July 2015 - galaxy-dev - lists.galaxyproject.org

Problem finding depency for none toolshed tools
by Christian Brenninkmeijer 03 Jul '15

03 Jul '15

Hi, I have been testing tools not yet ready for a tool-shed but had trouble finding the dependencies as there was no database entries to load these. The code in lib/galaxy/tools/deps/resolvers/galaxy_packages.py assumes that the env.sh or bin directory will be in dependency_dir/package/version when in fact it is often in dependency_dir/ package/version/owner/package_name/revision. I have created a pull request with some code to find the dependency in the sub directory https://github.com/galaxyproject/galaxy/pull/413 As I am relatively new to galaxy I have probably broken lots of rules/agreements on how I did the pull request. If so please let me know where I went wrong so I can redo it properly. Christian PS. This is my proposed change to lib/galaxy/tools/deps/resolvers/galaxy_packages.py: def _find_dep_versioned( self, name, version, type='package', **kwds ): #First try the way without owner/name/revision path = join( self.base_path, name, version ) package = self._galaxy_package_dep(path, version) if package != INDETERMINATE_DEPENDENCY: return package #now try with an owner/name/revision for owner in listdir(path): owner_path = path + "/" + owner for package_name in listdir(owner_path): if package_name.startswith("package_"+name): package_path = owner_path + "/" + package_name for revision in listdir(package_path): revision_path = package_path + "/" + revision package = self._galaxy_package_dep(revision_path, version) if package != INDETERMINATE_DEPENDENCY: return package return INDETERMINATE_DEPENDENCY

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cloudman launch
by Alexander Vowinkel 02 Jul '15

02 Jul '15

Hi Enis, I am trying to launch my cloudman instance with this launcher again: https://launch.usegalaxy.org/launch You created the flavor for me because it wouldn't load my galaxyIndices from the snaps.yaml in my default bucket. I thought, this problem was fixed, but it still creates a galaxyIndices from the default snapshot (600GB) when using the Standard flavor. When I use my flavor, it loads the snapshot, but it is a little outdated ;) So my question: Is this behaviour expected? If no, are you going to fix it soon? If not, could you update my flavor in the way that galaxyIndices gets created from snap-6f0b211d ? Further: Should I update CM? I am still on the version from Jun 22. I am still not sure what I need to change (my snaps.yaml) in order to have my clean cluster creation still functioning. Thanks, Alexander

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cloudman persist filesystem error
by Alexander Vowinkel 02 Jul '15

02 Jul '15

Hi, from IRC this question/bug report: (18:06:13) avowinkel: some cloudman guy here? enis? (18:06:30) avowinkel: AttributeError: 'NoneType' object has no attribute 'id' (18:06:50) avowinkel: when persisting galaxyIndices (18:07:43) avowinkel: snapshot is created, but it crashes when ... somewhen well after that (18:11:08) avowinkel: http://pastebin.com/SDp1p96K (18:11:10) mrscribe: Title: paster.log - Pastebin.com (at pastebin.com) Best, Alexander

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running tophat2 on local Galaxy - can't find bowtie2
by HARDING Simon 01 Jul '15

01 Jul '15

Hi I've set-up a local Galaxy instance and have been using the data manager / tool-shed to set up tools and indexes etc. I've installed both bowtie2 and tophat2 but when i come to run tophat 2 I get the following error: tophat2 --num-threads ${GALAXY_SLOTS:-4} /export/system0/home/galaxy/galaxy-dist/tool-data/mm9/bowtie2_index/mm9/mm9,/export/system0/home/galaxy/galaxy-dist/tool-data/mm9/bowtie2_index/mm9/mm9 "/export/system0/home/galaxy/galaxy-dist/database/files/000/dataset_14.dat" [2015-07-01 16:22:24] Beginning TopHat run (v2.0.9) ----------------------------------------------- [2015-07-01 16:22:24] Checking for Bowtie Bowtie 2 not found, checking for older version.. Error: Bowtie not found on this system. Clearly there is an issue here with tophat2 knowing where bowtie2 is. What I can fathom is where this is assigned and how to get this working. In my tool_dependency_dir/bowtie2 there are both 2.2.4 and 2.2.5 packages - this has confused me a bit, but i think it was because the 2.2.5 is a dependency of tophat2 and 2.2.4 a dependency of bowtie2. Thanks in advance for any insight and help - I suspect it's something trivial as i'm quite new to Galaxy. -- Simon D. Harding, PhD. MRC HGU MRC IGMM at University of Edinburgh Crewe Road, EDINBURGH, EH4 2XU -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Not seeing reference genome - Bowtie2
by McCully, Dwayne (NIH/NIAMS) [C] 01 Jul '15

01 Jul '15

Hello Everyone, Performed a data retrieval using the rsync method for mm10 and also downloaded the .loc files per the "Data Integration" page to the tool-data directory. The paths match in the .loc file for bowtie2 of the mm10 download directory. My problem is that I'm not seeing mm10 in the "Select Reference Genome" from within Bowtie2. Any tips would be appreciated Dwayne

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