June 2016 - galaxy-dev - lists.galaxyproject.org

Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt 28 Apr '17

28 Apr '17

Hi everyone, I just wanted to ask how the extra_file_path is handled in case of job running as the real user since the file_path is only writable by the galaxy user. Any clue? Thanks, L-A

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Python script can't can't import BioPython modules in Galaxy 16.01
by Makis Ladoukakis 17 Jan '17

17 Jan '17

Hello everyone, I've recently upgraded to Galaxy 16.01 and i have some issues with a python wrapper from a tool. When I run it via Galaxy I get the following error: Traceback (most recent call last): File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, in <module> from Bio import SeqIO ImportError: No module named Bio However when I click on the "view details" icon to copy the command from the tool and run it on my command line the tool works perfectly. In addition this issue occurs while I already have installed BioPython. When I type Python and write "from Bio import SeqIO" I get no error. Can this be an issue related to the virtual environment that is initialized each time Galaxy starts? Thank you in advance, Makis Ladoukakis

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Python ValueError: too many values to unpack
by Matthias De Smet 18 Oct '16

18 Oct '16

Hi all, I’m trying to develop a tool that lets you select a file on the server. I’m using the dynamic_options setting to let Galaxy render a dropdown list of available file. However, when I try to test the tool in its current form, I get the following error: <pre> galaxy.web.framework.decorators ERROR 2016-01-26 13:08:35,649 Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 260, in decorator rval = func( self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/tools.py", line 98, in build return tool.to_json(trans, kwd.get('inputs', kwd)) File "lib/galaxy/tools/__init__.py", line 2602, in to_json populate_state(trans, self.inputs, state_inputs, state_errors, params.__dict__) File "lib/galaxy/tools/__init__.py", line 2471, in populate_state state[input.name] = input.get_initial_value(trans, context, history=history) File "lib/galaxy/tools/parameters/basic.py", line 984, in get_initial_value value = [ optval for _, optval, selected in options if selected ] ValueError: too many values to unpack </pre> My tool xml looks like this: <pre> <tool id="archivetolibrary" name="Copy files" version="0.1.0"> <description>from the archive to a data library</description> <code file="list_files.py"/> <command interpreter="bash"> test.sh > $log </command> <inputs> <param name="archive_source" type="select" display="radio" label="Choose source archive"> <options from_file="archives.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> <param name="query" type="text" label="Search for files"/> <param name="selected_file" type="select" label="Choose your file" dynamic_options="list_files(archive_source,query)"/> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <test> </test> </tests> <help> This tool copies data from and archive folder to your history. Keep in mind this folder MUST be readable by Galaxy in order for this tool to work. </help> </tool> </pre> and the script called in the “code” tag looks like this <pre> def list_files(dir,query): listing=[] for fname in listdir(dir): fullpath = path.join(dir, fname) #only select datafiles, not md5 checksums if path.isfile(fullpath) and not fullpath.endswith(".md5"): listing.append( fname ) return listing </pre> This script should return a list with filenames that should be displayed in the dropdown list. I’m tracking Galaxy release 15.10, running on a Ubuntu 14.04.3 server Thanks for your help! Matthias

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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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Re: [galaxy-dev] how to create users through Galaxy API?
by Martin Čech 02 Sep '16

02 Sep '16

Hi, you specify username, password and email in the body (payload) of the POST as Key:Value pairs. Code from the API method: ( https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/ga…) username = payload[ 'username' ] email = payload[ 'email' ] password = payload[ 'password' ] There are also other conditions that need to be fulfilled (e.g. user creation has to be turned on in the configuration) - you will find these when you look at the source code of the method (because the documentation is not perfect yet, sorry). M. On Sun, Dec 29, 2013 at 11:22 PM, xlwang <xlwang_0903(a)163.com> wrote: > hi, > I still have some confusion. > post /api/users , when i use postman, it seems like this: > > > No other parameters? How to confirm the new user's information?Such as > user name, password. > Can you give me a example please?Thank you! > > At 2013-12-30 06:04:15,"Martin Čech" <marten(a)bx.psu.edu> wrote: > > Hello, > > to create a user through API you send a POST request to /api/users > > More information about User API here: > > > https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.… > > Martin > > > On Fri, Dec 27, 2013 at 5:11 AM, xlwang <xlwang_0903(a)163.com> wrote: > >> hello, >> I want to create users through Galaxy API.For example, I can get users >> information through url like this(use postman): >> http://localhost:8080/api/users?key=my_key >> But how to create a user? >> >> >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > > >

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Error running JBrowse
by Raymond Wan 16 Aug '16

16 Aug '16

Dear all, I'm trying to run the JBrowse tool within Galaxy. The installation was fine (I think), but when I run the tool, I get this error: Fatal error: Exit code 1 () Traceback (most recent call last): File "/d15/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/d022577ff9cf/jbrowse/jbrowse.py", line 11, in <module> from Bio.Data import CodonTable ImportError: No module named Does this mean I'm missing something? In the history, if I click the "(i)" icon for the incomplete job (in red), everything looks fine, except that it says: Tool Version: python: can't open file 'jbrowse.py': [Errno 2] No such file or directory However, "jbrowse.py" does exist in the path above. Any idea what could be wrong? Thank you! Ray

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Amazon Instance Types for Galaxy
by Lapointe, David 14 Jul '16

14 Jul '16

Are there instance types which will not work for Galaxy/Cloudman on AWS? EBS volumes for example. Thanks, David -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144 Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

2 1

Python tool wrapper with multiple input and output files
by Marco Tangaro 08 Jul '16

08 Jul '16

Dear experts, my name is Marco and I'm working to port our python tool to the Galaxy framework. The main script needs a rna.bam file as input, a reference fasta file, both mandatory. Finally, you can add a dna.bam file, but this is optional. Therefore an example command is: script.py -i rna.bam -f reference.fa -j dna.bam The outout is a tabular. Again the -j dna.bam option is completely optional. So quite soon it turned out that I had to use a python wrapper to parse our script. Now the wrapper works fine. The next step is to run the tool over multiple input file and we would like to avoid to use a workflow. The idea is that to each input file corresponds an output file. The reference is still the same. For instance, we have: rna_1.bam + dna_1.bam -> output_1.txt rna_2.bam + dna_2.bam -> output_2.txt rna_3.bam + dna_3.bam -> output_3.txt ... and so on. But I don't know the best strategy to give to my wrapper multiple input files. Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they correspond to the right rna_xyz.bam file. I would like to have as output a page which is showing as results the link to the single output files as suggested here. https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files planning to integrate a javascript interface. I've browsed a lot, but on multiple input file the posts are old. I'm using the last galaxy release (16_04). I'm quite new to the galaxy world... Thanks a lot for your suggestions, Marco

2 3

Auto detection of output format Galaxy custom tool
by Katherine Beaulieu 07 Jul '16

07 Jul '16

Hi everyone, I am looking to auto-detect the file format of a file outputted by a python tool I have written. Does anyone have any idea how to do this? I have tried setting the format attribute to "auto" with no luck. Let me know if you would like to see my tool config file. Cheers, Katherine

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Implementing iRODS with Galaxy
by Yip, Miu ki 01 Jul '16

01 Jul '16

Hello Galaxy Team, We're from the Bioinformatics Shared Resources (BSR) at Cold Spring Harbor Labs and we're looking to implement irods on a newly installed version of Galaxy. We want to incorporate iRODS (http://irods.org/) Is there a recommended way to do this, or no? Thanks in advance for the advice. Best, Miuki Yip

2 1

Docker for Mac
by Rathert, Philipp, Dr. 29 Jun '16

29 Jun '16

Dear all I was wondering if anybody has experience running a galaxy production server using docker for mac. I know it's beta testing at the moment but since the Virtual machine environment gave us such a hard time preserving and managing user data etc. I thought I try it anyway... However, it seems to be not as easy as expected. after installation of docker I pull the new docker galaxy image with docker pull quay.io/bgruening/galaxy:16.04 When I start a test container with net=host docker run -it --net=host quay.io/bgruening/galaxy:16.04) I am not able to connect to the galaxy web app and get this error: Starting ProFTP proftpd: ERROR (abnormal termination) and ==> /home/galaxy/logs/slurmd.log <== [2016-06-29T08:13:41.440] error: Unable to resolve "moby": Unknown host [2016-06-29T08:13:41.440] error: Unable to establish control machine address I then tried to use Kinematik and at least I get the web app running. However, I didn't find the option to change the network settings to net=host And I have the additional problem that I have to assign ownership rights to the folders in /export and I get the following error: chown -R postgres:postgres /postgresql chown: postgres: illegal group name I know these are many issues, but maybe one of you has experience with this and could provide some help. Thanks a lot, Philipp

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Doubts about Galaxy installation.
by Álvaro Rios 28 Jun '16

28 Jun '16

Dear Member of the Galaxy Team, My name is Álvaro Rios, I am Associate Professor of the North Fluminense State University, RJ, Brazil. I am a beginner in the use of Galaxy tools and, I would like to install my own Galaxy. However I am not familiarized with command lines for instation of Galaxy. My interest is to use tool like BS-seeker2 avaible into Toolshed. I am using a MacBook Pro (2,2 GHz Intel Core i7; 16G RAM). It is enough to work with Galaxy? I saw that I can download a zipped file version and install it. What file I need to click to install Galaxy? How can I become a administrador? Thank you for your attention, With Best Regards Álvaro Rios.

4 4

HTCondor tool runner configuration is not working properly on our Galaxy instance
by Vipin TS 28 Jun '16

28 Jun '16

Dear Galaxy Development team, I am deploying a clone of our public instance <https://galaxy.cbio.mskcc.org> on a new infrastructure in another data center. In the new setup, a master node with Galaxy application running and have another couple of slave nodes connected via htcondor tool runner. The master and slaves nodes are connected properly. I manually checked a job submission and it worked well. I upgraded the clone codebase to v16.04 stable release version. Found an issue in github issue tracker related to my case this <https://github.com/galaxyproject/galaxy/issues/2376> and made a comment but didn't get any response. When I submit a job for uploading a small file to the clone instance, the instance won't submit jobs and it stays idle stage. On my master node, when I use condor specific command to see the job status it is also not listing any jobs from galaxy user. I felt like the job preparation step is not done properly, The log file displays the following: galaxy.tools DEBUG 2016-06-28 17:47:58,213 Validated and populated state for tool request (23.232 ms) galaxy.tools.actions.upload DEBUG 2016-06-28 17:47:58,215 Persisted uploads (1.766 ms) galaxy.tools.actions.upload DEBUG 2016-06-28 17:47:58,256 Checked and cleaned uploads (40.963 ms) galaxy.tools.actions.upload_common INFO 2016-06-28 17:47:58,277 tool upload1 created job id 77960 galaxy.tools.actions.upload DEBUG 2016-06-28 17:47:58,315 Created upload job (58.474 ms) galaxy.tools.execute DEBUG 2016-06-28 17:47:58,315 Tool [upload1] created job [77960] (101.754 ms) galaxy.tools.execute DEBUG 2016-06-28 17:47:58,323 Executed 1 job(s) for tool upload1 request: (109.568 ms) Is there any public server running with condor as the cluster job runner? I would like to get some help to resolve my issue to connect the cluster via htcondor. Virtually enjoying the GCC2016 talks! Thank you for providing the links. Vipin | Rätsch Lab

1 0

CloudMap_Hawaiian_Variant & missing tools on new Galaxy instance
by Nikolaos Tur 28 Jun '16

28 Jun '16

Hi, imported from usegalaxy.org workflow CloudMap_Hawaiian_Variant_Mapping_with_WGS to local Galaxy instance (16.04) shows missing tools or their different versions. For instance: *Tool name* Add or Replace Groups, *id* toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0, *version* 1.56.0 *Tool name* Mark Duplicate reads, *id* toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0, *version* 1.56.0 Also it requires SNP 1.56 version. Our Galaxy instance has the latest tools version for 16.04. Does it mean I have to install older version of tools or modify workflow to use latest one? (As I see workflow asks for programs with different ids what was in older versions: picard_ARRG in 1.56 but it probably is already picard_AddOrReplaceReadGroups in 1.136. Or bedtools from aaronquinlan repository with id="bedtools_genomecoveragebed_bedgraph" and which is not available in 16.04 repositories but probably this program is in bedtools from iuc with id="bedtools_genomecoveragebed"). Also I see that tools on usegalaxy.org are even newer than our but this workflow is imported there without any errors. Does it mean that on usegalaxy.org there are many versions of the same tool but they are not visible in tools panel? Does some one have modified version of this workflow (or similar to try just cloudmap tests) to new Galaxy instance? Thanx, Nikolaos

2 2

GCC2016 will be streamed
by Dave Clements 28 Jun '16

28 Jun '16

Hello all, GCC2016 events started today with the coding and data hackathons. Training runs tomorrow and Monday, and the meeting will run on Tuesday and Wednesday. In past years we have made slides, posters and training materials, and sometimes video available online after the meeting. We’ll do that again this year (with slides and posters on the new Galaxy F1000 channel). This year, Indiana University is making it possible to go one step further: All GCC2016 training sessions <https://gcc16.sched.org/overview/type/D.x+Training+-+All> and conference talks <https://gcc16.sched.org/overview/type/E.x+Conference+-+All> will be streamed live during the events. URLs for streaming are on the conference FAQ <https://gcc2016.iu.edu/faq/index.php>. Enjoy the show, and hope to see you next year, Dave C, on behalf of the GCC2016 Exec -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

2 1

Creating a test for a Tool Shed tool
by Erika Gedvilaite 27 Jun '16

27 Jun '16

Dear Galaxy Dev, I am interested in FASTAptamer, t tool on the tool shed. I talked with Anton Netrutenko and he suggested I create some tests for the program. If you can help me set those up, it would be greatly appreciated. I have an admin rights for my own local galaxy at erikakelly13(a)gmail.com account . Thank you for all of the time and help. Sincerely, Erika Gedvilaite

1 0

Toolshed tool HiFive error running
by Bharath S 23 Jun '16

23 Jun '16

Hello, I, Bharath Saravanan (bharath.mh24(a)gmail.com) am unable to run HiFive tool from the tool shed with the following error being generated. Please help sort it out. Thank You Fatal error: Exit code 1 () Traceback (most recent call last): File "/mnt/galaxy/galaxy-app/.venv/bin/hifive", line 4, in <module> __import__('pkg_resources').run_script('hifive==1.0.2', 'hifive') File "/mnt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/pkg_resources.py", line 2716, in <module> working_set.require(__requires__) File "/mnt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/pkg_resources.py", line 685, in require needed = self.resolve(parse_requirements(requirements)) File "/mnt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/pkg_resources.py", line 588, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: hifive==1.0.2

1 0

tabular file displayed without tabs
by Ryan G 22 Jun '16

22 Jun '16

Hi - I have a tools that generates a tab-delimited text file as output. when I click the eye icon to view the data, all the fields are compressed as if there were no tabs. If I expand the history view, the little preview window shows the contents as tabbed. I've verified that the spaces are indeed '\t' tab characters. Why would Galaxy not display this file as a tab-delimited file?

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Ansible & Docker
by mark fernandes (IFR) 21 Jun '16

21 Jun '16

Given the usage of Ansible & Docker by this group - this may prove interesting. Ansible Container is undergoing rapid development. For now, Ansible Container can only be installed from source. See INSTALL.md for details. https://www.helpnetsecurity.com/2016/06/20/ansible-native-container-workflo… Red Hat launched Ansible Container under the Ansible project, which provides a simple, powerful, and agent-less open source IT automation framework. Available now as a technology preview, Ansible Container allows for the complete creation of Docker-formatted Linux containers within Ansible Playbooks, eliminating the need to use external tools like Dockerfile or docker-compose. Ansible's modular code base, combined with ease of contribution, and a community of contributors in GitHub, enables the powerful IT automation platform to manage today's infrastructure, but also adapt to new IT needs and DevOps workflows. Best, Mark Fernandes T: +44 (0)1603 255000 Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK www.ifr.ac.uk Facebook | Twitter | LinkedIn | YouTube The Institute of Food Research receives strategic funding from BBSRC

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Re: [galaxy-dev] Infinite recursion on conda dependency manager
by Rathert, Philipp, Dr. 20 Jun '16

20 Jun '16

Hi Björn, this is not working root@galaxy:/galaxy-central# export PATH=/galaxy-central/tool_deps/_conda/bin/:$PATH root@galaxy:/galaxy-central# conda install -y -q conda=3.19.3 bash: conda: command not found cheers, Philipp -----Original message----- From: Björn Grüning <bjoern.gruening(a)gmail.com> Sent: Monday 20th June 2016 13:21 To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de>; galaxy-dev(a)lists.galaxyproject.org Cc: Björn Grüning <bjoern.gruening(a)gmail.com> Subject: Re: [galaxy-dev] Infinite recursion on conda dependency manager Hi Philipp, you are inside of the Docker container? Can you do a: export PATH=/galaxy-central/tool_deps/_conda/bin/:$PATH conda install -y -q conda=3.19.3 Ciao, Bjoern Am 20.06.2016 um 13:01 schrieb Rathert, Philipp, Dr.: > Dear all, > > > > > > I am trying to install bowtie as a dependency for bismarck. however, I am getting the error posted below. > > > > Maybe somebody has an idea how to fix this. > > > > > > Thanks in advance, > > > > philipp > > > > > > In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: > SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)’: > SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ˆ > SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’: > SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ˆ > SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’: > SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: > SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)’: > SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TLeft>::Type TLeftValue; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: > SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’: > SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: > SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’: > SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Iterator<T, Standard>::Type TIterator; > ˆ > SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’: > SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: > SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’: > SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Id<TStringSet>::Type TId; > ˆ > In file included from SeqAn-1.1/seqan/index.h:82:0, > from ebwt_build.cpp:5: > SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)’: > SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue; > ˆ > SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)’: > SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue; > ˆ > SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize; > ˆ > SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)’: > SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value< Shape<TValue, TSpec> >::Type THValue; > ˆ > SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)’: > SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value< Shape<TValue, TSpec> >::Type THValue; > ˆ > SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)’: > SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value< Shape<TValue, TSpec> >::Type THValue; > ˆ > In file included from SeqAn-1.1/seqan/index.h:83:0, > from ebwt_build.cpp:5: > SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)’: > SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value< Shape<TValue, GappedShape> >::Type THValue; > ˆ > SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)’: > SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ˆ > SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)’: > SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ˆ > In file included from SeqAn-1.1/seqan/file.h:66:0, > from ebwt_build.cpp:7: > SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’: > SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Row<TAlign>::Type TRow; > ˆ > SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)’: > SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Position<TAlign>::Type TPosition; > ˆ > In file included from SeqAn-1.1/seqan/file.h:69:0, > from ebwt_build.cpp:7: > SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)’: > SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Row<TAlign>::Type TRow; > ˆ > In file included from ebwt.h:27:0, > from ebwt_build.cpp:11: > blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::buildSamples()’: > blockwise_sa.h:380:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ˆ > blockwise_sa.h: In member function ‘virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()’: > blockwise_sa.h:745:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ˆ > In file included from ebwt.h:1607:0, > from ebwt_build.cpp:11: > ebwt_search_backtrack.h: In member function ‘bool GreedyDFSRangeSource::backtrack(uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t*, uint8_t*, bool)’: > ebwt_search_backtrack.h:772:11: warning: variable ‘foundTarget’ set but not used [-Wunused-but-set-variable] > > .. > TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from alphabet.h:6, > from color_dec.cpp:11: > SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’: > SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from alphabet.h:6, > from color_dec.cpp:11: > SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’: > SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Iterator<T, Standard>::Type TIterator; > ˆ > SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’: > SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from alphabet.h:6, > from color_dec.cpp:11: > SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’: > SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Id<TStringSet>::Type TId; > ˆ > In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from color_dec.cpp:11: > SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’: > SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Row<TAlign>::Type TRow; > ˆ > SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)’: > SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Position<TAlign>::Type TPosition; > ˆ > In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from color_dec.cpp:11: > SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)’: > SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Row<TAlign>::Type TRow; > ˆ > color_dec.cpp: In function ‘void decodeHit(const char*, const char*, size_t, size_t, const char*, size_t, size_t, int, char*, char*, char*, int&, int&)’: > color_dec.cpp:187:6: warning: variable ‘lastOmin’ set but not used [-Wunused-but-set-variable] > int lastOmin = INT_MAX; > ˆ > In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from hit.h:11, > from hit.cpp:1: > SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)’: > SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ˆ > SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’: > SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ˆ > SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’: > SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from hit.h:11, > from hit.cpp:1: > SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)’: > SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TLeft>::Type TLeftValue; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from hit.h:11, > from hit.cpp:1: > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: > SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from hit.h:11, > from hit.cpp:1: > SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’: > SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from hit.h:11, > from hit.cpp:1: > SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’: > SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Iterator<T, Standard>::Type TIterator; > ˆ > SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’: > SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from hit.h:11, > from hit.cpp:1: > SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’: > SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Id<TStringSet>::Type TId; > ˆ > In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from hit.h:12, > from hit.cpp:1: > SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’: > SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Row<TAlign>::Type TRow; > ˆ > SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)’: > SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Position<TAlign>::Type TPosition; > ˆ > In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from hit.h:12, > from hit.cpp:1: > SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)’: > SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] > typedef typename Row<TAlign>::Type TRow; > ˆ > make: *** [bowtie] Error 1 > > > > > > > > > > > > -----Original message----- > From: Björn Grüning <bjoern.gruening(a)gmail.com> > Sent: Wednesday 15th June 2016 9:09 > To: Peter van Heusden <pvh(a)sanbi.ac.za>; galaxy-dev(a)lists.galaxyproject.org > Subject: Re: [galaxy-dev] Infinite recursion on conda dependency manager > > > Hi Peter, > > please install conda in version 3.19.3. Conda-4 has a bug when using > with --offline and --local. > > conda install conda=3.19.3 should work. > > https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L15 > > Thanks, > Bjoern > > Am 15.06.2016 um 00:44 schrieb Peter van Heusden: >> Hi there >> >> I've got a package in our lab conda channel (its still in testing phase) >> called goget. This is specified as a requirement for the build_ctb_gene >> tool like this: >> >> <requirements> >> <requirement type="package" version="0.0.1">goget</requirement> >> </requirements> >> >> When the tool runs, I see infinite recursion on the conda side: >> >> https://gist.github.com/pvanheus/c16a07a2c954741a311881cc7606df8d >> >> Any ideas? >> >> Thanks, >> Peter >> >> >> >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >

1 0

Re: [galaxy-dev] Infinite recursion on conda dependency manager
by Rathert, Philipp, Dr. 20 Jun '16

20 Jun '16

Dear all, I am trying to install bowtie as a dependency for bismarck. however, I am getting the error posted below. Maybe somebody has an idea how to fix this. Thanks in advance, philipp In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)’: SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’: SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’: SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)’: SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value<TLeft>::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’: SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’: SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator<T, Standard>::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’: SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’: SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] typedef typename Id<TStringSet>::Type TId; ^ In file included from SeqAn-1.1/seqan/index.h:82:0, from ebwt_build.cpp:5: SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)’: SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)’: SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize; ^ SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)’: SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape<TValue, TSpec> >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)’: SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape<TValue, TSpec> >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)’: SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape<TValue, TSpec> >::Type THValue; ^ In file included from SeqAn-1.1/seqan/index.h:83:0, from ebwt_build.cpp:5: SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)’: SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape<TValue, GappedShape> >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)’: SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)’: SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from ebwt_build.cpp:7: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’: SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] typedef typename Row<TAlign>::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)’: SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs] typedef typename Position<TAlign>::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from ebwt_build.cpp:7: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)’: SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] typedef typename Row<TAlign>::Type TRow; ^ In file included from ebwt.h:27:0, from ebwt_build.cpp:11: blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::buildSamples()’: blockwise_sa.h:380:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value<TStr>::Type TAlphabet; ^ blockwise_sa.h: In member function ‘virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()’: blockwise_sa.h:745:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value<TStr>::Type TAlphabet; ^ In file included from ebwt.h:1607:0, from ebwt_build.cpp:11: ebwt_search_backtrack.h: In member function ‘bool GreedyDFSRangeSource::backtrack(uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t*, uint8_t*, bool)’: ebwt_search_backtrack.h:772:11: warning: variable ‘foundTarget’ set but not used [-Wunused-but-set-variable] .. TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’: SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’: SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator<T, Standard>::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’: SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’: SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] typedef typename Id<TStringSet>::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from color_dec.cpp:11: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’: SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] typedef typename Row<TAlign>::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)’: SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs] typedef typename Position<TAlign>::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from color_dec.cpp:11: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)’: SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] typedef typename Row<TAlign>::Type TRow; ^ color_dec.cpp: In function ‘void decodeHit(const char*, const char*, size_t, size_t, const char*, size_t, size_t, int, char*, char*, char*, int&, int&)’: color_dec.cpp:187:6: warning: variable ‘lastOmin’ set but not used [-Wunused-but-set-variable] int lastOmin = INT_MAX; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)’: SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’: SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’: SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)’: SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value<TLeft>::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’: SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String<TTargetValue, TTargetSpec> TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’: SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’: SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator<T, Standard>::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’: SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’: SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] typedef typename Id<TStringSet>::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from hit.h:12, from hit.cpp:1: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’: SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] typedef typename Row<TAlign>::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)’: SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs] typedef typename Position<TAlign>::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from hit.h:12, from hit.cpp:1: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)’: SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] typedef typename Row<TAlign>::Type TRow; ^ make: *** [bowtie] Error 1 -----Original message----- From: Björn Grüning <bjoern.gruening(a)gmail.com> Sent: Wednesday 15th June 2016 9:09 To: Peter van Heusden <pvh(a)sanbi.ac.za>; galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] Infinite recursion on conda dependency manager Hi Peter, please install conda in version 3.19.3. Conda-4 has a bug when using with --offline and --local. conda install conda=3.19.3 should work. https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L15 Thanks, Bjoern Am 15.06.2016 um 00:44 schrieb Peter van Heusden: > Hi there > > I've got a package in our lab conda channel (its still in testing phase) > called goget. This is specified as a requirement for the build_ctb_gene > tool like this: > > <requirements> > <requirement type="package" version="0.0.1">goget</requirement> > </requirements> > > When the tool runs, I see infinite recursion on the conda side: > > https://gist.github.com/pvanheus/c16a07a2c954741a311881cc7606df8d > > Any ideas? > > Thanks, > Peter > > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

2 1

Re: [galaxy-dev] History is not up-to-date
by Rathert, Philipp, Dr. 20 Jun '16

20 Jun '16

Hi Carl, it looks like the time is not correct. System Time: 2016-06-20T09:30:00.038328386Z EventsListeners: 0 Init SHA1: Init Path: /usr/local/bin/docker Docker Root Dir: /mnt/sda1/var/lib/docker Labels: provider=virtualbox the clock on my mac says 11:25 Is there an easy way to fix this or do I need to run galaxy in a new container? I run the container with -privileged=true, so it should be possible but so far I didn't find how... Thanks for your help. Cheers, Philipp -----Original message----- From: Philipp Rathert <philipp.rathert(a)ibc.uni-stuttgart.de> Sent: Wednesday 15th June 2016 9:07 To: 'Carl Eberhard' <carlfeberhard(a)gmail.com> Cc: galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date HI Carl, I am travelling these days but will check on Monday. Thanks in advance. Cheers, Philipp From: Carl Eberhard [mailto:carlfeberhard@gmail.com] Sent: Tuesday, June 14, 2016 6:24 PM To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> Cc: galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date Hi, Phillip Quick questions: - is the time properly set on the computer where you've got Galaxy running in the browser? - is the time in the docker container also correct? From you terminal output it looks like the update time might be the issue and we can then take it from there. Thanks On Tue, Jun 14, 2016 at 11:28 AM, Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de <mailto:philipp.rathert@ibc.uni-stuttgart.de> > wrote: Dear All, I have a problem with my histories. We are running the Docker galaxy stable version 16.04 and when I start a tool the history does not show that it is running. it is not specific for any tool but for all. however, something is running in the back 129.69.102.30 - - [14/Jun/2016:12:57:21 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:21 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2) 129.69.102.30 - - [14/Jun/2016:12:57:25 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:25 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 1) 129.69.102.30 - - [14/Jun/2016:12:57:29 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:29 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:33 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:33 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:37 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:37 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3) I am not sure how to fix this and I am happy for any suggestion. Cheers, Philipp ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>

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Re: [galaxy-dev] History is not up-to-date
by Rathert, Philipp, Dr. 20 Jun '16

20 Jun '16

Dear Nicola, I am using the 16.04 release. did you implement changes in this one recently? Cheers, Philipp -----Original message----- From: Nicola Soranzo <nsoranzo(a)tiscali.it> Sent: Monday 20th June 2016 12:16 To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de>; 'Carl Eberhard' <carlfeberhard(a)gmail.com> Cc: galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date Hi Philipp, this has been fixed in the mean time on the release_16.04 branch of Galaxy, see https://github.com/galaxyproject/galaxy/pull/2506 Can you try to update your Galaxy server in the container and check if it's working? Cheers, Nicola On 20/06/16 10:31, Rathert, Philipp, Dr. wrote: Hi Carl, it looks like the time is not correct. System Time: 2016-06-20T09:30:00.038328386Z EventsListeners: 0 Init SHA1: Init Path: /usr/local/bin/docker Docker Root Dir: /mnt/sda1/var/lib/docker Labels: provider=virtualbox the clock on my mac says 11:25 Is there an easy way to fix this or do I need to run galaxy in a new container? I run the container with -privileged=true, so it should be possible but so far I didn't find how... Thanks for your help. Cheers, Philipp -----Original message----- From: Philipp Rathert <philipp.rathert(a)ibc.uni-stuttgart.de> Sent: Wednesday 15th June 2016 9:07 To: 'Carl Eberhard' <carlfeberhard(a)gmail.com> Cc: galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date HI Carl, I am travelling these days but will check on Monday. Thanks in advance. Cheers, Philipp From: Carl Eberhard [mailto:carlfeberhard@gmail.com] Sent: Tuesday, June 14, 2016 6:24 PM To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> Cc: galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date Hi, Phillip Quick questions: - is the time properly set on the computer where you've got Galaxy running in the browser? - is the time in the docker container also correct? From you terminal output it looks like the update time might be the issue and we can then take it from there. Thanks On Tue, Jun 14, 2016 at 11:28 AM, Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> wrote: Dear All, I have a problem with my histories. We are running the Docker galaxy stable version 16.04 and when I start a tool the history does not show that it is running. it is not specific for any tool but for all. however, something is running in the back 129.69.102.30 - - [14/Jun/2016:12:57:21 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:21 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2) 129.69.102.30 - - [14/Jun/2016:12:57:25 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:25 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 1) 129.69.102.30 - - [14/Jun/2016:12:57:29 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:29 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:33 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:33 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:37 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:37 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3) I am not sure how to fix this and I am happy for any suggestion. Cheers, Philipp ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

1 0

Building Galaxy Tool: cannot find 'is_of_type'
by Nikolaos Tur 19 Jun '16

19 Jun '16

Hi, according to https://planemo.readthedocs.io/en/latest/writing_how_do_i.html#check-input-… and https://bitbucket.org/galaxy/galaxy-central/pull-requests/457/allow-cheetah… there is simple function for data type checking: is_of_type() after running job is not prepared and fail with: galaxy.jobs.runners ERROR 2016-06-19 18:46:16,257 (66) Failure preparing job Traceback (most recent call last): File "/home/galaxy/lib/galaxy/jobs/runners/__init__.py", line 169, in prepare_job job_wrapper.prepare() File "/home/galaxy/lib/galaxy/jobs/__init__.py", line 889, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/home/galaxy/lib/galaxy/tools/evaluation.py", line 445, in build raise e NotFound: cannot find 'is_of_type' while searching for 'is_of_type' where part of wrapper with is_of_type() is: <command> <![CDATA[ #if $reads.is_of_type('fastq'): ln -s "$reads" rInput1.fq && #set $reads = 'rInput1.fq' #end if ... where am I wrong? Or that is a Galaxy bug? Galxy is 16.04 and is_of_type() function is defined in lib/galaxy/tools/wrappers.py Thanx, Nikolaos

1 0

flexbar v2.7 & required format extension
by Nikolaos Tur 18 Jun '16

18 Jun '16

Hi, does someone use latest version of flexbar 2.7 with Galaxy? It seems newest flexbar changes way how it works with data. Now it requires format extension for data. But Galaxy operates data with .dat extension in database/files/. Also there is flexbar wrapper for version 2.7, so it should be somehow integrated to the Galaxy. Our Galaxy is 16.04. Thanx, Nikolaos

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GalaxyAdmins Meetup This Thursday
by Dave Clements 16 Jun '16

16 Jun '16

Hello all, The June online meetup of GalaxyAdmins will be this Thursday <https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_06_16>. This month features two talks: *1. Galaxy in Production at the University of Minnesota* [image: Minnesota Supercomputing Institute] <https://www.msi.umn.edu/> [image: Galaxy Radio Telescope] <https://github.com/galaxyproject/galaxy/pull/2455> Galaxy has been deployed in several contexts by the Minnesota Supercomputing Institute (MSI) <https://www.msi.umn.edu/> at the University of Minnesota - Twin Citites <https://www.umn.edu/>. This month Evan Bollig <https://www.msi.umn.edu/staff/evan> and JJ Johnson <https://www.msi.umn.edu/staff/jj> of MSI will discuss several aspects of this work relevant to the GalaxyAdmins <https://wiki.galaxyproject.org/GalaxyAdmins> group: - customizations made to Galaxy that enable MSI to leverage it as a Tier I service <https://www.msi.umn.edu/services> for our users (e.g., scheduling, quotas, billing, and sharing). - Pulsar <https://github.com/galaxyproject/pulsar> for Galaxy-P <https://usegalaxyp.org/> tools on Windows. - the CLIA-certified <http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/IVDRegulatory…> pipelines and how Galaxy is integrated into clinical workflows *2. Galaxy Radio Telescope* The GRT <https://github.com/galaxyproject/galaxy/pull/2455> aims to collect job run information from Galaxy servers that opt into the process. Galaxy Admins can sign in to the GRT, register their Galaxy servers, and get back API keys per-Galaxy instance. Then they set up a cron job (preferably weekly, but we may explore options here later), and submit job data to the GRT. See https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_06_16 for full details and links. The conference room link will be posted an hour before the meetup. GalaxyAdmins is a discussion group for Galaxy community members that administer Galaxy installations. Hope to see you (online) on Thursday, Dave Clements and Hans-Rudolf Hotz -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

2 1

fail to install pulsar on windows machine
by Jun Fan 15 Jun '16

15 Jun '16

Dear all, I used to utilize LWR on a windows machine to run windows-only tools. As recently I upgrade the Galaxy to the latest stable version 16_01, Galaxy indicated that no LwrJobRunner available. Therefore I had to install Pulsar. When I followed the instruction at https://pulsar.readthedocs.io/en/latest/install.html and failed. 1. From PyPI option: after executing pulsar-config and two files app.yaml and server.ini being generated, the command pulsar returns the error saying 'pulsar' is not recognized as an internal or external command, operable program or batch file. 2. From Source option: it failed at run.bat step and got the main error message as "ImportError: No module named grp". My python is 2.7.11 and in the python shell, the command "import grp" gives the same error. Any help is welcome Best regards! Jun

1 0

Infinite recursion on conda dependency manager
by Peter van Heusden 15 Jun '16

15 Jun '16

Hi there I've got a package in our lab conda channel (its still in testing phase) called goget. This is specified as a requirement for the build_ctb_gene tool like this: <requirements> <requirement type="package" version="0.0.1">goget</requirement> </requirements> When the tool runs, I see infinite recursion on the conda side: https://gist.github.com/pvanheus/c16a07a2c954741a311881cc7606df8d Any ideas? Thanks, Peter

2 1

History is not up-to-date
by Rathert, Philipp, Dr. 15 Jun '16

15 Jun '16

Dear All, I have a problem with my histories. We are running the Docker galaxy stable version 16.04 and when I start a tool the history does not show that it is running. it is not specific for any tool but for all. however, something is running in the back 129.69.102.30 - - [14/Jun/2016:12:57:21 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:21 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2) 129.69.102.30 - - [14/Jun/2016:12:57:25 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:25 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 1) 129.69.102.30 - - [14/Jun/2016:12:57:29 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:29 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:33 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:33 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:37 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:37 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3) I am not sure how to fix this and I am happy for any suggestion. Cheers, Philipp

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Re: [galaxy-dev] how to get raw input from GUI
by Dooley, Damion 14 Jun '16

14 Jun '16

A general note, besides <sanitize> which sounds like a fine choice, a technique I've used where the form's input might have some wonky characters in it, including carriage returns, but these need to be received and processed via a command line, is to use encode(): $rules.encode('base64').replace('\n','') Then over in receiving python script Rules = rulesparam.decode('base64') D. >Message: 3 >Date: Mon, 13 Jun 2016 17:12:05 -0700 >From: Beginner TI <ruiwang.sz(a)gmail.com> >To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> >Subject: [galaxy-dev] how to get raw input from GUI >Message-ID: > <CAPNcnp5B8uzQbAHLqA7ak4NMpQZ+CDitvNDg0J9ZS+bS5A06OQ(a)mail.gmail.com> >Content-Type: text/plain; charset="utf-8" > >Hi, > >I am working on a wrapper for gatk and including > > <repeat name="filters" title="filter names and expressions" >help="--filterName, --filterExpression"> > <param name="filter_name" type="text" value="" >title="Filter name to be included in the analysis" /> > <param name="filter_exp" type="data" value="" >title="Filter >expression to be included in the analysis" /> > </repeat> > >in it, however, when I reference it using > >${filter.filter_exp} > >it would translate 'FS > 30.0' into XXXFS __gt__ 30.0XXX > >is there a way that I could keep the original text string 'FS > 30.0'? I >did a quick lookup online but didn't see anything in cheetah's user guide >or other places. > >Thanks, >Rui

1 0

Re: [galaxy-dev] cleanup datasets error
by Rathert, Philipp, Dr. 14 Jun '16

14 Jun '16

Hi Bjoern, I edited the galaxy.ini directly and started the script. Unfortunately I get a different error: Traceback (most recent call last): File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in <module> main() File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main app = CleanupDatasetsApplication( config ) File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in __init__ self.model = galaxy.model.mapping.init( config.file_path, config.database_connection, engine_options={}, create_tables=False, object_store=self.object_store ) File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init engine = build_engine( url, engine_options, database_query_profiling_proxy, trace_logger ) File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py", line 20, in build_engine engine = create_engine( url, proxy=proxy, **engine_options ) File "/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py", line 386, in create_engine return strategy.create(*args, **kwargs) File "/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 75, in create dbapi = dialect_cls.dbapi(**dbapi_args) File "/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 579, in dbapi import psycopg2 ImportError: No module named psycopg2 Can I install the python-psycopq2 module via apt-get in the container and would this help to fix thee issue? Cheers, Philipp -----Original message----- From: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> Sent: Tuesday 14th June 2016 9:56 To: Bjoern Gruening <bjoern.gruening(a)gmail.com> Cc: galaxy-dev <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] cleanup datasets error Hi Bjoern, This is wired. It worked before... I will add this to the galaxy.ini in the config folder and try again. Cheers, Philipp ---Philipp on the road--- Am 14.06.2016 um 09:50 schrieb Bjoern Gruening <bjoern.gruening(a)gmail.com <mailto:bjoern.gruening@gmail.com> >: Hi, I don't think this will work with the script. This script reads the config file you specify config/galaxy.ini. And hence it needs to be added in this file, not via -e variables. This is probably something we should improve. Ciao, Bjoern > cleanup datasets error > > HI Björn, > > > > I have added these to the galaxy.ini via the docker specific e- > variables during startup of the container. > > > > How can I check if they are broken? > > > > Cheers, > > > > Philipp > > > > *From:*Bjoern Gruening [mailto:bjoern.gruening@gmail.com] *Sent:* > Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr. > <philipp.rathert(a)ibc.uni-stuttgart.de>; galaxy-dev > <galaxy-dev(a)lists.galaxyproject.org> *Subject:* Re: [galaxy-dev] > cleanup datasets error > > > > Hi Philipp, > > have you followed this from the readme? > > > Note that if you would like to run any of the cleanup scripts ><https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%2…>, > you will need to add the following to > |/export/galaxy-central/config/galaxy.ini|: > > |database_connection = > postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path = > /export/galaxy-central/database/files| > > Or is this broken? Cheers, Bjoern > > On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote: > > Dear all, > > > > when I want to start the cleanup datasets script I get the following > error. > > > > (.venv)root@galaxy:/galaxy-central# python > /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py > config/galaxy.ini -d -10 -1 > > Traceback (most recent call last): > > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", > line 544, in <module> > > main() > > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", > line 99, in main > > for key, value in config_parser.items( "app:main" ): > > File "/usr/lib/python2.7/ConfigParser.py", line 642, in items > > raise NoSectionError(section) > > ConfigParser.NoSectionError: No section: 'app:main' > > > > > > We are using the docker galaxy stable 16.04 version. Before this > script always worked without producing any error. > > > > It would be great if anybody has an idea how to fix this... > > > > Thank you very much in advance. > > > > Cheers, > > > > Philipp > > > > > > -----Original message----- *From:* Marius van den Beek > <m.vandenbeek(a)gmail.com> <mailto:m.vandenbeek@gmail.com> *Sent:* > Tuesday 7th June 2016 14:06 *To:* Marco Tangaro > <ma.tangaro(a)gmail.com> <mailto:ma.tangaro@gmail.com> *Cc:* galaxy-dev > <galaxy-dev(a)lists.galaxyproject.org> > <mailto:galaxy-dev@lists.galaxyproject.org> *Subject:* Re: > [galaxy-dev] Python tool wrapper with multiple input and output > files > > > Hi Marco, > > > > you've got an interesting use-case there. > > You may want to use either a dataset list (if you only supply > rna_n.bam), > > or a paired dataset list (rna_n.bam and dna_n.bam). > > I would probably implement a conditional, where the user selects > either a dataset list or a paired dataset list. > > The output would then be another collection of output files. > > Have a look at the test tool folder, and see if any of the tools > named collection_*.xml fits what you would like to do > > https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools > > > These two may be a good basis for what you want to achieve: > >https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/coll… > > > [this one creates an output collection] > >https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/coll… > > > [this one has a conditional to either select a list or a paired list as input] > > > > Let us know if you need more help! > > > > Cheers, > > Marius > > > > On 7 June 2016 at 09:50, Marco Tangaro <ma.tangaro(a)gmail.com > <mailto:ma.tangaro@gmail.com>> wrote: > > Dear experts, my name is Marco and I'm working to port our python > tool to the Galaxy framework. The main script needs a rna.bam file as > input, a reference fasta file, both mandatory. Finally, you can add a > dna.bam file, but this is optional. Therefore an example command is: > > script.py -i rna.bam -f reference.fa -j dna.bam > > The outout is a tabular. Again the -j dna.bam option is completely > optional. So quite soon it turned out that I had to use a python > wrapper to parse our script. Now the wrapper works fine. > > > The next step is to run the tool over multiple input file and we > would like to avoid to use a workflow. > > The idea is that to each input file corresponds an output file. The > reference is still the same. For instance, we have: > > rna_1.bam + dna_1.bam -> output_1.txt rna_2.bam + dna_2.bam -> > output_2.txt rna_3.bam + dna_3.bam -> output_3.txt ... and so on. > > > But I don't know the best strategy to give to my wrapper multiple > input files. Moreover I have to be sure, when the dna_xyz.bam files > are uploaded, that they correspond to the right rna_xyz.bam file. > > I would like to have as output a page which is showing as results the > link to the single output files as suggested here. > https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files > planning to integrate a javascript interface. > > I've browsed a lot, but on multiple input file the posts are old. I'm > using the last galaxy release (16_04). > > I'm quite new to the galaxy world... Thanks a lot for your > suggestions, Marco > > > ___________________________________________________________ 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: https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > > > > > > ___________________________________________________________ > > 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: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

3 3

cleanup datasets error
by Rathert, Philipp, Dr. 14 Jun '16

14 Jun '16

Dear all, when I want to start the cleanup datasets script I get the following error. (.venv)root@galaxy:/galaxy-central# python /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d -10 -1 Traceback (most recent call last): File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 544, in <module> main() File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 99, in main for key, value in config_parser.items( "app:main" ): File "/usr/lib/python2.7/ConfigParser.py", line 642, in items raise NoSectionError(section) ConfigParser.NoSectionError: No section: 'app:main' We are using the docker galaxy stable 16.04 version. Before this script always worked without producing any error. It would be great if anybody has an idea how to fix this... Thank you very much in advance. Cheers, Philipp -----Original message----- From: Marius van den Beek <m.vandenbeek(a)gmail.com> Sent: Tuesday 7th June 2016 14:06 To: Marco Tangaro <ma.tangaro(a)gmail.com> Cc: galaxy-dev <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] Python tool wrapper with multiple input and outputfiles Hi Marco, you've got an interesting use-case there. You may want to use either a dataset list (if you only supply rna_n.bam), or a paired dataset list (rna_n.bam and dna_n.bam). I would probably implement a conditional, where the user selects either a dataset list or a paired dataset list. The output would then be another collection of output files. Have a look at the test tool folder, and see if any of the tools named collection_*.xml fits what you would like to do https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools These two may be a good basis for what you want to achieve: https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/coll… [this one creates an output collection] https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/coll… [this one has a conditional to either select a list or a paired list as input] Let us know if you need more help! Cheers, Marius On 7 June 2016 at 09:50, Marco Tangaro <ma.tangaro(a)gmail.com <mailto:ma.tangaro@gmail.com> > wrote: Dear experts, my name is Marco and I'm working to port our python tool to the Galaxy framework. The main script needs a rna.bam file as input, a reference fasta file, both mandatory. Finally, you can add a dna.bam file, but this is optional. Therefore an example command is: script.py -i rna.bam -f reference.fa -j dna.bam The outout is a tabular. Again the -j dna.bam option is completely optional. So quite soon it turned out that I had to use a python wrapper to parse our script. Now the wrapper works fine. The next step is to run the tool over multiple input file and we would like to avoid to use a workflow. The idea is that to each input file corresponds an output file. The reference is still the same. For instance, we have: rna_1.bam + dna_1.bam -> output_1.txt rna_2.bam + dna_2.bam -> output_2.txt rna_3.bam + dna_3.bam -> output_3.txt ... and so on. But I don't know the best strategy to give to my wrapper multiple input files. Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they correspond to the right rna_xyz.bam file. I would like to have as output a page which is showing as results the link to the single output files as suggested here. https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files planning to integrate a javascript interface. I've browsed a lot, but on multiple input file the posts are old. I'm using the last galaxy release (16_04). I'm quite new to the galaxy world... Thanks a lot for your suggestions, Marco ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>

3 4

how to get raw input from GUI
by Beginner TI 13 Jun '16

13 Jun '16

Hi, I am working on a wrapper for gatk and including <repeat name="filters" title="filter names and expressions" help="--filterName, --filterExpression"> <param name="filter_name" type="text" value="" title="Filter name to be included in the analysis" /> <param name="filter_exp" type="data" value="" title="Filter expression to be included in the analysis" /> </repeat> in it, however, when I reference it using ${filter.filter_exp} it would translate 'FS > 30.0' into XXXFS __gt__ 30.0XXX is there a way that I could keep the original text string 'FS > 30.0'? I did a quick lookup online but didn't see anything in cheetah's user guide or other places. Thanks, Rui

2 2

Re: [galaxy-dev] Deploying custom genome in Galaxy for use with ANNOVAR (Peter Briggs)
by David Kovalic 13 Jun '16

13 Jun '16

Peter, Thanks! The blog post is very helpful. David > ---------- Forwarded message ---------- > From: Peter Briggs <peter.briggs(a)manchester.ac.uk> > To: galaxy-dev(a)lists.galaxyproject.org > Cc: > Date: Wed, 8 Jun 2016 08:25:03 +0100 > Subject: Re: [galaxy-dev] Deploying custom genome in Galaxy for use with > ANNOVAR > Hello David > > I don't think it will answer all your questions, however: I wrote up my > experiences with installing ANNOVAR in Galaxy last year which might be > useful as a starting point: > > > http://galacticengineer.blogspot.co.uk/2015/03/installing-annovar-in-galaxy… > > As I recall all the databases we installed were standard ones from > ANNOVAR. However the above instructions might be useful in at least > getting started. > > Apologies if I've misunderstood your question and this doesn't help, > > Best wishes > > Peter > > On 07/06/16 17:48, David Kovalic wrote: > > All, > > > > From my read of the command line docs for ANNOVAR I believe that the > > program needs so ancillary files for its operation (e.g. GenePred file, > > transcripts fasta file, etc...). > > > > Does anyone have any experience deploying custom genomes in Galaxy for > > use with ANNOVAR? Specifically what files need to go where in order to > > enable the Galaxy ANNOVAR front end? > > > > Thanks, > > > > David > > > > > > ___________________________________________________________ > > 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: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > -- > Peter Briggs peter.briggs(a)manchester.ac.uk > Bioinformatics Core Facility University of Manchester > B.1083 Michael Smith Bldg Tel: (0161) 2751482 > > > >

1 0

Compiler & OS questionnaire
by Björn Grüning 13 Jun '16

13 Jun '16

Hi, the conda community is currently doing a survey on the buildchain requirements of the scientific community and want to know if we need binaries that run under old systems like CentOS-5 or if CentOS-6 and newer is sufficient. Galaxy supports conda since a few releases and we have plans to advertise this dependency resolver more and more in the near future. It would be great to know how many of you run Galaxy on an old system like CentOS-5 or if it would be ok if it would be ok to only support systems newer than CentOS-6. Please fill out this survey: https://t.co/q0l2mkS5Na Thanks a lot! Bjoern

1 0

Trinity installation
by Jose Juan Almagro Armenteros 10 Jun '16

10 Jun '16

Hello, I am having troubles installing the last version of the tool Trinity. I found that I have the same error as this issue ( https://github.com/galaxyproject/galaxy/issues/1947) so I tried the suggested solution. It didn't work, so I posted the error in the issue. Then, I tried to change the tmp folder to another one in the same filesytem (and undoing the previous solution). Again it didn't work, but it gave a different error: File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 123, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 108, in install_and_build_package initial_download=False ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 845, in execute_step destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 864, in move_directory_files shutil.move( source_file, destination_file ) File "/usr/lib/python2.7/shutil.py", line 130, in copy2 copyfile(src, dst) File "/usr/lib/python2.7/shutil.py", line 82, in copyfile with open(src, 'rb') as fsrc: [Errno 21] Is a directory: '/steno-internal/projects/galaxy/galaxy-dist/tmp/tmp-toolshed-mtd8Exq2w/trinityrnaseq-2.1.1/trinity-plugins/jellyfish' I am using the Galaxy release *16.01. *Do you know how could I solve this problem?

2 2

Using session parameters in Galaxy tools
by Amelia Ireland 09 Jun '16

09 Jun '16

Is it possible to access session parameters and use them in Galaxy tool wrappers? If so, how? I am integrating Galaxy with a local system, and I need the current session ID to be able to access user and session-specific data. I am already getting the user email as $__user_email__ (from https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccommand.3E_… ). Any suggestions gratefully received. Thanks!

2 1

Xenopus genome
by Kurtenbach, Stefan 09 Jun '16

09 Jun '16

Dear Galaxy team, First, thanks for your great work! I want to use Bowtie2 to align ChIPseq data to the Xenopus laevis genome. However, It's not listed. The tool said that if the desired genome is not in the list to contact the galaxy team, so here I am :) Could you add this? Thanks! Stefan

2 1

Re: [galaxy-dev] How to get the encoded ID from the HistoryDatasetAssociation?
by Malcolm Tobias 08 Jun '16

08 Jun '16

Thanks Martin! With your hint and the example from graphviz.mako I was able to get this to work. Cheers, Malcolm On Wednesday, June 08, 2016 03:23:31 PM Martin Čech wrote: Hello Malcolm, encoded_id is a database row id that has been ran through this method (https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/security/__…) using the 'secret' from galaxy.ini config. You should be able to do something like this in the mako: ${trans.security.encode_id( hda.id[2] )} thank you for using Galaxy Martin On Wed, Jun 8, 2016 at 11:16 AM Malcolm Tobias <mtobias(a)wustl.edu[3]> wrote: hda.name[4] and hda.id[2] I can see various properties of thedataset, but not the encoded ID. Any suggestions on how to do this? Thanks in advance. Malcolm --Malcolm Tobias314.362.1594 ___________________________________________________________Please keep all replies on the list by using "reply all"in your mail client. To manage your subscriptions to thisand other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/[5] http://galaxyproject.org/search/mailinglists/[6] -- Malcolm Tobias 314.362.1594 -------- [1] https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/security/__… [2] http://hda.id [3] mailto:mtobias@wustl.edu [4] http://hda.name [5] https://lists.galaxyproject.org/ [6] http://galaxyproject.org/search/mailinglists/

1 0

Any way to prime the value of a tool text field parameter dynamically?
by Dooley, Damion 08 Jun '16

08 Jun '16

I have a need to have the default value of a text parameter : <param name="statements" label="Statements" type="text" area="true" value="???"> Set dynamically, as powered by say a call to a function in <code file="tool_form.py" /> , much like a dynamic_options="get_rule_section(recipe_file)" call. Has anyone done that somehow without hacking Galaxy code? A user can then edit the text. The default depends on a previous selection (e.g. recipe_file input). Thanks, Damion

1 0

not sure what I can do about this...
by Fernandez Edgar 08 Jun '16

08 Jun '16

Hello Gents, So someone asked me to install the package Prokka on Galaxy. I did and everything went well! However, the following error comes up, when they try to work with Prokka: Fatal error: Exit code 2 () [tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version. [20:20:53] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.10 from http://www.vicbioinformatics.com' -Z outdir\/prokka\.err -i outdir\/prokka\.fsa 2> /dev/null According to a google search, there is very little on this error. And it has been around for a while but I didn't find a posted solution. Any suggestions? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218

7 22

How to replace 'BioMart Central server' in the "Get Data" tools ?
by Hans-Rudolf Hotz 08 Jun '16

08 Jun '16

Hi As you probably know, the central BioMart server is currently unavailable (see: http://www.biomart.org/notice.html) Hence, the "Get Data -> BioMart Central server" tool in our local Galaxy installation does not work anymore - well, this is also the case on usegalaxy.org. We can easily switch the tool to point to a different Mart server, i.e.: Change: <inputs action="http://www.biomart.org/biomart/martview" .... to: <inputs action="http://www.ebi.ac.uk/uniprot/biomart/martview" .... However, we would like to switch to the ensembl Mart server: http://www.ensembl.org/biomart/martview It looks like the ensembl Mart server is nowadays embedded in the ensembl web site, and the requests are not send to Galaxy, but end up on the ensembl web page, where they cause a "Error 404 - Page not found". Unfortunately, I am not that savvy about the inner works of the ensembl web site anymore ;) Has anyone else looked into this problem and found already a solution? Thank you very much for any help Hans-Rudolf

2 5

How to get the encoded ID from the HistoryDatasetAssociation?
by Malcolm Tobias 08 Jun '16

08 Jun '16

I'm really close to having a way to visualize radiological images in Galaxy, but need help in getting past the final hurdle. In the mako file, I can see how to pass parameters to the javascript that does the visualization. It's expecting a URL to the dataset, like: params["images"] = ["/datasets/78176dfc865c8302/display/"]; >From what I can gather 78176dfc865c8302 is the encoded ID for the dataset. >From variables like hda.name and hda.id I can see various properties of the dataset, but not the encoded ID. Any suggestions on how to do this? Thanks in advance. Malcolm -- Malcolm Tobias 314.362.1594

2 1

Deploying custom genome in Galaxy for use with ANNOVAR
by David Kovalic 08 Jun '16

08 Jun '16

All, >From my read of the command line docs for ANNOVAR I believe that the program needs so ancillary files for its operation (e.g. GenePred file, transcripts fasta file, etc...). Does anyone have any experience deploying custom genomes in Galaxy for use with ANNOVAR? Specifically what files need to go where in order to enable the Galaxy ANNOVAR front end? Thanks, David

2 1

Error installing cummeRbund tool
by Raymond Wan 07 Jun '16

07 Jun '16

Dear all, I'm trying to install a Galaxy tool (cummeRbund; the one from devteam) and I'm getting the following error during installation: ----- Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request POST /admin_toolshed/prepare_for_install. Reason: Error reading from remote server ----- In paster.log, I see this: ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 35420) Traceback (most recent call last): File "/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 332, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib64/python2.6/SocketServer.py", line 628, in __init__ self.finish() File "/usr/lib64/python2.6/SocketServer.py", line 671, in finish self.wfile.flush() File "/usr/lib64/python2.6/socket.py", line 303, in flush self._sock.sendall(buffer(data, write_offset, buffer_size)) error: [Errno 32] Broken pipe ---------------------------------------- Does this mean there's a problem on our side, or perhaps there is a file missing from the tool (or the connection to the Toolshed has a problem)? Any suggestions as to what I should look for? I first tried 2 days ago and waited until now to try again -- still the same problem. Thank you! Ray

2 3

Auto-registration and database session issue
by Durdevic, Marija 06 Jun '16

06 Jun '16

Dear all, I am using LDAP authentication and auto registration options. LDAP authentication passed successfully, but I got error message during auto-registration process: File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.IntegrityError: (psycopg2.IntegrityError) duplicate key value violates unique constraint "ix_role_name" DETAIL: Key (name)=(marija.durdevic(a)medunigraz.at) already exists. [SQL: 'INSERT INTO role (create_time, update_time, name, description, type, deleted) VALUES (%(create_time)s, %(update_time)s, %(name)s, %(description)s, %(type)s, %(deleted)s) RETURNING role.id'] [parameters: {'update_time': datetime.datetime(2016, 6, 6, 12, 43, 29, 93304), 'description': u'Private Role for marija.durdevic(a)medunigraz.at', 'deleted': False, 'create_time': datetime.datetime(2016, 6, 6, 12, 43, 29, 93290), 'type': 'private', 'name': u'marija.durdevic(a)medunigraz.at'}] [pid: 22823|app: 0|req: 2/2] 10.17.16.180 () {54 vars in 1129 bytes} [Mon Jun 6 14:43:29 2016] POST /user/login?use_panels=False => generated 0 bytes in 74 msecs (HTTP/1.1 500) 1 headers in 63 bytes (0 switches on core 1) After that, user appear in database and I am able to login. Anyhow, I would like to solve this issue and to register without errors. I tried to debug Galaxy code... It looks like that problem is somewhere with sessions... Script: Lib/galaxy/security/__init__.py Function: create_private_user_role( self, user ) In this line: self.sa_session.flush() Anny suggestion what can be wrong? Thanks in advance, Marija Mag. Marija Đurđević Core Facility Computational Bioanalytics Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria Phone: +43 316/385-73024 Fax:+43 316/385-73009 Email: marija.djurdjevic(a)medunigraz.at Email: marija.djurdjevic(a)klinikum-graz.at Web: https://zmf.medunigraz.at/

1 0

setting metadata externally failed for HistoryDatasetAssociation
by Anthony Underwood 06 Jun '16

06 Jun '16

Jobs that I run on a local Galaxy install on a Fedora 23 machine are completing but are erroring with the message below. Any idea why the metadata can not be written? Thanks galaxy.jobs.runners.local DEBUG 2016-06-03 17:30:02,044 execution finished: /home/anthony.underwood/galaxy/database/jobs_directory/000/142/galaxy_142.sh galaxy.model.metadata DEBUG 2016-06-03 17:30:02,158 setting metadata externally failed for HistoryDatasetAssociation 158: [Errno 2] No such file or directory galaxy.jobs.runners.local ERROR 2016-06-03 17:30:02,235 Job wrapper finish method failed Traceback (most recent call last): File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/__init__.py", line 1257, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/anthony.underwood/galaxy/lib/galaxy/datatypes/binary.py", line 339, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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The state of the MOTHUR merge?
by Peter van Heusden 03 Jun '16

03 Jun '16

PR #429 on tools-iuc contains the updated MOTHUR toolsuite for Galaxy. https://github.com/galaxyproject/tools-iuc/pull/429 It *looks* like it is ready to merge - what is still needed before it merges into tools-iuc? Thanks! Peter

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Re: [galaxy-dev] LDAP authentication
by mark fernandes (IFR) 03 Jun '16

03 Jun '16

Don't know if this helps or not but here's the link to Novell's entry on LDAP support for eDirectory https://www.novell.com/documentation/edir873/?page=/documentation/edir873/e… Mark Fernandes T: +44 (0)1603 255000 Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK www.ifr.ac.uk Facebook | Twitter | LinkedIn | YouTube The Institute of Food Research receives strategic funding from BBSRC

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atlas 3.10 IUC error
by Olivier CLAUDE 03 Jun '16

03 Jun '16

Hello again, I am truly sorry to bother everyone again but i still experience problems: This time with atlas 3.10 owned by iuc At the beginning without modifying anything, the error log was saying " mkdir : cannot create directory ATLAS/build : No such file or directory" After that I tried to modify the tool_dependencies.xml : L48 : "mkdir ATLAS/build &&" changed to "mkdir build &&" The error is "/bin/sh: 4 : cannot open /host/static_full_blas_lapack.diff: No such file" I can see it, if I go with a web browser, but I cannot download it manually nor click on it without crashing the web browser. Any idea? Thanks again, M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 – Equipe 2 Faculté de médecine Pitié-Salpêtrière 91, bld de l'Hôpital - 3ème étage - Porte 305 75013 Paris - FRANCE

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