- galaxy-dev - lists.galaxyproject.org

Installing Cairo into Gakaxy
by Christian Brenninkmeijer 13 Oct '15

13 Oct '15

Hi All, Has anyone got a working example tool_dependencies.xml to install the Cairo package into R. (I actually need a package that depends on R Cairo but the current issue is Cairo) I am having the cairo.h not found issue I have cloned https://toolshed.g2.bx.psu.edu/view/devteam/package_cairo_1_12_14/b39299b4b… (and its dependencies) As well as https://toolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/9f2fddb9d6e2 I am trying to use <action type="setup_r_environment"> But can not get the package_cairo to be seen by the R I have tried <action type="set_environment_for_install"> both inside and outside of the setup_r_environment but it does not appear to be working, Full attempted tool_dependencies.xml attached, Thanks in advance Christian University of Manchester

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updated eggs needed for OS X El Capitan compatibility
by Wolfgang Maier 12 Oct '15

12 Oct '15

Hi, today, there was a complaint on the Galaxy Biostar forum that Galaxy fails to start under the new OS X El Capitan (https://biostar.usegalaxy.org/p/14492/) I had noticed this last week already, and that post prompted me to investigate the problem in more detail. The result (now checked on our own Galaxy instance) is that compatibility with El Capitan requires updates to two eggs - amqp and kombu - in the sense that, at least, you can start Galaxy after fixing these two. I haven't checked to see if there are additional run time problems. Hope that information helps, Wolfgang

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GCC2016 Training Day Topic Nominations are now open
by Dave Clements 12 Oct '15

12 Oct '15

Hello all, The 2016 Galaxy Community Conference (GCC2016) <https://wiki.galaxyproject.org/Events/GCC2016> features two full days of training on June 26-27. Each day will have multiple tracks, with each track featuring several sessions throughout the day. GCC2016 will be held at Indiana University <http://indiana.edu/> in Bloomington, Indiana, United States. *GCC2016 Training topics <https://wiki.galaxyproject.org/Events/GCC2016/Training> are nominated by you <http://bit.ly/gcc2016tdnom>, the Galaxy Community.* Please give some thought to what topics you would like to see offered, or that you would like to offer, and then submit them as topic nominations <http://bit.ly/gcc2016tdnom>. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see - Topics nominated for GCC2015 <http://bit.ly/gcc2015vote> - Topics nominated for GCC2014 <http://bit.ly/1s6NtMN> - Topics nominated for GCC2013 <http://bit.ly/1i2j1gN> - The Galaxy Events page <https://wiki.galaxyproject.org/Events>, which lists what training the community is offering outside of GCCs. - Topics that have already been nominated for GCC2016 <https://wiki.galaxyproject.org/Events/GCC2016/Training#Nominated_Topics> *Please nominate a topic now! <http://bit.ly/gcc2016tdnom> * Nominated topics will be published as they come in <https://wiki.galaxyproject.org/Events/GCC2016/Training#Nominated_Topics>. *Topic nomination closes Friday, October, 16.*. Topics will be compiled into a uniform list by the GCC2016 Organizing Committee, and topics will be voted on by the Galaxy Community from October 26 through November 6. Topics will then be selected and scheduled based on topic interest, and the organisers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. Looking forward to a stellar set of nominations, and hoping to see you in Bloomington, GCC2016 Exec Committee <https://wiki.galaxyproject.org/Events/GCC2016/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Get the working directory within the ncbi_blastp_wrapper.xml file
by Ryan Johnson 12 Oct '15

12 Oct '15

Hello all, We are setting up a galaxy instance that will submit jobs to our cluster. We could not get pbs_python to work so we have added all PBS logic to the cheetah template wrapper ncbi_blastp_wrapper.xml. Currently, all jobs are running out of the home directory. We want to add logic to the wrapper which will get the working directory from the JobWrapper class and then change to that directory and run from there. Can anyone help us to access the JobWrapper.working_underscore value? Or suggest a better way to do this? Thank you very much, Ryan -- Ryan S. Johnson, PhD Applications Scientist Center for Advanced Research Computing P: (650) 430-6194 E: rjohns03(a)carc.unm.edu

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Workflow 'Input Dataset' Ressolution Issue
by Marco Albuquerque 12 Oct '15

12 Oct '15

Hello Galaxy Dev, Consider the workflow found in 'Strelka_Workflow_Sequential' image Here it is in a different view 'Strelka_Sequential_Workflow_Different_View' Notice That the first input dataset links to the fetch_interval tool and the first preprocess tool. And the second input dataset links only to the second preprocess tool. When you run the workflow, what actually happens is the first input dataset goes to the fetch_interval tools and the second input dataset goes to both preprocessing tools. (Look at final two images). They have essentially executed the same tool twice. Where it should be an execution with a normal file and an execution with a tumour file. Why is this happening? What can I do to fix this? Thanks, Marco Albuquerque

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Question about using dynamic options and refresh_on_change for rendering 2 associated select lists
by Greg Von Kuster 09 Oct '15

09 Oct '15

Hello all, I’m working on adding support to the Galaxy framework for datatypes in the constructive solid geometry (CSG) space and I have several working Galaxy tools and a visualization plugin that deal with 3d shapes in this environment. All of this work will soon be contributed to open source. For one of the tools, I need to provide 2 select lists on the tool form that are associated in such a way that when an option in select list 1 is chosen, the options in select list 2 are altered and re-rendered. This behavior would probably use a combination of dynamic options and refresh_on_change between the 2 associated select lists. I’ve not seen a tool that does this precisely, so I’m hoping that if it is currently possible to do this within Galaxy tools, someone will point me to an example. If it is not currently possible, I will contribute a PR for supporting it, but would like some input as to how it should be done. Dynamic options are currently rendered using 4 approaches; from_file, from_dataset, from_parameter and from_data_table. One or more of several filters can then be applied to the options to alter them if desired. Since these CSG tools involve new datatypes, I have flexibility into how the metadata elements are set up that are needed to render these 2 select lists. A dictionary may work where the metadata element contents look like this: {a: [‘1’, ‘2’], b: [‘3’, ‘4’] } The options in select list 1 would be ‘a’ and ‘b’. When ‘a’ is selected, select list 2 would have options ‘1’ and ‘2’, and when ‘b’ is selected, select list 2 would have options ‘3’ and ‘4’. To support this approach, perhaps dynamic options could be enhanced to include a from_dict option. There would be some complxity involved in associating the lists using refresh_on_change so that select list 2 is refreshed with the correct options when select list one is changed. I haven’t yet worked out these details. Also, using a dictionary will not keep order for the options, so perhaps a list of tuples would be better? [ [ ‘a’, [‘1’, ‘2’]], [‘b’, [‘3’, ‘4’]]] Can someone let me know if this is currently possible, and if so, an example tool that does it? If it’s not possible, does the above approach seem reasonable, or is there a better way? Thanks very much, Greg Von Kuster ___________________________________________________________ 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/ <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] Puzzling error in program using Bioblend
by mark fernandes (IFR) 09 Oct '15

09 Oct '15

And it’s Nicola for the win…! I deleted the two tabular files and re-uploaded them and my code works! ☺ Following on from this does this error state happen very often or have I just been unlucky? If the former is true, any suggestions on how best to trap it and report back to user to fix? Thanks Nicola. I was beginning to wonder if I had blundered in my Python. 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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package_picard_1_136 installation error
by Sven E. Templer 09 Oct '15

09 Oct '15

Hello list, installing the dependency package_picard_1_136 results in the following error: --- File "/beegfs/common/galaxy/home/galaxy-15.07/lib/tool_shed/galaxy_install/install_manager.py", line 142, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict ) File "/beegfs/common/galaxy/home/galaxy-15.07/lib/tool_shed/galaxy_install/install_manager.py", line 100, in install_and_build_package initial_download=True ) File "/beegfs/common/galaxy/home/galaxy-15.07/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step initial_download=initial_download ) File "/beegfs/common/galaxy/home/galaxy-15.07/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step checksums = self.get_dict_checksums( action_dict ) File "/beegfs/common/galaxy/home/galaxy-15.07/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 223, in url_download archive = CompressedFile( file_path ) File "/beegfs/common/galaxy/home/galaxy-15.07/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract print "foo" [Errno 2] No such file or directory: './database/tmp/tmp-toolshed-mtdBC1_TE/picard-tools-1.136/picard-tools-1.136/' --- Checking the directory './database/tmp/tmp-toolshed-mtdBC1_TE/picard-tools-1.136' returns: $ ls -a ./database/tmp/tmp-toolshed-mtdBC1_TE/picard-tools-1.136 . .. htsjdk-1.136.jar libIntelDeflater.so picard-lib.jar picard.jar The same thing happens with 'package_picard_1_126_0', whereas 'package_picard_1_56_0' installs fine. Is there an issue with '<source_directory>.</source_directory>' (in 126 and 136) vs '<source_directory>picard-tools-1.56</source_directory>'? I changed this in my local xml but it had no effect. Any ideas? Sven

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User API keys with External (LDAP) authentication disabled?
by Ryan G 08 Oct '15

08 Oct '15

Hi all - I have external authentication established with our enterprise wide LDAP working with Galaxy. I just noticed that I can no longer manage API keys for users from the Admin Page -> API Keys. I get "Access to Galaxy user controls is disabled. User controls are disabled when Galaxy is configured for external authentication" We basically have a 'nobody' user in Galaxy that populates the Data Library with new data from a proprietary system. We were using a user's API key (mine) to do this but want to switch over to a daemon style user key. In order to do so, I need to generate an API key for the dummy user. Is there no way to get API keys from the Admin interface with external authentication?

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Puzzling error in program using Bioblend
by mark fernandes (IFR) 08 Oct '15

08 Oct '15

Hi, I'm hoping that the list can help me out. I'm trying to write some tools to capture elements to ease migration from a course development server to a training server. I'm using the Bioblend API which I am a newbie at using. In the code for extracting the data files from shared data libraries all is well except for 'Tabular' data (e.g. fasta and txt are OK). The error seems to be at the stage where the program calls the Bioblend .datasets.download_dataset() function. NB The tabular files in question can be downloaded fine from the server on the appropriate Galaxy page. (My code is at the end of this message - Please forgive the quality of my Python code). If a tabular data file is present then I get the following output & errors from my program:- Root path: /usr/users/fr009/fernande/gal_exports/data Library: Intro Galaxy Training No. of items in library 11 >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Getting_started/NBARC/BM361007.fasta << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Getting_started/NBARC/NB_domains.tabular << --------------------------------------------------------------------------- DatasetStateException Traceback (most recent call last) <ipython-input-36-8f38351db9f4> in <module>() 52 filepath = os.path.join(rootpathplus,fname.strip("/")) 53 print '>>',filepath,'<<' ---> 54 gi.datasets.download_dataset(items['id'],filepath,False) /usr/local/lib/python2.7/dist-packages/bioblend/galaxy/datasets/__init__.pyc in download_dataset(self, dataset_id, file_path, use_default_filename, wait_for_completion, maxwait) 81 dataset = self.show_dataset(dataset_id) 82 if not dataset['state'] == 'ok': ---> 83 raise DatasetStateException("Dataset not ready. Dataset id: %s, current state: %s" % (dataset_id, dataset['state'])) 84 85 # Galaxy release_13.01 and earlier does not have file_ext in the dataset DatasetStateException: u'Dataset not ready. Dataset id: 1cd8e2f6b131e891, current state: error' Also note that : g_vers = gi.config.get_config() g_vers['version_major'] Outputs]: u'15.03' Any help/elucidation gratefully received (I'm on a learning curve here) :-) Thanks in anticipation. Mark Fernandes #####Code omitting the template files###### --------------------------------------------------------- import bioblend.galaxy import os # Ipython Notebook version - MAF Oct 2015 # Server specific bit. in Real code get this from environ & args (argv) server = 'http://N85460.nbi.ac.uk:8080/' api_key = 'secret_squirrel' rootpath = os.path.join(os.environ['HOME'],'gal_exports/data') print 'Root path: ',rootpath #connect to galaxy server instance gi = bioblend.galaxy.GalaxyInstance(url=server, key=api_key) #fetch names info about data libraries dl = gi.libraries.get_libraries() # for each library, get the folder names for each set & create the sub-dirs if they do not exist for libs in dl: print 'Library: ', libs['name'] rootpathplus = os.path.join(rootpath,libs['name']) # Code to check directory pre-esistence and create it if it doesn't # Move this out to a support module in finished code.... try: os.makedirs(rootpathplus, 0755) except OSError: if not os.path.isdir(rootpathplus): raise # for each library, get the folder names for each set & create the sub-dirs if they do not exist fold = gi.libraries.get_folders(libs['id']) print 'No. of items in library',len(fold) if len(fold) > 1: for items in fold: dirpath = os.path.join(rootpathplus,os.path.normpath(items['name'].strip("/"))) try: os.makedirs(dirpath, 0755) except OSError: if not os.path.isdir(dirpath): raise # # for each folder create the sub-dir off of user rootdir cl = gi.libraries.show_library(libs['id'],True) for items in cl: if items['type']=='file': fname = os.path.normpath(items['name']) file_ext = os.path.splitext(fname)[1] # check for tabular data file and omit to avoid error message if file_ext != '.tabular': # Swap above if with this one to let the bad stuff happen... # if file_ext != '.untrapped': filepath = os.path.join(rootpathplus,fname.strip("/")) print '>>',filepath,'<<' gi.datasets.download_dataset(items['id'],filepath,False) Root path: /usr/users/fr009/fernande/gal_exports/data Library: Intro Galaxy Training No. of items in library 11 >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Getting_started/NBARC/BM361007.fasta << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Getting_started/Pinfestans/PinfestansAVH9.fasta << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Getting_started/Pinfestans/PinfestansAVRblb1.fasta << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Getting_started/Pinfestans/PinfestansAVRblb2.fasta << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Getting_started/Test.fasta << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Interval_operations/SNPsDensity/UCSC_Human_chr22_SNPs.txt << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Interval_operations/SNPsDensity/UCSC_Human_refGene_chr22_Exons.txt << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Interval_operations/TAF1/TAF1_ChIP << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Interval_operations/TAF1/TAF1_ChIP_chr11 << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Interval_operations/TAF1/UCSC_Human_RefGene_chr11_Promoters << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Interval_operations/TAF1/UCSC_Human_refGene_chr11 << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/data_visualisation/www.compsysbio.org_bacteriome_dataset_functional_interactions.txt << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/loading_data/Local_data/truseq_exome_targeted_regions.hg19.bed.chr22.bed << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/loading_data/BioMart_Homo_sapiens_genes_GRCh37p13_chr22.txt << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/loading_data/TAF1_ChIP.txt << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/loading_data/UCSC_Human_refGene_chr22_Exons.txt << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/loading_data/illumina_truseq_exome_targeted_regions_hg19_chr22.txt << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/workflows/UCSC_Human_chrX_SNPs.txt << >> /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/workflows/UCSC_Human_refGene_chrX_Exons.txt << Library: New data library No. of items in library 1 ---------------------------------------------------------------------------------- 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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