- galaxy-dev - lists.galaxyproject.org

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 24 Aug '11

24 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 24 Aug '11

24 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 24 Aug '11

24 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 24 Aug '11

24 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 24 Aug '11

24 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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visualization tool
by shashi shekhar 24 Aug '11

24 Aug '11

Hi All, I want to add my own Visualization tool in local instance of galaxy .how i will do it in galaxy ? i want to integrate jmol in galaxy. Regards shashi

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Boolean options in toolconfigs: yes/no vs. give/omit flag.
by Samuel Lampa 23 Aug '11

23 Aug '11

Hi, I'm trying to parse the XML toolconfig format, for generating a lightweight command config wizard in an Eclipse based product. I wonder: Boolean parameters for some tools (such as the emboss/textsearch one), seems to allow always giving the parameter's flag at all times, and just change the following value between "yes" and "no" for these params, like: textsearch -caseinsensitive yes or textsearch -caseinsensitive no On the other hand, I guess there are many tools which tell such boolean options just by giving the flag itself, so it would by analogy be: textsearch -caseinsensitive or textsearch My question is, how can I see the difference between these two cases, in the tool config file? (Unfortunately I don't know any of the wrapped tools good enough to know where to look for a flag of the latter kind). Cheers // Samuel -- System Expert / Bioinformatician SNIC-UPPMAX HPC Center Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa(a)scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se

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Fwd: [SOLVED] Re: DRMAA broken following SGE update. How to fix?
by Roman Valls 23 Aug '11

23 Aug '11

I'm glad it worked Chris, I'm keeping thread on the mailing list for future reference... -------- Original Message -------- Subject: Re: [galaxy-dev] DRMAA broken following SGE update. How to fix? Date: Tue, 23 Aug 2011 11:56:13 +0100 From: Chris Cole <chris(a)compbio.dundee.ac.uk> Organization: University of Dundee To: Roman Valls <brainstorm(a)nopcode.org> Hi, The SGE_ROOT variable was the same as always, but it turns out I had a DRMAA_LIBRARY_PATH path that was still pointing to the old path. It's such a long time since I set up galaxy that I'd forgotten about it. Changed it and Galaxy is working again. Thanks to you and Remy for pointing me in the right direction. Chris On 23/08/11 09:32, Roman Valls wrote: > Did you adjust the SGE_ROOT environment variable to point to the > libdrmaa for SGE (probably /opt/sge_62u5_gr/bin/lx24-amd64) ? > > This is of course just a guess, could you please provide some error > messages/logs ? > > Cheers, > Roman > > On 2011-08-23 10:20, Chris Cole wrote: >> BUMP >> >> Does anyone have any idea on this? Our Galaxy is currently out of action >> until this is sorted. >> Thanks, >> >> Chris >> >> On 22/08/11 10:08, Chris Cole wrote: >>> Hi, >>> >>> Following a recent update to our SGE, DRMAA is failing to load in >>> galaxy. The reason being that the path has changed. How do I change the >>> path for galaxy to find the libdrmaa module? >>> Cheers, >>> >>> Chris >>> >>> >> >> ___________________________________________________________ >> 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/ > ___________________________________________________________ > 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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Brad's GFF parser in a Biopython repository
by Peter Cock 23 Aug '11

23 Aug '11

Hi Brad, I managed to do a git script to select out the GFF code and tests from your bcbb repository and get it into the Biopython source tree. The folder changes made it interesting ;) Input: https://github.com/chapmanb/bcbb (master branch) Output: https://github.com/peterjc/biopython/tree/brad_gff The tests pass, but that is as far as I have got with this. Brad, could you have a look at this new branch for sanity checking please? Peter

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