July 2016 - galaxy-dev - lists.galaxyproject.org

hide password xml tag
by Mohamed Kassam 15 Jul '16

15 Jul '16

Dear all, I would like to hide when typing a password in a tool I develloped. Do you have the tag I have to use, I tried type="password" but it does not work. Thanks in advance,

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Amazon Instance Types for Galaxy
by Lapointe, David 14 Jul '16

14 Jul '16

Are there instance types which will not work for Galaxy/Cloudman on AWS? EBS volumes for example. Thanks, David -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144 Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

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Swiss German Galaxy Tour/Day 2016 - Freiburg (Germany), 20/21 October
by Hans-Rudolf Hotz 13 Jul '16

13 Jul '16

Dear all After the big success of the “Swiss German Galaxy Tour” in 2014, we are going to organize a similar event again in October this year. This time we meet for two days in Freiburg (Germany): https://wiki.galaxyproject.org/Events/SG2016 It is our great pleasure to announce that Dannon Baker, a core developer of the Galaxy team from Johns Hopkins will join us again on both days. Like last time, the aim is to discuss the status of the Galaxy project, new developments, interface to other systems, extensions and best practice in reproducible research. We also welcome participants who are using other workflow management systems and tool developers who are looking for such systems to offer their tools to a wider audience. The program is as follows: Thursday, October 20th: 3rd Swiss Galaxy Workshop. we intend to have a full day of talks from you. We encourage you to design your talk problem-centric and use the experience of other participants to solve them. please provide a preliminary title for a 20-minutes talk or a short presentation, when you register. Friday, October 21st: 2nd German Galaxy Developer Workshop this day is more on the technical side, with presentation and hands on exercises. please provide suggestion for topics to be covered during this day, when you register. Registration is now open (space is limited). We recommend you register soon to secure your spot on one or both days of the SG2016Tour: http://tinyurl.com/SG2016-reg Looking forward to see many of you in Freiburg Regards, Bjoern and Hans-Rudolf

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Writing test for dataset collection
by Cristel Thomas 11 Jul '16

11 Jul '16

Dear galaxy developers, Can someone point me to a resource explaining how to write the test section of the xml for tools dealing with dataset collections? as input as well as output. Thanks much, Cris

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Motif Alignment and Search Tool - MAST
by KIRILL PANKOV 08 Jul '16

08 Jul '16

Hello, I was hoping to use MAST, a part of the MEME Suite collection of tools, in Galaxy: http://meme-suite.org/doc/mast.html?man_type=web While I have found the MEME Suite, I have been unable to locate the specific MAST tool in the tool shed. I was wondering if it was currently available for use in Galaxy? Thanks, Kirill Pankov

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user login web page with welcome one
by Nikolaos Tur 08 Jul '16

08 Jul '16

Hi. What to tell Galaxy to have user login web page with login frame and welcome frame? I try to modify login.js in galaxy/client/galaxy/scripts to comment part of code as suggested there: // TODO: remove iframe for user login (at least) and render login page from here // then remove this redirect if( !options.show_welcome_with_login ){ var params = jQuery.param({ use_panels : 'True', redirect : redirect }); window.location.href = Galaxy.root + 'user/login?' + params; return; } It creates two frames but... it continues to create them in infinity loop in every welcome frame. How to solve this? I saw many local Galaxy instances have this and it works. Galaxy is 16.04. Thanx, Nikolaos

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showing progress on running tasks
by Ryan G 08 Jul '16

08 Jul '16

Hi all - I know this isn't currently a feature, but wanted to find out about what it would take to implement.... We developed some custom tools that are long running....multiple hours. The tools run through various steps of an analysis. Is there a way to display progress of a task in the history? Possibly as a small progress bar? Or provide some feedback via an html page in the main frame? Ryan

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Can't stop uwsgi processes with supervisod
by Marco Tangaro 08 Jul '16

08 Jul '16

Dear experts, I've a strange behaviour with uWSGI and supervisor. This is my settings in galaxy.ini file: [uwsgi] processes = 3 socket = 127.0.0.1:4001 stats = 127.0.0.1:9191 #socket = /var/log/galaxy/uwgi.sock pythonpath = /home/galaxy/galaxy/lib pythonhome = /home/galaxy/galaxy/.venv threads = 4 logto = /var/log/galaxy/uwsgi.log And this is my supervisord settings: [program:galaxy_web] command = /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini directory = /home/galaxy/galaxy umask = 022 autostart = true autorestart = true startsecs = 20 user = galaxy environment = VIRTUAL_ENV="/home/galaxy/galaxy/.venv",PATH="/home/galaxy/galaxy/.venv/bin:%(ENV_PATH)s",PYTHONHOME="/home/galaxy/galaxy/.venv" numprocs = 1 stopsignal = INT startretries = 15 The problem is that when I run galaxy with "supervisorctl start galaxy:" I've 4 galaxy process (ps -aux | grep uwsgi): galaxy 28795 13.0 1.0 1465320 177332 ? Sl 16:42 0:12 /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini galaxy 28950 1.2 1.0 1465320 170108 ? Sl 16:42 0:01 /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini galaxy 28951 1.1 1.0 1465320 170108 ? Sl 16:42 0:01 /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini galaxy 28953 0.0 1.0 1465320 166060 ? S 16:42 0:00 /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini Once I did "supervisorctl stop galaxy:" I've: galaxy 28953 0.0 1.0 1465320 166060 ? S 16:42 0:00 /home/galaxy/galaxy/.venv/bin/uwsgi --ini-paste /home/galaxy/galaxy/config/galaxy.ini there is still a uwsgi process (sometimes more, it depends on the uwsgi process number). I'm able to stop only those processes which have a "Sl" in the STAT column of "ps -aux | grep uwsgi": S Interruptible sleep (waiting for an event to complete) l is multi-threaded (using CLONE_THREAD, like NPTL pthreads do) (ps wiki) The problem is that I can't stop all the uwsgi processes, therefore I'm unable to restart galaxy, without killing all uwsgi processes. Thanks a lot, Marco.

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Metadata access using tool config
by Katherine Beaulieu 08 Jul '16

08 Jul '16

Hi everyone, I am working on a tool which attempts to create a file which stores all the metadata associated with a job execution. The things I know how to access right now are the file extension, name history id, dataset id. I'd like to know how to access other things like the job id, uuid, file size, job command-line, job end time, job start time, core allocated, job runtime and any other important information associated with tool execution. I would prefer to get this information from the tool config file or my tool script and not have the user create an api key which they have to submit as a parameter to my tool. Let me know if you guys have any ideas! Katherine

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Python tool wrapper with multiple input and output files
by Marco Tangaro 08 Jul '16

08 Jul '16

Dear experts, my name is Marco and I'm working to port our python tool to the Galaxy framework. The main script needs a rna.bam file as input, a reference fasta file, both mandatory. Finally, you can add a dna.bam file, but this is optional. Therefore an example command is: script.py -i rna.bam -f reference.fa -j dna.bam The outout is a tabular. Again the -j dna.bam option is completely optional. So quite soon it turned out that I had to use a python wrapper to parse our script. Now the wrapper works fine. The next step is to run the tool over multiple input file and we would like to avoid to use a workflow. The idea is that to each input file corresponds an output file. The reference is still the same. For instance, we have: rna_1.bam + dna_1.bam -> output_1.txt rna_2.bam + dna_2.bam -> output_2.txt rna_3.bam + dna_3.bam -> output_3.txt ... and so on. But I don't know the best strategy to give to my wrapper multiple input files. Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they correspond to the right rna_xyz.bam file. I would like to have as output a page which is showing as results the link to the single output files as suggested here. https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files planning to integrate a javascript interface. I've browsed a lot, but on multiple input file the posts are old. I'm using the last galaxy release (16_04). I'm quite new to the galaxy world... Thanks a lot for your suggestions, Marco

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