galaxy-dev April 2016

galaxy-dev@lists.galaxyproject.org

47 participants
55 discussions

Re: [galaxy-dev] Question: Cannot start local Galaxy after upgrade to v16.01
by Scott Szakonyi 19 Apr '16

19 Apr '16

Hi Daniel, I'm a relative novice at Galaxy administration, but at first blush it looks like you're missing (or the Galaxy user doesn't have permissions on) the paste process. You can try a GIT status or diff to see if something just didn't download right. Otherwise, check to make sure that your entire galaxy install directory is owned by the Galaxy user and the group that the Galaxy user belongs to. Hope this helps! pkg_resources.DistributionNotFound: Paste -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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novice galaxy user needs help retrieving MIA history
by ryan stueve 19 Apr '16

19 Apr '16

Greetings, I am a novice Galaxy user. I was getting along perfectly this morning (made some mistakes, deleted some steps) and got to alignment steps in my RNAseq analysis. Went to some afternoon meetings, returned & logged back in- MY HISTORY WAS EMPTY! can you advise? Instance: MAIN/publicUsername/email: jnkaccnt1(a)outlook.comHistory name: something like "LUAD RNA-seq"; definitely had "LUAD" in title also, here is one of the steps/filenames that should be in history (I downloaded before meeting):"Galaxy240-[H1648_TopHat_on_data_164_and_data_163__accepted_hits].bam" any help sincerely appreciated

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Issue with GATK in workflow
by Scott Szakonyi 18 Apr '16

18 Apr '16

Hello all, We have indexed a genome using the appropriate data manager, for GATK, and our reference is showing up and working for individual walkers in GATK 2.8. When designing a workflow, however, the reference genome is not appearing as an option for many walkers, including indel realigner and realigner target creator. It is appearing for haplotype caller. Again outside of the workflow environment the indexed references show up for all walkers. Any thoughts on this issue? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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Order of element in datasetcollection "List"
by julie dubois 18 Apr '16

18 Apr '16

Hi all, I've created a tool which takes a collection List as input. This tool iterate on this collection with a "for" loop. I'd like to know the order of my datasets in this collection for the next treatment in my tools. For example, when I take dataset number 1 and number 2 and number 3 to create my collection. When I iterate on it : what is the first element? the number 1 or the number 3. I ask it because I've seen that when a tool works on a dataset collection, the first job in the history (number of dataset in history is the lowest) ran on dataset number3 and not on dataset number 1 as I expected ! Thanks in advance. Julie Chevalier

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Allow users to see the job queue?
by Raymond Wan 15 Apr '16

15 Apr '16

Dear all, I know Galaxy is independent of the underlying queuing system but is it possible to display the status of the queue to users via the Galaxy interface? I understand that the jobs are submitted under the name of the owner of the Galaxy process. And that there is a way to fix this [1], but I think I'm fine with leaving it as-is. I guess it would be nice if users can see how long the queue is. The naive way that I'm thinking about is to have a cronjob that runs "squeue" (we are using SLURM) periodically. Its output is cleaned up by a script and a "static" HTML file is generated for Galaxy to display. I don't know if there is a more sensible way that fits within the framework of Galaxy. Is this approach acceptable or is there a better / easier way that I've completely missed? Thank you! Ray [1] https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_…

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Data removal after ftp import.
by Zuzanna K. Filutowska 15 Apr '16

15 Apr '16

Dear All, is there any option to not remove files that has been imported to Galaxy from FTP directory and to not remove files that haven't been imported since 3 days? -- Regards, -- Zuzanna K. Filutowska, HPC Systems Administrator Poznan Supercomputing and Networking Center Institute of Bioorganic Chemistry Polish Academy of Sciences Seize the day boys! Make your lifes extraordinary! --John Keating

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Tool shed tools, manual dep installation
by David Trudgian 15 Apr '16

15 Apr '16

Hi All, I'm currently caught between the requests of our Galaxy users to install things from main tool-shed, and our information security dept's concerns r.e. the automated installation of tool-deps on our systems. Due to restrictive web access policies for servers here our galaxy server can't access SourceForge, where many tool-dep downloads are. A request to unblock this for a particular tool-dep package led to our infosec justifiably raising concerns r.e. a tool-dep package that is quite out of date (details sent off list previously). We're now currently unable to install tool-shed tools that users have requested. The current proposal from our infosec dept is to get all our deps from system repos etc. However the way I'm aware of implementing this for tool-shed tools, which need to run across our cluster, would be something pretty arduous like: * Clone the tool from the upstream toolshed repo * Edit the tool code to remove the package requirements * Identify and install all the requirements on the cluster as system pkgs / environment modules - with attention to versions so things work as expected * Edit the tool code so it knows to load the right environment modules / set right PATH when it runs * Install the tool into our galaxy 'tools' dir , not the 'shed_tools' * Manually add the tool to galaxy's tool_conf.xml.main * Schedule downtime to restart galaxy * Test things out .... or we have to host our own tool shed, import tools we want from upstream, edit out the package requirements, provide the deps ourselves. These have all the headaches of merging things in when upstream shed-tools change. Just wondering if I'm missing anything? I know you can turn off 'handle repository dependencies' when installing a tool, but the tool still defines 'requirements' in its XML file and shows 'Missing repository/tool dependencies' in the Admin. Has anyone had any experience of dealing with this kind of situation? Many thanks! -- David Trudgian Ph.D. Computational Scientist, BioHPC Lyda Hill Department of Bioinformatics UT Southwestern Medical Center Dallas, TX 75390-9039 Tel: (214) 648-4833 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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tool shed bug on uploading incorrect files
by Christian Brenninkmeijer 14 Apr '16

14 Apr '16

Hi All, There is a bug in the toolshed code when you upload a file with an error. For example a jar file containing an tool_dependency.xml which refers to a non existing dependency. The toolshed correct refuses to except the upload and stays at the old version, However the files are added to the database/community_files/xxx/repo_yyy directory. If I then later upload a different jar with different files the previous files are NOT deleted. If you try to delete there from the webbrouser you get an error. Quick Fix is to go into database/community_files/xxx/repo_yyy and delete the files manually. Christian University of Manchester PS. I was able to replicate this with a brand new toolshed. create admin user, category ect create a tool and add a jar with a tool_dependecy.xml file with which reference a dependency not there upload a different jar which does not include a tool_dependency.xml file browse ...tip file mark tool_dependency.xml which is showing and attempt to delete.

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Planemo test with SGE
by D K 12 Apr '16

12 Apr '16

Hi, I posted this question to biostars but didn't get an answer.... Is it possible to use "planemo test" functionality on an SGE cluster? I can correctly run a custom tool on an SGE cluster when I manually run a job through the galaxy interface. If I change the job_conf.xml so that the job is run locally, I can use "planemo test" successfully, but if I change the job_conf.xml so that Galaxy uses the SGE cluster, planemo fails: Traceback (most recent call last): File "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py", line 289, in test_tool self.do_it( td ) File "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py", line 38, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line 43, in stage_data_in_history upload_wait() File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line 280, in wait while not self.__history_ready( history_id ): File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line 298, in __history_ready return self._state_ready( state, error_msg="History in error state." ) File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line 361, in _state_ready raise Exception( error_msg ) Exception: History in error state. -------------------- >> begin captured stdout << --------------------- History with id 2891970512fa2d5a in error - summary of datasets in error below. -------------------------------------- | 1 - MTB_Genes.fasta (HID - NAME) | Dataset Blurb: | tool error | Dataset Info: | The cluster DRM system terminated this job | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- --------------------- >> end captured stdout << ---------------------- Is this a problem with my configuration or a limitation of planemo? Thanks!

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Re: [galaxy-dev] init scripts version 16.01
by Eric Kuyt 11 Apr '16

11 Apr '16

Thanks, works like a charm! Clean easy fix, Now why I couldn't come up with this myself. On 2 April 2016 at 11:49, Marius van den Beek <m.vandenbeek(a)gmail.com> wrote: > ld have been mentioned with the release notes. > I didn't test this, but it might be sufficient to replace > PYTHON="/usr/bin/python" > with PYTHON="<path/to/venv/bin/python>". > If that is sufficient for you, let us know and we will update the wiki and > adjust the script in > -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt(a)wur.nl Web: http://www.cvi.wur.nl

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galaxy-dev April 2016