- galaxy-dev - lists.galaxyproject.org

Workflow step IDs: out of order?
by Freek de Bruijn 15 Sep '14

15 Sep '14

Hi everyone, The Galaxy API is a great way to interact with a Galaxy server and I've been using it to run workflows (supported by the blend4j library, since I'm working on a Java project). Recently, I ran into a challenge with the workflow step IDs. When retrieving the metadata of a Galaxy workflow (using the API and blend4j), the order of the workflow step IDs appears to be random (or at least, not what I expected). This makes it complicated to specify parameters when you run a workflow via the API, because the step ID and parameter name normally are a nice way to pick the parameter you want to set (blend4j method: WorkflowInputs.setStepParameter). Is is possible to determine which step ID is assigned to - for example - the second workflow step? >From a few tests and looking at the Galaxy source code, it looks to me like the workflow steps are sorted according to their position in the workflow editor (in ascending order of sqrt(sqr(position.x) + sqr(position.y))). When storing the workflow in the database, the ID field for each step is assigned a unique unpredictable number (by SQLAlchemy or the database?). But in addition to the ID, there is also a nice order_index field, which contains the indices in the expected order! Would it be possible to add the order_index field to the API and would that solve the step order issue? Cheers, Freek ------ Freek de Bruijn Scientific programmer | VU University medical center

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custom datatypes
by Calvin Morrison 13 Sep '14

13 Sep '14

Hi, I just want a simple data type for my 'custom' datatype (it's just a trained matrix in a specific format generated by my database building tool), so that my tools which use this database will only see ones with that format in the dropdown select list. in my datatypes.xml i have this: <datatype extension="gz" type="galaxy.datatypes.quikrdb" mimetype="application/octet-stream" display_in_upload="true" description="A database trained with quikr." /> then in my tool xml files i have <outputs> <data name="output" format="quikrdb" /> </outputs> which seems to be fine, but my tools which use it still show me all my data, not just trained db's <param name="dbname" type="data" format="quikrdb" label="custom trained database"/> Am i doing something wrong? Calvin Morrison

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Incorrect revision getting referenced in a complex tool dependency - why?
by Melissa Cline 12 Sep '14

12 Sep '14

Hi Folks, Okay, I really need debugging ideas on this one. I have three repositories I'm developing under the test toolshed. They're named start_xena, xena_import and xena_find_datasets (they're all under visualization). start_xena contains a simple tool dependency to a package named installXena. xena_import and xena_find_datasets contain complex dependencies to installXena. I've installed these tools on two computers. On one, everything works great - amazingly well, in fact! Kudos, Development Team! On the other computer, the env.sh files associated with the complex dependencies keep referencing the wrong version of start_xena/installXena. Here are the gory details. The start_xena tool is installed in testtoolshed.g2.bx.psu.edu/repos/melissacline/start_xena/82755b0ee5a5/start…. I'm a bit confused about the revision part of the path, because the latest revision is different (75c7d80df9c1), and I have uninstalled and re-installed the tool since its last update. Its package, installXena, is installed under tool_dependencies at tool_dependencies/installXena/1.0/melissacline/start_xena/82755b0ee5a5/. That directory contains all the files I'd expect to be there, and its env.sh file contains all the environment variables I'd intended to set. So far, so good. xena_import is installed on my computer at testtoolshed.g2.bx.psu.edu/repos/melissacline/xena_import/dc42b6bbc22b/xena…. Its tool_dependencies.xml reference installXena under start_xena as: <?xml version="1.0"?> <tool_dependency> <package name="installXena" version="1.0"> <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="start_xena" owner="melissacline" changeset_revision="82755b0ee5a5"/> </package> </tool_dependency> (Aside: is it necessary to have the changeset_revision in there? I'm a bit worried about the maintenance task of updating it for all of my dependent tools every time I update start_xena, but as I'll explain, it's not clear that this revision info is getting used). The tool dependency dir for xena_import is at tool_dependencies/installXena/1.0/melissacline/xena_import/dc42b6bbc22b/. Its env.sh reads: if [ -f /Users/melissacline/src/galaxy-dist/tool_dependencies/installXena/1.0/melissacline/start_xena/0676a227dbc6/env.sh ] ; then . /Users/melissacline/src/galaxy-dist/tool_dependencies/installXena/1.0/melissacline/start_xena/0676a227dbc6/env.sh ; fi Notice that the wrong revision number is in there. The 06 revision was an older one. Needless to say, the files and environment variables I need aren't in the 06 directory. Where does this incorrect revision number come from? I've deleted all the 06 directories, repeatedly. I've deleted and reinstalled the tools, and verified that after deletion, the directories in question were in fact gone. I've tried resetting the metadata for these tools under the Galaxy Admin menu. Now I need new ideas. As I mentioned, all of this works beautifully on a second computer. It's as if the first Galaxy installation, on the first computer, got stuck with some outdated information, and I haven't figured out how to clear it out. Thanks! Melissa

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Tool Errors
by Calvin Morrison 12 Sep '14

12 Sep '14

Hi guys, I am trying to write a tool with a conditional and for whatever reason the results, well aren't any results. It just says 'no seek', which totally bewildering. Does anyone know what this means? Thank you, Calvin my xml file: <tool id="quikr" name="Quikr"> <description>Classify with Quikr</description> <command> # if $qdb.dbtype == "user" quikr -v -k 0 -s ${qdb.dbname} -i ${input} -o ${output} # else quikr -v -k 0 -s "${qdb.dbname}${qdb.dbsize}".mat.gz -i ${input} -o ${output} # end if </command> <inputs> <param name="input" type="data" format="fasta" label="input fasta file"/> <conditional name="qdb"> <param name="dbtype" type="select" label="Genomes to score against"> <option value="default" selected="true">Pretrained databases</option> <option value="user">Custom trained quikr database</option> </param> <when value="user"> <param name="dbname" type="data" format="quikrdb" label="custom trained database"/> <param name="dbsize" type="hidden" label="mer size"> <option value="5">5</option> </param> </when> <when value="default"> <param name="dbname" type="select" label="Choose database"> <option value="/data/galaxy/data/gg91">Green Genes 91%</option> <option value="/data/galaxy/data/gg94">Green Genes 94%</option> <option value="/data/galaxy/data/rdp">RDP Trained Set</option> </param> <param name="dbsize" type="select" label="mer size"> <option value="5">5</option> <option value="6">6</option> <option value="7">7</option> <option value="8">8</option> </param> </when> </conditional> <param name="lambda" type="integer" size="6" value="10000" label="lambda" help="default 10000"/> </inputs> <outputs> <data name="output" format="tabular" /> </outputs> <help> </help> </tool>

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Amazon cloud setup for galaxy training
by Anne Pajon 12 Sep '14

12 Sep '14

Dear, I am setting up with my colleague Jing an Introductory Galaxy training course at the University of Cambridge due to on the 24th September. I am looking for help on how to setup the cloud to have a smooth user experience during the workshop. Would you have any links with information to recommend or any advices on how to set it up? Many thanks in advance. Kindest regards, Anne. -- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon(a)cruk.cam.ac.uk | +44 (0)1223 769 631

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Installing Galaxy on Freebsd 10.0
by ashish damania 11 Sep '14

11 Sep '14

# sh run.shSome eggs are out of date, attempting to fetch...Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetchedWarning: simplejson (a dependent egg of bioblend) cannot be fetchedsimplejson 2.1.1 couldn't be downloaded automatically. You can trybuilding it by hand with: python scripts/scramble.py -e simplejsonFetch failed.Traceback (most recent call last): File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 38, in app_factory from galaxy.app import UniverseApplication File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/app.py", line 12, in <module> from galaxy.visualization.data_providers.registry import DataProviderRegistry File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py", line 2, in <module> from galaxy.visualization.data_providers import genome File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 17, in <module> from pysam import !csamtools, ctabix File "/usr/home/ec2-user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg/pysam/__init__.py", line 1, in <module> from csamtools import *ImportError: /usr/home/ec2-user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg/csamtools.so: Undefined symbol "__ks_insertsort_heap"So I have tried running this scriptpython scripts/scramble.py -e simplejsonTraceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/scramble.py", line 60, in scramble raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, new_egg ) )galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for simplejson did not appear to fail, but no egg found to copy from expected path: /usr/home/ec2-user/galaxy-dist/scripts/scramble/build/py2.7/simplejson/dist/simplejson-2.1.1-py2.7.eggI found that I have file named: "simplejson-2.1.1-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg" in the "../scripts/scramble/build/py2.7/simplejson/dist/" folder. I renamed that file simplejson-2.1.1-py2.7.egg but it gives me that same error when I execute "sh run.sh".Is it ok to run Galaxy under Freebsd 10.0? Are there any compatibility issues?Thanks you.

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no capsule export from a local tool shed
by Christophe Antoniewski 11 Sep '14

11 Sep '14

Hi, Here is a question maybe to Greg: Since the GCC2014 we started a local toolshed following the instructions in http://gregvonkuster.org/galaxy-tool-shed-framework-building-galaxy-tools/ It works nicely, except that today I tried to export repository capsules ("export this revision") from the local toolshed and it returns the following error (see below). I cannot remember whether I had ever tested this particular action since the local tool shed set up. Thus I even cannot say whether the bug is due to an original misconfiguration or it happened later on. I can add that the local toolshed is served by apache with rewriting rules (I am saying this because in addition it is not possible to download repositories as gz archives etc... and suspect that there is maybe a problem, in addition, with the apache config). Any help appreciated ! Regards Christophe --------------- URL: http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0be… Module galaxy.web.framework.middleware.error:*149* in __call__ >> <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0be…> app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.debug.prints:*106* in __call__ >> <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0be…> environ*,* self*.*app*)* Module paste.wsgilib:*543* in intercept_output >> <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0be…> app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*84* in __call__ >> <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0be…> *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ >> <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0be…> *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ >> <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0be…> *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*190* in handle_request >> <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0be…> body *=* method*(* trans*,* ****kwargs *)* Module galaxy.webapps.tool_shed.controllers.repository:*1249* in export >> <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0be…> repositories_archive_filename *=* os*.*path*.*basename*(* repositories_archive*.*name *)* *AttributeError: 'NoneType' object has no attribute 'name'* Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 christophe.antoniewski(a)upmc.fr http://bio-dev.snv.jussieu.fr/ Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org http://www.sciencesenmarche.org/

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BAMtools in Galaxy
by Anton Nekrutenko 11 Sep '14

11 Sep '14

Derek: Just to let you know that I just wrapped BAMTools for Galaxy: GitHub -> https://github.com/nekrut/bamtools GalaxyToolShed -> https://toolshed.g2.bx.psu.edu/view/anton/bamtools Galaxt Test Server -> https://test.galaxyproject.org (look for BAMTools on the left pane). We will roll them out on the main site soon. Thanks for a great package! anton -- Anton Nekrutenko Professor of Biochemistry and Molecular Biology http://nekrut.bx.psu.edu (814) 826-3051

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Keeping Galaxy up to date
by Thomas Bellembois 11 Sep '14

11 Sep '14

Hello, I try to keep our Galaxy instance up to date. Very often, some tools disappear and other do not work anymore. This breaks some users workflows. I may miss something. Is there a "best update pratice" to keep a Galaxy instance and the tool-sheds fully functionnal ? Regards, Thomas -- Thomas Bellembois, Network and System Administrator, IGFL (France) http://perso.ens-lyon.fr/thomas.bellembois - +33 4 26 73 13 67 (IGFL internal IT doc: http://itdoc.igfl.ens-lyon.fr/itdoc)

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ToolShed test failure: NotFound: cannot find 'ucsc_display_sites' while searching for 'APP.config.ucsc_display_sites'
by Peter Cock 11 Sep '14

11 Sep '14

Hi all, I'm wondering why my samtools_depad repository tests have failed, and since I have not changed this recently presume this is due to a Galaxy change or general TestToolShed problem not specific to my tool: https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad Tests that failed Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterj…) Stderr: Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 114, in test_tool self.do_it( td ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 35, in do_it self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 75, in _verify_outputs galaxy_interactor.verify_output( history, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 82, in verify_output self._verify_metadata( history_id, hid, attributes ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 103, in _verify_metadata raise Exception( msg ) Exception: Dataset metadata verification for [file_ext] failed, expected [bam] but found [None]. Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/web/framework/decorators.py", line 243, in decorator rval = func( self, trans, *args, **kwargs) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/webapps/galaxy/api/history_contents.py", line 188, in show return self.__show_dataset( trans, id, **kwd ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/webapps/galaxy/api/history_contents.py", line 214, in __show_dataset hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/web/base/controller.py", line 855, in get_display_apps for display_app in hda.get_display_applications( trans ).itervalues(): File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/model/__init__.py", line 1754, in get_display_applications return self.datatype.get_display_applications_by_dataset( self, trans ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/data.py", line 445, in get_display_applications_by_dataset value = value.filter_by_dataset( dataset, trans ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/display_applications/application.py", line 200, in filter_by_dataset if link_value.filter_by_dataset( data, trans ): File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/display_applications/application.py", line 78, in filter_by_dataset if fill_template( filter_elem.text, context = context ) != filter_elem.get( 'value', 'True' ): File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1410263883_33_43576.py", line 82, in respond NotFound: cannot find 'ucsc_display_sites' while searching for 'APP.config.ucsc_display_sites' requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/993bad2fe35335db/contents/7fbe67cfae825002?key=edc04240db9605fb7edc7bab44d3404c HTTP/1.1" 500 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): 127.0.0.1 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/993bad2fe35335db/contents/7fbe67cfae825002/provenance?key=edc04240db9605fb7edc7bab44d3404c HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): 127.0.0.1 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/993bad2fe35335db/contents/7fbe67cfae825002/provenance?key=edc04240db9605fb7edc7bab44d3404c HTTP/1.1" 200 None Any thoughts? Thanks, Peter

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