- galaxy-dev - lists.galaxyproject.org

strange submit script
by Nikolaos Tur 04 May '17

04 May '17

Hi, Galaxy 16.04, sge as batch system. There is strange submit script from one job which replicates whole Galaxy home directory to the working directory for jobs and does this 2 times. Am I correct that tool_script.sh file is generated automatically by Galaxy or still user can add something there? If it generates automatically then is this a bug? cat tool_script.sh: #!/bin/bash # The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi PACKAGE_BASE=/home/galaxy/tools/dependencies/samtools/1.2/iuc/package_samtools_1_2/f6ae3ba3f3c1; export PACKAGE_BASE; . /home/galaxy/tools/dependencies/samtools/1.2/iuc/package_samtools_1_2/f6ae3ba3f3c1/env.sh; MEM=`expr "${GALAXY_SLOTS:-16}" \* 48 - 16` ; workdir=`pwd`; echo "workdir is $workdir"; cd $LOCAL; echo "Running Trinity from `pwd`"; Trinity --max_memory "${MEM}G" --CPU "${GALAXY_SLOTS:-16}" --bflyHeapSpaceMax "32G" --bflyHeapSpaceInit "2G" --bflyGCThreads "6" --left /home/galaxy/database/files/000/dataset_81417.dat --right /home/galaxy/database/files/000/dataset_81418.dat --seqType fq --SS_lib_type RF --group_pairs_distance 500 > /home/galaxy/database/files/000/dataset_81515.dat 2>&1 || (ec=$? ; cp -pr . $workdir; cd $workdir; cat /home/galaxy/database/files/000/dataset_81515.dat >&2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit $ec); cp -pr . $workdir; cd $workdir Output is: workdir is /home/galaxy/database/jobs_directory/000/51718/working Running Trinity from /home/galaxy It means that in "cd $LOCAL" LOCAL variable is undefined. And then there is a bunch of copies from home directory. Thanx for the help, Nikolaos

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Re: [galaxy-dev] unable to install tools
by Briand, Sheldon (NRC/CNRC) 03 May '17

03 May '17

Hi, Here are, I think, the relevant lines from my nginx.conf: location / { proxy_pass http://galaxy_app; proxy_set_header X-Forwarded-Host $host:$server_port; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; proxy_set_header X-URL-SCHEME https; } >From galaxy.ini: nginx_x_accel_redirect_base = /_x_accel_redirect nginx_x_archive_files_base = /_x_accel_redirect I have checked the start-up logs and both the admin_toolshed controllers are enabled on start-up. I've also tried a fresh python venv environment which didn't help. I was able to install tools in the past. Has anyone run into this recently? Thanks, -Sheldon From: Briand, Sheldon (NRC/CNRC) Sent: Tuesday, May 02, 2017 5:30 PM To: 'galaxy-dev(a)lists.galaxyproject.org' <galaxy-dev(a)lists.galaxyproject.org> Subject: unable to install tools Hi, I've updated to Galaxy 17.01 from Galaxy 16.07. Today I am having trouble installing or updating tools. Whenever I pick the option to install a tool from the main toolshed I get a page that says: "NOT FOUND The requested url /admin_toolshed/prepare_to_install was not found on this server" Is there a setting that I need to change on my server? I do run through a nginx proxy server. I can provide it's configuration if it's relevant. Thanks, -Sheldon Sheldon Briand Computer Systems and Applications Analyst National Research Council/Government of Canada Sheldon.briand(a)canada.ca/<mailto:Sheldon.briand@canada.ca/> Tel: (902) 426-1677

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unable to install tools
by Briand, Sheldon (NRC/CNRC) 02 May '17

02 May '17

Hi, I've updated to Galaxy 17.01 from Galaxy 16.07. Today I am having trouble installing or updating tools. Whenever I pick the option to install a tool from the main toolshed I get a page that says: "NOT FOUND The requested url /admin_toolshed/prepare_to_install was not found on this server" Is there a setting that I need to change on my server? I do run through a nginx proxy server. I can provide it's configuration if it's relevant. Thanks, -Sheldon Sheldon Briand Computer Systems and Applications Analyst National Research Council/Government of Canada Sheldon.briand(a)canada.ca/<mailto:Sheldon.briand@canada.ca/> Tel: (902) 426-1677

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May 2017 Galaxy News: GCC2017 deadlines, sponsors & BoFs; new papers, openings, tutorials...
by Dave Clements 02 May '17

02 May '17

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keeping the original file name from the FTP pop-up
by Nikolay Aleksandrov Vazov 02 May '17

02 May '17

Hi, I am using a third-party software to upload huge files (> 100 GB) into Galaxy which emulates the ftp upload procedure. The files come up into the FTP upload pop-up as long id-strings (see attached). which are then used for the filename in the history panel. Displaying the original file name in the pop-up was easy (see attached - Real Name column), but propagating it to the history panel has been more challenging :) I finally found a way to keep the original file name in the history panel, but the method does not look very elegant. At the same time, I discovered that the file name can be explicitly set by using the param NAME in in ../data_source/upload.xml <param name="NAME" type="hidden" help="Name for dataset in upload"></param> I need to push it to the tool inputs from the FTP pop-up but I can't find the way to do it? Does anybody have had some experience with this? Best regards Nikolay =============== Nikolay Vazov, PhD Department for Research Computing, University of Oslo

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uWSGI dataset request error
by Dawes, Gwen 01 May '17

01 May '17

Hi all, We have a simple Galaxy instance running on a webserver on our cluster. Recently, we've seen an upswing of student usage, and I'm trying to look into switching over from a single paster instance to a system using uWSGI to spread the load. Currently we're running the 17.01 release, but we saw this same behaviour on the 16.10 one. I've followed all the steps on the wiki related to setting up uWSGI, but we're encountering the following problem, in the words of one or our primary users: "It is not possible to download/save files from a history. Nothing happens when clicking the floppy disk icon. ... It is possible to view files (clicking the eye icon) that are displayed other than as raw data: tables, html. png does not work. Preview of large text files (i.e. fastq) works, but when selecting display all, the same error message is shown. The small preview in the history (dataset-peek) works." We see the following issue when trying to view raw data: The requested URL /datasets/<a_dataset_id>/display/ was not found on this server. Currently apache (2.4.6) is configured using mod_proxy_uwsgi using: ProxyPass / uwsgi://localhost:14001/ I can see that the requests are being sent over to uwsgi (in its logs): [pid: <pid>|app: 0|req: 95/241] <my_ip> (<my_user>) {82 vars in 1983 bytes} [Mon May 1 15:19:16 2017] GET /datasets/<a_dataset_id>/display?to_ext=fasta => generated 0 bytes in 50 msecs (HTTP/1.1 200) 6 headers in 281 bytes (1 switches on core 1) But we see that it's giving a zero length response. Does anyone know what's going on here? I can't find a way to increase logging further to debug this error, but it's preventing us from using uwsgi to scale out this service. If anyone can make a good suggestion or wants extra details, please let me know. Thanks, Gwen Dawes

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Combine different resolvers for one tool
by Ignacio EGUINOA 30 Apr '17

30 Apr '17

Hi all, I'm setting up a Galaxy server which consists of a Galaxy head node and a Docker engine (swarm) running on top of an OpenNebula cloud. So, ideally I would like to run everything using this Docker engine. For tools that only have 1 dependency, the Docker resolver works perfectly. But, in the case of tools having more than 1 dependency, if I activate mulled containers (enable_beta_mulled_containers = True) it will just try to run the tool script using the container corresponding to the 1st dependency found, which of course fails. What is the correct approach for resolving several dependencies using Docker? I tried activating the involucro which (as far as I understood) builds the docker container on-the-go based on the conda environment which results from the merge of all the dependencies. I know it's a beta feature but still, couldn't make it work...besides setting the path and auto_init to True, what am I supposed to put in the containers_resolvers_config_file ? Beside this, would it be possible to combine the dependencies in another way? Is it possible in the current version to load the conda environment inside a I know it may sound redundant and unnecessary in terms of dependency resolution but in cases like I the one I described, where you have the Docker swarm already running. I tried this with a few tools, using one of the containers as base and loading the rest of the dependencies using conda environment. Would it be possible to do this in an automatic way, using a general base container? Anyway, the general question is where are things going regarding dependency resolution, so that I can get an idea of what to expect in the future and how to collaborate with development of these features. I found a thread on github about this ( [ https://github.com/galaxyproject/galaxy/issues/3299 | https://github.com/galaxyproject/galaxy/issues/3299 ] ) but don't know the resolutions taken about it (if any). Thanks in advance for the help. Ignacio Ignacio Eguinoa - Predoctoral fellow Applied Bioinformatics And Biostatistics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 36 95 [ http://www.psb.ugent.be/ | www.psb.ugent.be ]

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Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt 28 Apr '17

28 Apr '17

Hi everyone, I just wanted to ask how the extra_file_path is handled in case of job running as the real user since the file_path is only writable by the galaxy user. Any clue? Thanks, L-A

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Environmental Variable in <version_command>
by D K 25 Apr '17

25 Apr '17

Is it possible to use environment variables within <version_command>? I'm trying to use git commit information as the version ID in galaxy where the path $GITREPO can change: e.g. <version_command>git --git-dir="$GITREPO/project.git" log -n 1 origin/master | grep -P "commit|Author|Date"</version_command> Thanks!

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Additional Information about users in the API
by Milen Kouylekov 25 Apr '17

25 Apr '17

Dear Team, Hi, my name is Milen Kouylekov and I am working on the galaxy portal customized for natural language technology applications. http://lap.clarino.uio.no. I wrote an reporting script that uses Galaxy API to summarize the user activity. The idea of the script is to send regular reports with the information available to the reporting server as well as additional information like queries that failed to execute etc. I have managed to retrieve using the API most of the relevant information except the following: 1) User creation date. 2) User last access date. I have investigated that user object and see that information is part of it. My question is: Is there a way to access this information through the API? If not can I make a feature request? It is an information useful for administration of a galaxy instance. Cheers Milen

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