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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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output filter bugs
by Alexander Vowinkel 30 Jun '15

30 Jun '15

Hi, I have a tool with filtered outputs (<data [..]><filter>[...]</data>). A) As I understood the filters are pure python. But if I put it in "<![CDATA[", it doesn't work. I think this should work even better ;) B) The workflow generator doesn't interpret the filters. When I put the tool in a workflow, all possible outputs are shown. This doesn't change when I change an option that would change the output choice. Can someone fix this? ;) Best, Alexander

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Job still waiting - Command Line None - SGE
by Gildas Le Corguille 30 Jun '15

30 Jun '15

Hi, We have a problem on our production instances since one or two years (never found the time to write it and we still hope to find by ourself). Some jobs stay in "waiting" status (grey) indefinitely. Job ID User Last Update Tool State Inputs Command Line Job Runner PID/Cluster ID 63094 foo(a)bar.fr 10 hours ago toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4 new 123250 setting_metadata None None None 63093 foo(a)bar.fr 10 hours ago toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4 new 123249 setting_metadata None None None 63088 foo(a)bar.fr 14 hours ago testtoolshed.g2.bx.psu.edu/repos/jjohnson/trinityrnaseq/trinityrnaseq_norm/… new 123250 setting_metadata, 123249 setting_metadata None None None Our scheduler is SGE. We tried to found the origin of this issue : - there is not relevant clues in the log files - sometimes, a restart make start those jobs - sometimes, kill a job make the others start - sometimes, there is no choice than resubmit Is anyone can propose an idea to fix this behaviour ? Thanks Gildas

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planemo shed_update - error
by Alexander Vowinkel 29 Jun '15

29 Jun '15

Hi, I'm running: planemo shed_update --check_diff --shed_target toolshed and get a python error message (see below). shed_diff and shed_lint are working fine. planemo, version 0.12.2 Best, Alexander Traceback (most recent call last): > File "/usr/local/bin/planemo", line 11, in <module> > sys.exit(planemo()) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 664, > in __call__ > return self.main(*args, **kwargs) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 644, > in main > rv = self.invoke(ctx) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 991, > in invoke > return _process_result(sub_ctx.command.invoke(sub_ctx)) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 837, > in invoke > return ctx.invoke(self.callback, **ctx.params) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 464, > in invoke > return callback(*args, **kwargs) > File "/usr/local/lib/python2.7/dist-packages/click/decorators.py", line > 64, in new_func > return ctx.invoke(f, obj, *args[1:], **kwargs) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 464, > in invoke > return callback(*args, **kwargs) > File > "/usr/local/lib/python2.7/dist-packages/planemo/commands/cmd_shed_update.py", > line 52, in cli > tsi = shed.tool_shed_client(ctx, **kwds) > File "/usr/local/lib/python2.7/dist-packages/planemo/shed/__init__.py", > line 331, in tool_shed_client > key = prop("key") > File "/usr/local/lib/python2.7/dist-packages/planemo/shed/__init__.py", > line 323, in prop > return kwds.get("shed_%s" % key, None) or shed_config.get(key, None) > AttributeError: 'NoneType' object has no attribute 'get'

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Galaxy API to upload files to data library
by Ryan G 29 Jun '15

29 Jun '15

Hi all - I'm trying to figure out how to script the ability to upload data (fastq) files to Galaxy via the API. I can get the Library's root_folder_id, but am unsure of what the API call is to upload a file. I'm constructing this dictionary: data = {} data['folder_id'] = galaxyFolderId data['create_type'] = 'file' data['file_type'] = 'fastq' data['upload_option'] = 'upload_paths' data['filesystem_paths'] = fileToUpload data['link_data_only'] = 'link_to_files' I assume this is the correct format based on other code I've seen, but I'm not sure what the actual submit call should be. 'api/libraries/' or 'api/folders'????

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LDAP and new history creation
by Erwan DELAGE 29 Jun '15

29 Jun '15

Dear all, We have a galaxy instance that uses LDAP for authentication and it works fine. The only problem is that a new history is created each time a user log in. When we disable LDAP to use the classical authentication method, the problem goes away. Any idea of what could happen here ? Thanks Erwan

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Download of hg19 genome by data manager fails
by Tobias Zimmermann 29 Jun '15

29 Jun '15

Dear All, I have some problems with the download of genome files by the data manager. I tried to download some genome files from the UCSC server with the data manager of galaxy ( name: data_manager_fetch_genome_all_fasta, revision: cca219f2b212), but it fails because of a timeout. Our galaxy server is in an internal network without connection to the Internet. To access the Internet we are required to go trough a http-proxy before any web-services can be accessed. The file /shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py manages the download of the file. Line 183 shows the problem. Here the FTP item from the python ftplib module tries to establishes the connection to the UCSC ftp server. This connection fails. So here is my question: How can i download data by the data manager with a http-proxy? Thanks for help! Tobias

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Set build when discovering output in collection
by Alexander Vowinkel 27 Jun '15

27 Jun '15

Hi, as many of you probably know by now, I have a tool that creates an output collection by discovering the datasets in this collection like propsed there: [1] Specifically I have a fastq input with set build information (a ref genome). The output is a collection of fastq files. After I managed to give them the same format like the input (hacky version), I now want them to adopt the build ID. How can I do that? Thanks, Alexander [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/634/allow-tools-to…

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