July 2014 - galaxy-dev - lists.galaxyproject.org

bioblend problem trying to use run_tool function
by Olivia Doppelt 24 Jul '14

24 Jul '14

Dear Developers, I would like to use bioblend to export the result of a galaxy workflow. To do that, we want to use an implemented tool called export_data; which enables the copy of a result file from galaxy arborescence to a local directory which belong to the user making the analysis and the export. We tried to launch this tool using the run_tool function but it doesn't work. giOlivia.tools.run_tool(history_id='xxxxxxxxxxx',tool_id='yyyyyyyy/export_data/export/2.2',tool_inputs={'input':'id_data','name':"data"}) I get an error message which is very long and attached to this email. Please help me on that it is the final step of several ones using bioblend. Have a nice day, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur

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How to configure galaxy with a cluster
by 王渭巍 24 Jul '14

24 Jul '14

Hello, everyone, I am new here, and I am trying to configure galaxy with a cluster. I have 3 servers. One for galaxy server, two for cluster computing. And I followed "Running Galaxy Tools on a Cluster" done the configuration. Now I have 2 questions: 1. How to vertify whether I have configured the galaxy cluster successfully? For example, I don't see there is any cluster options in "NGS mapping (bowtie2) ", but I see cluster options in a web galaxy. 2. And any other work I should do for configuring galaxy with a cluster? Thank you for any help. Ben

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Once-run galaxy archives
by Eric Rasche 23 Jul '14

23 Jul '14

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Test ToolShed Down
by Mark Lindsay 23 Jul '14

23 Jul '14

Dear All apologies. Another simple question. When I attempt to load tools from the test toolshed it give a relocation error. Are these links currently down (or am I making a mistake) and if so, does anybody have an idea as to when these will be re-instated. I am particular keen to install the Tophat2 indexer (part of data_manager) Many thanks for your time Mark

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writing datatypes
by Eric Rasche 22 Jul '14

22 Jul '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I'm trying to add a new datatype to my galaxy instance for genbank files, however I'm running into various issues. I've followed the tutorial (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes) however that example subclasses tabular, and I'd like to subclass Text as they're plain text files, and I'd like to be able to define a sniffer for them (not possible if your type=galaxy.datatypes.data:Text) I figured the call ought to be something like <datatype extension="gb" type="galaxy.datatypes.data:Genbank" subclass="True" /> however, everything I try fails with > Error importing datatype module galaxy.datatypes.data: 'module' object has no attribute 'Genbank' To avoid this particular issue, I tried writing a separate datatype just for genbank files (type="galaxy.datatypes.genbank:Genbank"), however that fails with the same error: > galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error importing datatype module galaxy.datatypes.genbank: 'module' object has no attribute 'genbank' > Traceback (most recent call last): > File "/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py", line 206, in load_datatypes > module = getattr( module, mod ) > AttributeError: 'module' object has no attribute 'genbank' Here's my lib/galaxy/datatypes/genbank.py looks like: > import pkg_resources > pkg_resources.require( "bx-python" ) > import logging > from galaxy.datatypes import data > log = logging.getLogger(__name__) > > class Genbank( data.Text ): > file_ext = "gb" > > def sniff( self, filename ): > header = open(filename).read(5) > return header == 'LOCUS' To debug this, I've tried copying the tabular data type completely, removed all the classes other than Tabular, and renamed it "Genbank", however this fails too with the same error. Can anyone offer some insight? Cheers, Eric -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (GNU/Linux) iQIcBAEBAgAGBQJTxCHwAAoJEMqDXdrsMcpVmbsQAJ3eFIhZtZmVP9LCz/F9Ywg/ 148NJZy4lmxZU0KScJlc8kVDCDSADXIHd0Db/kpJwuUKEX7zei9q2uXfO7sWl3yt yxrFEdtX/a5SMVsa6F5WZuKwBs0zfvfsnIUoraOgh6nXeJnr53l9mYeWaKB6bi3Z xAlgJG/kdIR1jRjAimuQf4vMjNgtDQPOmotYBQTytbhsV6/nRzGI8RZAYwQ7GnVs XYOWFyhzrBgALndVI3BjI21rbRqguhrqr2t7i0Ma7Pp2JmAnNjmUaq70NN3Rueh6 DvnTtxInM1dVOQY+Yam6MCMmAedV1cG+rNGdpP2l82MajQAsMtbXckBXXKcSgyTq WCFoLVURYO1tHkWyq4ikamfFDHtJp1DogBYhUiPMyRw+CV+3sOvr0U5DcyRdiDsJ Xcm3ygqYVLGwauNmuN3yGcQcnfypDOOeFs1lppbNe3lw0w3ikZN4Zmu1ec5s1ITK MEcgBrGYgZrKDRXkx53lnABGpv6mYflYpag7fguDNL8j0lh9beaaNmHr4tmeEcug VZ1b1EWoLMj/ikJ/vZcluiHPTSTheiAP8Ttvh1WAayq4rKwVtZygaI9IDauqqBQ1 Dgotes3vcomlTQXDUEZACyOZDxl7wbAUh0LZVaa2fYNIOoPNPOItUFSjf6YveF88 dLiw3ddVm+BFmczJzRpt =4m2j -----END PGP SIGNATURE-----

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Video Datatypes
by Eric Rasche 22 Jul '14

22 Jul '14

Howdy all, This is probably only of interest to a tiny subset of you who work with microscopy and microscope video, but I've added video datatypes and an associated viz plugin for viewing .mp4 files. Please feel free to submit bugs/feature requests/PRs on these https://github.com/erasche/galaxy-video-viz-plugin https://github.com/erasche/galaxy-video-datatypes I plan to add more video datatypes as time permits, as well as tools for working with those datasets (e.g., ffmpeg wrapper). Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Texas A&M Univesity College Station, TX 77843 Ph: 4046922048

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Galaxy error
by Beck, Emily A 22 Jul '14

22 Jul '14

Hello, I have repeatedly gotten the following error message when attempting to use both the mapping and pileup functions in Galaxy. I am using files that I have previously used successfully with these functions, and cannot fix it. Thank you. ~Emily Beck user username emilybeck quota_percent 19 total_disk_usage 52086193970 nice_total_disk_usage 48.5 GB email emily-beck(a)uiowa.edu is_admin false tags_used model_class User id 03f0554e2314759e source HDACollection(f313d1d65c4ee57e,451) xhr readyState 4 responseText {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0} responseJSON err_msg Uncaught exception in exposed API method: err_code 0 status 500 statusText Internal Server Error responseHeaders Server nginx/1.4.7 Date Wed, 16 Jul 2014 15:19:52 GMT Content-Type application/json Transfer-Encoding chunked Connection keep-alive Cache-Control max-age=0,no-cache,no-store options data parse true emulateHTTP false emulateJSON false Emily Beck PhD Candidate Llopart Lab 469 Biology Building Iowa City, IA 52242 Lab: (319)335-3430

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getting API key from user/pass
by Eric Rasche 22 Jul '14

22 Jul '14

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Schema downgraded but galaxy won't launch
by Kandalaft, Iyad 22 Jul '14

22 Jul '14

Hello everyone I tried a galaxy update on my development instance of galaxy. It failed due to a schema change coupled with a mysql version change. Don't worry about why it failed - that has been resolved. I have a backup copy of the database that I restored, which was based on schema 118. I issued a "hg update *revision*" to revert back to a code base using the 118 schema. I verified that the model folder now only contains up to 118_....py. When I try to start galaxy, it tells me that the code requires schema 120 and that I should upgrade using db_manage.sh. I tried running "db_manage.sh downgrade 118" but since the database is already v118, it just exists without any output. What am I doing wrong? Regards, Iyad Kandalaft Bioinformatics Application Developer Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: Iyad.Kandalaft(a)agr.gc.ca<mailto:Iyad.Kandalaft@agr.gc.ca> Telephone | Téléphone 613- 759-1228 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada

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Basic Questions
by Mark Lindsay 22 Jul '14

22 Jul '14

Apologies if this sounds like a basic question or if I am enquiring of the incorrect list. I have just had a local instance of galaxy installed on my MacPro. Could somebody inform me of the best options for loading large BAM files (5Gb) from the same hard drive into this instance of Galaxy. It states o that it is not possible to load files > 2Gb and that you must use either a URL or FTP. My scripting knowledge is virtually non-existant….although I have access to people that do. Cheers Mark

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