- galaxy-dev - lists.galaxyproject.org

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

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question using PICRUSt COG vs. KEGG
by Ana Weil 01 Jul '16

01 Jul '16

Hello, I have a general question. A metagenome prediction in PICRUSt worked fine when I ran it requesting KEGG output (running on MAIN), but I got the below error when requesting COG output. I could not find in the on-line forums or other areas of support what may be needed regarding a different input file or change in the normalization by copy number in order to get COG instead of KEGG output? Thank you very much for your help! Ana Traceback (most recent call last): File "/n/galaxy/www/galaxy_hutlab14/galaxy-hutlab14-20150109/tools/picrust_galaxy/scripts/predict_metagenomes.py", line 337, in <module> main() File "/n/galaxy/www/galaxy_hutlab14/galaxy-hutlab14-20150109/tools/picrust_galaxy/scripts/predict_metagenomes.py", line 171, in main ids_to_load=ids_to_load,verbose=opts.verbose,transpose=True) File "/n/galaxy/www/galaxy_hutlab14/galaxy-hutlab14-20150109/tools/picrust_galaxy/scripts/predict_metagenomes.py", line 113, in load_data_table genome_table_fh = gzip.open(data_table_fp,'rb') File "/n/hutlab11/tools/python2.7.8/lib/python2.7/gzip.py", line 34, in open return GzipFile(filename, mode, compresslevel) File "/n/hutlab11/tools/python2.7.8/lib/python2.7/gzip.py", line 94, in __init__ fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb') IOError: [Errno 2] No such file or directory: '/usr/local/galaxy-python/lib/python2.7/site-packages/picrust/data/cog_13_5_precalculated.tab.gz'

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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.

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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

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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

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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/

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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

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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

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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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