- galaxy-dev - lists.galaxyproject.org

building indexes
by Nikolaos Tur 03 Oct '16

03 Oct '16

Hi, I try to build indexes for ch38 (GRCh38.84 Toplevel) using data managers for BWA-MEM and TwoBit. Both failed. Error building index: Error in faToTwoBit, index overflow at CHR_HSCHR4_5_CTG12. The 2bit format does not support indexes larger than 4Gb, please split up into smaller files. [bwa_index] Update BWT... [bwt_bwtupdate_core] Failed to allocate 46629609168 bytes at bwtindex.c line 135: Cannot allocate memory Error building index. So, how to split genome for TwoBit and how much RAM is needed for BWA indexes? These errors are from runs on machine with 45GB RAM. Thanx, Nikolaos

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Install error of package_bioconductor_limma_3_28_10
by Alexandre Defelicibus 03 Oct '16

03 Oct '16

Hi all, I got this error when I tried to install the package package_bioconductor_limma_3_28_10 <https://toolshed.g2.bx.psu.edu/repository/browse_repositories?sort=name&ope…> : Error downloading from URL https://depot.galaxyproject.org/software/limma/limma_3.28.10_src_all.tar.gz: HTTP Error 404: Not Found Could someone help me? Best regards, Alexandre

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News of the Galaxy: October 2016
by Dave Clements 03 Oct '16

03 Oct '16

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New Galaxy Australia community opens registrations for GAMe 2017
by Dave Clements 03 Oct '16

03 Oct '16

>From the GAMe 2017 Organising Committee <https://www.embl-abr.org.au/game2017/organisers/>: Today we officially launch the Galaxy Australia <https://www.embl-abr.org.au/galaxyaustralia/> community with the opening of registrations for the Galaxy Australasia Meeting 2017 (GAMe 2017) being held in Melbourne over 3-9 February. Australian Galaxy users and administrators will now have more opportunities to interact and collaborate to identify and address the needs of the local community. The community will also be a hub for Australian Galaxy training courses and offer a catalog of Australian Galaxy servers. The establishment of Galaxy Australia is supported by the EMBL Australia Bioinformatics Resource (EMBL-ABR) in its appointed role of supporting the development of skills and training in the Australian life science research community. At the EMBL-ABR Hub, hosted at the Victorian Life Sciences Computation Initiative (VLSCI), Galaxy is used extensively for teaching and data analysis directly as well as through the Australian-made Genomics Virtual Laboratory <https://www.genome.edu.au/>. VLSCI’s expert bioinformaticians and professional staff will help promote community activities and training. Galaxy Australia has a Twitter feed (@GalaxyAustralia <https://twitter.com/galaxyaustralia>) for announcements and discussion relevant to the community. *Galaxy Australasia Meeting 2017 (GAMe 2017)* The Community’s first major activity is to organise the Galaxy Australasia Meeting 2017 (GAMe 2017), 3-9 February in Melbourne. We are pleased to announce that early registration <https://www.embl-abr.org.au/game2017/registration/> and talk and poster abstract submission <https://www.embl-abr.org.au/game2017/submit-your-talkposter/> are now open for the GAMe 2017. This meeting will bring together biomedical researchers, bioinformaticians, infrastructure providers, and data producers from across Australia and Asia to share expertise across many levels. The conference <https://www.embl-abr.org.au/game2017/conference/> starts 4 February and features two full days of keynotes, accepted and sponsor talks, poster and sponsor sessions, birds-of-a-feather gatherings, a conference dinner and lots of opportunities for networking. Prior to the conference we are offering a Researcher Training Day <https://www.embl-abr.org.au/game2017/training-day/> on 3 February, aimed at biomedical researchers who need to analyse their biological data. The conference is followed by a four day workshop on Galaxy server administration <https://www.embl-abr.org.au/game2017/training-for-admin-workshop/> for those working at that level. Talk abstracts are due 30 November <https://www.embl-abr.org.au/game2017/submit-your-talkposter/> and early registration ends 31 December <https://www.embl-abr.org.au/game2017/registration/>. Register now and save up to 43% off regular registration rates. There are also scholarships available for eligible students and postdocs <https://www.embl-abr.org.au/game2017/registration/#scholarships>. The scholarship application deadline is 18 November. We look forward to welcoming you to Melbourne. Remember to pack for our fabulous February weather! *GAMe 2017 Organising Committee <https://www.embl-abr.org.au/game2017/organisers/> (#game_2017)* -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Workflow ID, Galaxy Instance URL, API Key in Galaxy Tool Config
by Katherine Beaulieu 30 Sep '16

30 Sep '16

Hi everyone, We are trying to obtain the three things in the tile of this post to enable a tool to use the bioblend api and get the .ga file so that any user can go back into our system, get the workflow associated with the end file, get the input parameters which are tags associated with the end file, and rerun that workflow if necessary. So simply put I am asking if there is a way to access a galaxy instance through the bioblend api from within a tool's config xml file. I have asked about getting the .ga file beforehand but still have not solved this problem so if anyone has any experience with this please let me know. Cheers, Katherine

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Galaxy Feature Request: Input naming deficiencies
by Ziphozakhe Mashologu 30 Sep '16

30 Sep '16

Hi All In using Galaxy, I would like to be able to keep track of the input dataset name down the analysis chain. This is a similar if not the same issue raised by Eric in https://github.com/galaxyproject/galaxy/issues/2752, to which he proposes in the context of a workflow that, "the rename dataset action should support usage of all the dataset names from Input Dataset elements, rather than just input files to the particular tool." Please see the issue for more details. There are other similar issues raise scattered all over regarding the same issue: Enhancements: 1. Ability to name datasets using the element identifier: https://github.com/galaxyproject/galaxy/issues/2006 2. Ability to define the collection name in a workflow: https://github.com/galaxyproject/galaxy/issues/2398 3. Name datasets according to both collection name and element identifier: https://github.com/galaxyproject/galaxy/issues/2140, https://github.com/galaxyproject/galaxy/issues/2023 Bug Fixes: 1. Renaming using the input from paired dataset collections: https://github.com/galaxyproject/galaxy/issues/1675, https://github.com/galaxyproject/galaxy/issues/1686 I have created a github issue regarding the above, in effort to try and consolidate all these related above issues. https://github.com/galaxyproject/galaxy/issues/2980 Can we use the above issue to discuss the best approach on these issues, point out work being done on the area and perhaps define clear milestones for each? Galaxy Devs please provide me some guidance to best tackle this. (particularly of tracking the input dataset names along the analysis chain). Thanks, Zipho

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workflow import error
by Tony Schreiner 30 Sep '16

30 Sep '16

We have 2 galaxy instances running one is v15.05-74-gf6b894a the other is v15.10-30-g6a47d2d a user is trying to import a workflow file, it works on the older one, but raises an error on the newer one. URL: http://redacted.edu:8080/workflow/import_workflow <http://prince.bc.edu:8080/workflow/import_workflow> File '/cluster/home/galaxy/galaxy/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File '/cluster/home/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/cluster/home/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/cluster/home/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/cluster/home/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 191 in handle_request body = method( trans, **kwargs ) File '/cluster/home/galaxy/galaxy/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 921 in import_workflow workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source=src, add_to_menu=add_to_menu ) File '/cluster/home/galaxy/galaxy/lib/galaxy/web/base/controller.py', line 1111 in _workflow_from_dict publish=publish File '/cluster/home/galaxy/galaxy/lib/galaxy/managers/workflows.py', line 159 in build_workflow_from_dict module, step = self.__module_from_dict( trans, step_dict, secure=False ) File '/cluster/home/galaxy/galaxy/lib/galaxy/managers/workflows.py', line 605 in __module_from_dict module.save_to_step( step ) File '/cluster/home/galaxy/galaxy/lib/galaxy/workflow/modules.py', line 592 in save_to_step step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app ) File '/cluster/home/galaxy/galaxy/lib/galaxy/tools/__init__.py', line 1980 in params_to_strings return params_to_strings( self.inputs, params, app ) File '/cluster/home/galaxy/galaxy/lib/galaxy/tools/parameters/__init__.py', line 92 in params_to_strings value = params[ key ].value_to_basic( value, app ) File '/cluster/home/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py', line 574 in value_to_basic rval[ self.test_param.name ] = self.test_param.value_to_basic( value[ self.test_param.name ], app ) KeyError: 'uncol' i'm not able conclude much from this dump. Can anyone suggest some steps to debug this. Cheers Tony Schreiner

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Problem with conda on galaxy 16.07
by Léo Biscassi 30 Sep '16

30 Sep '16

Hi folks, Today after perform some tests with conda on galaxy 16.07 the follow message was returned in my terminal: "*Conda dependency seemingly installed but failed to build job environment.* " The error occurs when *build_isolated_environment()* function is call. Below some variable values: *is_installed* = *True* *job_directory* = */home/leobiscassi/programs/galaxy/job_work_dir/000/17* *env_path* = */home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env* *exit_code* = *127* Analyzing inside of the *build_isolated_environment()*, the *exec_create() *function is executed because *path* variable ( */home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env*) don't exists, the command executed by *exec_create* is showed below: *deps/_conda/bin/conda create -y --unknown --offline --prefix /home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env --file ./database/tmp/jobdepsIGslWfe2bd2345d2ec1bb4aeb81211183570bae7db28a3bea4f7ff9e8e75074719a7ee/__mgltools(a)1.5.6 > /dev/null* Some important values: *env* = *{'HOME': 'deps/_conda', 'CONDARC': '/home/leobiscassi/programs/galaxy/deps/_condarc'}* The command return is '*/bin/sh: 1: deps/_conda/bin/conda: not found*', but the binary exist. Anyone can help me with this? Thanks in advance. -- Best regards, *Léo Biscassi*

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compilation fails in pyBamTools & pyBamParser dependency packages
by Nikolaos Tur 30 Sep '16

30 Sep '16

Hi, installing tool dependency package_pybamtools_0_0_2 as well as package_pybamparser_0_0_1 cause below mansion errors. Following the tool_dependencies.xml file: <action type="shell_command">hg clone -r ba0341816b15fff5e0a554658d6579a60e1b12b1 https://bitbucket.org/dan/pybamtools pyBamTools</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR</action> I can download this package and manually compile it without errors under Galaxy environments. Question is what are sources of these errors and how to solve them using standard Galaxy installation procedure? After googling this errors there were mentions that it can be due to deprecated package `distribute' in new version of python and it is better to use `setuptools'. It is also described in pybamtools sources and after small modification to use `setuptools' in setup.py script it is also manually compiled without problems. Thanx, Nikolaos Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz Extracting in /tmp/tmpDIcsTL Now working in /tmp/tmpDIcsTL/distribute-0.6.38 Building a Distribute egg in /home/galaxy/galaxy/database/tmp/tmp-toolshed-mtdFbEf6k/pyBamTools Traceback (most recent call last): File "setup.py", line 248, in <module> scripts = scripts, File "/home/galaxy/python27/python/2.7.9/lib/python2.7/distutils/core.py", line 111, in setup _setup_distribution = dist = klass(attrs) File "/tmp/tmpDIcsTL/distribute-0.6.38/setuptools/dist.py", line 225, in __init__ _Distribution.__init__(self,attrs) File "/home/galaxy/python27/python/2.7.9/lib/python2.7/distutils/dist.py", line 287, in __init__ self.finalize_options() File "/tmp/tmpDIcsTL/distribute-0.6.38/setuptools/dist.py", line 257, in finalize_options ep.require(installer=self.fetch_build_egg) File "/tmp/tmpDIcsTL/distribute-0.6.38/pkg_resources.py", line 2027, in require working_set.resolve(self.dist.requires(self.extras),env,installer)) File "/tmp/tmpDIcsTL/distribute-0.6.38/pkg_resources.py", line 2237, in requires dm = self._dep_map File "/tmp/tmpDIcsTL/distribute-0.6.38/pkg_resources.py", line 2466, in _dep_map self.__dep_map = self._compute_dependencies() File "/tmp/tmpDIcsTL/distribute-0.6.38/pkg_resources.py", line 2499, in _compute_dependencies common = frozenset(reqs_for_extra(None)) File "/tmp/tmpDIcsTL/distribute-0.6.38/pkg_resources.py", line 2496, in reqs_for_extra if req.marker_fn(override={'extra':extra}): File "/tmp/tmpDIcsTL/distribute-0.6.38/_markerlib/markers.py", line 109, in marker_fn return eval(compiled_marker, environment) File "<environment marker>", line 1, in <module> NameError: name 'sys_platform' is not defined /home/galaxy/galaxy/database/tmp/tmp-toolshed-mtdFbEf6k/pyBamTools/distribute-0.6.38-py2.7.egg Traceback (most recent call last): File "setup.py", line 9, in <module> use_setuptools() File "/home/galaxy/galaxy/database/tmp/tmp-toolshed-mtdFbEf6k/pyBamTools/distribute_setup.py", line 152, in use_setuptools return _do_download(version, download_base, to_dir, download_delay) File "/home/galaxy/galaxy/database/tmp/tmp-toolshed-mtdFbEf6k/pyBamTools/distribute_setup.py", line 132, in _do_download _build_egg(egg, tarball, to_dir) File "/home/galaxy/galaxy/database/tmp/tmp-toolshed-mtdFbEf6k/pyBamTools/distribute_setup.py", line 123, in _build_egg raise IOError('Could not build the egg.') IOError: Could not build the egg.

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why modified workflow doesn't save?
by Nikolaos Tur 30 Sep '16

30 Sep '16

Hi, after modification of workflow it does not save in workflow editor. Just shows saving bar for ever. In logs there are not so much info, just mentions that using version of tools are different from specified in this workflow. I work with "CloudMap Hawaiian ..." workflow. Galaxy is 16.04 with version of tools at June/July time. Workflow file is a text file and potentially can be modified by hands. In this case on what I have to pay attention to change it in text editor. Is there any tutorial for this? Thanx, Nikolaos.

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