August 2011 - galaxy-dev - lists.galaxyproject.org

latest checkout (today) does not have Help or User
by Joseph Hargitai 24 Aug '11

24 Aug '11

Hi, built a new server today to test a few things. a, Help is not clickable via Apache2 proxy 2, when you use an apache2 proxy is it for granted that local authentication cannot be used? I tired remote-user = False hoping i can use load-balancing and proxy but retain local authentication. But User remains unclickable. 3, Using Nginx anyone has a full nginx config script? The wiki has the snippets which I am not sure where to fit in nginx nomenclature - does it go in conf or virtual sites enabled. I am assuming the local authentication can be done with nginx as is done on the cloud version. Which would be the goal. thanks, joe

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Launching a JAVA or external app
by Bossers, Alex 24 Aug '11

24 Aug '11

Hello all, would it be possible to launch for instance a JAVA app with preloaded parameters and files from galaxy that needs interaction/display? For instance a gui based annotation editor? It necessarily doesn't have to support saving of files back to galaxy. Sort of end stage. Any help or pointers appreciated. thanks Alex

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Installing local instance hiccup
by Stephen Doyle 24 Aug '11

24 Aug '11

Hello, I am in the process of installing a local instance, and I can't seem to be able to build the bx_python egg, even with scramble.py. Any ideas to get around this? Cheers, Steve --------------------------------- Dr Stephen R. Doyle Postdoctoral Researcher Genetics Department | La Trobe University | Bundoora 3086 Australia T: +61 3 9479 3087 | F: +61 3 9479 2480 | E: s.doyle(a)latrobe.edu.au<mailto:s.doyle@latrobe.edu.au> | W: http://www.latrobe.edu.au/genetics/staff/stephen_doyle.htm La Trobe University - ranked top in Victoria for student satisfaction (Sweeney Uni Student Report, 2009) CRICOS Provider 00115M J Please kindly consider your environment before printing this e-mail Warning to recipients: This email and any attachments are confidential and subject to copyright. If you are not the intended recipient any use, disclosure or copying is unauthorised. If you have received this email in error please advise us immediately by reply email and delete all copies. It is your responsibility to examine this email and any attachments for viruses. Any personal information in this email must be handled in accordance with the Information Privacy Act 2000 (Vic).

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How to get tool id in runner file (local.py)
by shashi shekhar 24 Aug '11

24 Aug '11

Hi, I have local instance of Galaxy and i am doing some modification in Galaxy .So i need tool id id in local.py file . How i will get this information in runner file (local.py). Regards shashi shekhar

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Apache configuration problem
by Joachim Jacob 24 Aug '11

24 Aug '11

Hi all, I am trying to set up httpd to serve galaxy from the root url and to serve static content as described on http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy. I will not serve Galaxy under a subdirectory. I have added to /etc/httpd/conf.d/ a file galaxy.conf with contents (CentOS system): RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P] Everything works after firing up httpd! :-) But when adding following rewrite rules: RewriteRule ^/static/style/(.*)/home/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*)/home/galaxy/galaxy_dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*)/home/galaxy/galaxy_dist/static/$1 [L] RewriteRule ^/favicon.ico/home/galaxy/galaxy_dist/static/favicon.ico [L] RewriteRule ^/robots.txt/home/galaxy/galaxy_dist/static/robots.txt [L] I get a page which is totally scrambled. At first sight, seems to be file permission problems. The apache log file (/var/log/httpd/error_log) shows (last two lines, but the lines before these are similar): *[Tue Aug 02 15:26:03 2011] [error] [client x.x.x.x] File does not exist: /home/galaxy/galaxy_dist, referer: http://x.x.x.x/root/tool_menu [Tue Aug 02 15:26:03 2011] [error] [client x.x.x.x] File does not exist: /home/galaxy/galaxy_dist, referer: http://x.x.x.x/history* Has anybody a clue on what I should do? I thought I will try these steps: - I changed the group owner of several of the directories recursively to the apache group - I have set the SELinux permissions with *chcon -R -h -t httpd_sys_content_t static* but no joy! :-( Thanks for any hint. Joachim

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Error uploading files through filesystem paths: MacOS, Postgres and galaxy-central
by Camille Stephan 23 Aug '11

23 Aug '11

Hello, I just installed postgres in my machine and things seem to work fine except for the "Upload files from filesystems paths" option which gives the following error: "Invalid paths: /path/to/file.fasta " The path is correct and I tried with different files and file formats. I have the most recent version from galaxy-central. Any idea what could be causing this? Thanks! Camille -- *** Camille Stephan-Otto Attolini, PhD Senior Research Officer, Bioinformatics and Biostatistics unit IRB Barcelona Tel (+34) 93 402 0553

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Re: [galaxy-dev] database/files/_metadata_files
by Chorny, Ilya 23 Aug '11

23 Aug '11

Great, thanks!! From: Daniel Blankenberg [mailto:dan@bx.psu.edu] Sent: Tuesday, August 23, 2011 1:26 PM To: Chorny, Ilya Subject: Re: [galaxy-dev] database/files/_metadata_files Run a tool (or auto-detect metadata) that creates any BAM or MAF output file. The file will originally be created in a temporary location and then moved into the final location in Galaxy's job finish methods. On Aug 23, 2011, at 4:20 PM, Chorny, Ilya wrote: I am setting metadata externally so how do I get a file to be generated in that directory? From: Daniel Blankenberg [mailto:dan@bx.psu.edu]<mailto:[mailto:dan@bx.psu.edu]> Sent: Tuesday, August 23, 2011 1:18 PM To: Chorny, Ilya Cc: galaxy-dev(a)lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] database/files/_metadata_files Hi Ilya, Tools should not ordinarily write to this directory, but will often read from it. These files are generated by Galaxy's Metadata functionality. If you are setting metadata externally (settings in universe_wsgi.ini) and using a cluster, then this will occur as part of the tool/job script, as a separate entry (calling set_metadata.sh) in the e.g. .sh file submitted to pbs. Certain filetypes, e.g. BAM and MAF, use these for storing index data. Thanks for using Galaxy, Dan On Aug 23, 2011, at 4:04 PM, Chorny, Ilya wrote: Can someone point me to a tool which writes to this directory? I made some changes to the code to run as actual user but cannot find a tools that writes to this directory. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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"multiple" inputs in tools used in workflows?
by Duddy, John 23 Aug '11

23 Aug '11

While snooping around the Galaxy code, I noticed that some tool features are not supported in workflows, only in histories. Is there a list somewhere that lists the restrictions? Specifically, are "multiple" inputs supported? John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

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database/files/_metadata_files
by Chorny, Ilya 23 Aug '11

23 Aug '11

Can someone point me to a tool which writes to this directory? I made some changes to the code to run as actual user but cannot find a tools that writes to this directory. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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collect_associated_files and umask
by Chorny, Ilya 23 Aug '11

23 Aug '11

When I run galaxy as the actual user using the code I committed to my fork, I run into a problem with dataset_*.dat files that have associated data wherein the associated data files are copied from the job_working_directory into the files directory. That directory is owned by the actual user and not by the galaxy user. I don't have a problem with the ownership but the permissions of the directory and associated files get changed to 777. Any thoughts on why the permissions get changed. The permissions are 755 and 644 for dirs and files respectively when in the working directory so why do they change when the directory is moved? Any help would be greatly appreciated. Best, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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