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Local: BWA 0.5.9. SA Coordinate/Segmentation fault
by Moritz Juchler 30 Jul '13

30 Jul '13

Hey, 1 I installed Galaxy locally. 2 I also have BWA installed and then used the 3 shed repository to get the bwa wrapper. 4 I have the reference genome now I'm stuck with the calculate SA coordinate. Segmenation fault. Google tells me that it could be a problem with -space (I have 4GB left) -the version I use. (I use 0.5.9 and did a succesful alignment with 0.7.5a, but the tool shed says 0.5.9, hence *could I just change to the current version* (without Galaxy knowing it), with which I did a succesful alignment?) Best Moritz

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Re: [galaxy-dev] CloudMan Error
by Dannon Baker 30 Jul '13

30 Jul '13

The warning message printed by the first ssh attempt indicates that you have no cloudman_key_pair.pem in the directory you executed the ssh command from. Find this file (or create a new one) and you'll be able to ssh. Good luck, and please keep threads on the list instead of emailing directly. Thanks! -Dannon On Mon, Jul 22, 2013 at 1:36 PM, <denizere(a)gmail.com> wrote: > Hi- the share string appears to be loading, but I am unable to ssh into my > instance using the provided command, or anything like it. Instead I get the > following: > > denizerezyilmaz$ ssh -i cloudman_key_pair.pem > ubuntu(a)ec2-54-242-61-164.compute-1.amazonaws.com > Warning: Identity file cloudman_key_pair.pem not accessible: No such file > or directory. > > OR: > > denizerezyilmaz$ ssh ec2-54-242-61-164.compute-1.amazonaws.com > Permission denied (publickey). > > What am I missing? Thank you, Deniz >

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Re: [galaxy-dev] Number of outputs = number of inputs
by Shafer, Christina 30 Jul '13

30 Jul '13

My question is related to this post <http://dev.list.galaxyproject.org/Number-of-outputs-number-of-inputs-td4656…> in the archive. As recommended, I referred to http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_… for some guidance on how to achieve multiple output files, specifically one set of six files per number of times the <repeat> tag is called. The example provided isn't that informative, however, as it doesn't show what the example_tool.sh command script is doing so I can make my perl wrapper script do the same thing. If I have six files total, do I only specify one in the <outputs> tag and then have the remaining 5 named according to the scheme in the perl wrapper? Or is it Galaxy that does the naming of the remaining files automatically? Is there a perl equivalent to the "$__new_file_path__" variable that I can use, or is this the literal resolved file path (e.g. "/opt/galaxy/... etc)? Right now, upon execution of my tool, if a user has two entries (so number of times <repeat> has executed is twice), my perl wrapper is called twice (good), but on the second call, Galaxy uses the same output filenames as the first run such that the first set of output files are all overwritten by the second execution (bad). How do I make sure that each <repeat> iteration results in a unique set of output files? Thanks for your help! Christina Shafer, Ph.D Regenerative Biology Laboratory Morgridge Institute for Research

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job_conf.xml about running Galaxy tools on a cluster.
by shenwiyn 30 Jul '13

30 Jul '13

Hi everyone， I am a newer in Galaxy. I installed my Galaxy with Torque2.5.0 . I used my job_conf.xml for a test ,my Galaxy seems to work with TORQUE by the interface of pbs_modoule ( _pbs.so) successfully. In my test job_conf.xml , it seems that we should use <tools>collection of <tool id="bwa_wrapper" destination="multicorejobs4"/>to specify bwa to run as multicorejobs4. But I do not sure wheather all the tools in Galaxy we should specify their destination (such as, regularjobs,longjobs), or all the tools would work with a default destination(<destinations default="regularjobs">).,unless we specify them. Could anyone give me some help please? This is my test job_conf.xml: <?xml version="1.0"?> <job_conf> <plugins workers="4">  <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="8"/> </plugins> <handlers default="batch">  <handler id="node01" tags="batch"/> <handler id="node02" tags="batch"/>  </handlers> <destinations default="regularjobs">  <destination id="local" runner="local"/> <destination id="regularjobs" runner="pbs" tags="cluster">  </destination> <destination id="longjobs" runner="pbs" tags="cluster,long_jobs">  </destination> <destination id="shortjobs" runner="pbs" tags="cluster,short_jobs">  </destination> <destination id="multicorejobs" runner="pbs" tags="cluster,multicore_jobs">  </destination> <destination id="real_user_cluster" runner="pbs"> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="dynamic" runner="dynamic">  <param id="type">python</param> <param id="function">interactiveOrCluster</param> </destination> </destinations> <tools>  <tool id="bwa_wrapper" destination="multicorejobs"/> </tools> <limits>  <limit type="registered_user_concurrent_jobs">500</limit> <limit type="unregistered_user_concurrent_jobs">1</limit> <limit type="concurrent_jobs" id="local">1</limit> <limit type="concurrent_jobs" tag="cluster">200</limit> <limit type="concurrent_jobs" tag="long_jobs">200</limit> <limit type="concurrent_jobs" tag="short_jobs">200</limit> <limit type="concurrent_jobs" tag="multicore_jobs">100</limit> </limits> </job_conf> shenwiyn

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How to display tool instead of html WWFSMD page at start-up?
by Neil.Burdett＠csiro.au 30 Jul '13

30 Jul '13

Hi, When Galaxy is started the centre column displays the "Hello world! It's running ..." WWFSMD? Html Page. How can this be changed so that a tool i.e. get data tool is shown up on start-up with all its text boxes etc rather than the default html file? Is this possible? Thanks Neil

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importing data from other public websites into galaxy
by Prasun Dutta 30 Jul '13

30 Jul '13

Hi, I wish to import data into my local instance of galaxy from another website. Kindly let me know how to achieve that and what all is required. I want to import data from a chemoinformatic database (mainly compound structures) into galaxy and run my own analysis tools on them. Regards, Prasun Dutta MSc (Bioinformatics) School of Biological Sciences University of Edinburgh, UK

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Auto hide tool and history panels
by Neil.Burdett＠csiro.au 30 Jul '13

30 Jul '13

Hi When starting Galaxy the tool panel and history panels appear as default. On the bottom of these panels are two arrows to minimise / hide the panels. Can someone show me how to make the panels be hidden by default rather than shown ? Thanks Neil

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Does the xml tool wrapper language have ifs or functions?
by Ben Gift 29 Jul '13

29 Jul '13

I'm finding it hard to deal with mutually exclusive options that also share many options between them for certain command line tools. Functions of if statements could solve this copy/pasting problem. Thanks

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Tool Shed test framework breaking where run_functional_tests.sh works
by Peter Cock 29 Jul '13

29 Jul '13

On Thu, May 9, 2013 at 10:49 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: > > Hi Dave, > > As you hoped, these test now shows up on the tool page (as expected > they are test failures - apparently my install script isn't quite right yet): > > ... > > This one is more interesting, and appears to be a problem with the > test framework (both tests pass locally via run_functional_tests.sh): > > http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 > Functional test results for changeset revision 16a1a5ae98e9 of seq_rename > 0 tests passed, 2 tests failed, 0 tests missing test components. > > I'll raise that on a new thread, Here's the output from the (Test) Tool Shed where the tests fail: Tests that failed *Tool id:* seq_rename *Tool version:* seq_rename *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 1320, 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 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['2']' in form 'tool_form' threw exception: cannot find value/label "2" in list control control: <SelectControl(new_column=[1])> 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. *Tool id:* seq_rename *Tool version:* seq_rename *Test:*test_tool_000001 ( 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 1320, 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 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> 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. Both tests fail with the following assertion: AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> 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. Both tests pass on my development machine run via: $ ./run_functional_tests.sh -id seq_rename The two tests are defined as follows - identical bar the style used for the column arguments - I was wondering if the Tool Shed testing was stricter about numeric column names, but that does not seem to be relevant: <tests> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="1" /> <param name="new_column" value="2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="c1" /> <param name="new_column" value="c2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> </tests> I can retest with the latest galaxy-dist once this issue is resolved: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.html Peter

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Cloudman - When will the symlinks be resolved ?
by Ravpreet Setia 29 Jul '13

29 Jul '13

I am referring to the following bug: https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-t… We are waiting for this bug to resolve before we fix any other issues with our Cloudman scripts. I am wondering when you think this bug will be resolved so I can plan my time. Thanks.

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