Tool Shed with NumPy :( The updated no-ATLAS numpy is revision f0490401cfff http://testtoolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 My tools using NumPy via Biopython 1.62 do seem to be picking up this new NumPy package, which is good. However, the install of NumPy seems to be failing in strange and *different* ways - which I suspect points to a Tool Shed test framework bug, perhaps in sharing the dependencies between tools? ---------------------- http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id /9e9e3b860aa0 Looks like partial NumPy install? Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Traceback (most recent call last): File "setup.py", line 463, in <module> setup(**setup_args) File "/usr/lib/python2.7/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "setup.py", line 216, in run if check_dependencies_once(): File "setup.py", line 123, in check_dependencies_once _CHECKED = check_dependencies() File "setup.py", line 163, in check_dependencies if is_Numpy_installed(): File "setup.py", line 282, in is_Numpy_installed return bool(can_import("numpy")) File "setup.py", line 274, in can_import return __import__(module_name) File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py", line 137, in <module> import add_newdocs File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py", line 13, in <module> from polynomial import * File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/polynomial.py", line 11, in <module> import numpy.core.numeric as NX AttributeError: 'module' object has no attribute 'core' ---------------------- http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/9e9e3b860aa0 Apparently the same error: Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Traceback (most recent call last): File "setup.py", line 463, in <module> setup(**setup_args) File "/usr/lib/python2.7/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "setup.py", line 216, in run if check_dependencies_once(): File "setup.py", line 123, in check_dependencies_once _CHECKED = check_dependencies() File "setup.py", line 163, in check_dependencies if is_Numpy_installed(): File "setup.py", line 282, in is_Numpy_installed return bool(can_import("numpy")) File "setup.py", line 274, in can_import return __import__(module_name) File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py", line 137, in <module> import add_newdocs File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py", line 13, in <module> from polynomial import * File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/polynomial.py", line 11, in <module> import numpy.core.numeric as NX AttributeError: 'module' object has no attribute 'core' ---------------------- http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/d08767ae73ce Looks like a different partial NumPy install? Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Traceback (most recent call last): File "setup.py", line 393, in <module> if is_Numpy_installed(): File "setup.py", line 282, in is_Numpy_installed return bool(can_import("numpy")) File "setup.py", line 274, in can_import return __import__(module_name) File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py", line 137, in <module> import add_newdocs File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py", line 4, in <module> from type_check import * File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/type_check.py", line 8, in <module> import numpy.core.numeric as _nx File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/core/__init__.py", line 42, in <module> __all__ += shape_base.__all__ AttributeError: 'module' object has no attribute '__all__' ---------------------- http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/834cf6618a14 Looks like yet another different partial NumPy install? Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Bio/Cluster/clustermodule.c: In function ‘py_median’: Bio/Cluster/clustermodule.c:2164:31: error: ‘PyArray_NOTYPE’ undeclared (first use in this function) Bio/Cluster/clustermodule.c:2164:31: note: each undeclared identifier is reported only once for each function it appears in Bio/Cluster/clustermodule.c: In function ‘py_mean’: Bio/Cluster/clustermodule.c:2230:31: error: ‘PyArray_NOTYPE’ undeclared (first use in this function) error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 ---------------------- http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/308ec20faefb My old favourite, listed under "Latest revision: failing tool tests" but with no visible test results or install failure - but as this also depends on Biopython and NumPy so it probably failed installation too. Regards, Peter

4 18

RFC: Streamlined Uploading
by John Chilton 22 Oct '13

22 Oct '13

This question is vaguely related to the following pull request put together by Gert Hulselmans. https://bitbucket.org/galaxy/galaxy-central/pull-request/171/avoid-corrupti… I think it makes sense to add this option. But I also I think the upload form is getting quite complicated and it only promises to get more complicated (looking ahead to things like advanced handling of compressed datasets or dataset collections). So I have the outline of a plan that could potentially address some of this that I would be interested in feedback on: 1) We merge this pull request. 2) Rename (or re-describe I guess): "Upload File from your computer" to "Advanced Upload Tool" (still with id upload1 to keep things as simple as possible). 3) We then create several news tools, which would appear before "Advanced Upload Tool" in the "Get Data" section: "Upload file from your computer" "Import files from the web via URLs" "Import FTP uploaded files" "Paste file contents" Each of these has just the form element they need (upload box, textbox, or FTP selector) as well for genome selection box. They also have a checkbox conditional for advanced options for "Convert tabs to spaces", the new "Posix lines", and perhaps "File format" (we could default to *auto* and make specification an advanced option). More thought should be given to what is considered a advanced option in each of these cases. If you are pasting content, you do not need the new "posix lines" option, but replace spaces with tabs might be a very common option. Whereas for uploaded files the inverse is sort of true. 4) To further streamline things, we could replace "Your history is empty. Click 'Get Data' on the left pane to start" in the empty history section with something with links: "Your history is empty. To get started, import data from [your computer], [web links], [your clipboard], [FTP], or by choosing an external data source from the 'Get Data' section in the left panel". I kind of find the big upload form daunting and I consider myself something of a Galaxy expert, I assume new users must find it even more so. I have no data to back this however, so let me know if you think I am way off base here. I would be really interested for perspectives from people who work closely with new users. Also it is potentially confusing that to upload data via URLs for instance you click a link that says "Upload File from your computer". This could simplify that as well. Thoughts? Thanks for your time, -John

3 2