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Re: [galaxy-dev] Problem installing tool_ Galaxy local
by Greg Von Kuster 05 Dec '13

05 Dec '13

Hi Valeria, Please always replay-all to keep email threads on the original list. Your setting for tool_dependency_dir should not be as you've stated: > tool_dependency_dir = tool_dependencies It should be an actual path on your local file system, something like: tool_dependency_dir = ../tool_dependencies If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory. I cannot guarantee that this change will solve your problem, but it will be a step in the right direction. After making this change, let us know if you still see problems. Greg Von Kuster On Dec 5, 2013, at 12:13 PM, Valeria Parreira Pinto <vparreir(a)uoguelph.ca> wrote: > Hi Greg, > > Unfortunately, it is not working...sorry bug you again. > I know nothing about programming...this is what I have done: ( I have tried to follow http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies) > > In universe_wsgi.ini modified > #tool_dependency_dir = None > tool_dependency_dir = tool_dependencies > > In shell > > Valerias-MacBook-Pro:galaxy-dist vrparreira$ cd tool_dependencies > Valerias-MacBook-Pro:tool_dependencies vrparreira$ mkdir smart > Valerias-MacBook-Pro:tool_dependencies vrparreira$ cd > Valerias-MacBook-Pro:~ vrparreira$ cd galaxy-dist > Valerias-MacBook-Pro:galaxy-dist vrparreira$ sh run.sh --reload > > > This is what I see on the shell (I am not sure that is necessary): > > 127.0.0.1 - - [05/Dec/2013:11:52:59 -0400] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=613e73b56070623c&changeset_revisions=b6481845eb0d HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories?status=done&messag…." "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > tool_shed.util.tool_util DEBUG 2013-12-05 11:53:16,026 Loading new tool panel section: S-MART > tool_shed.util.shed_util_common DEBUG 2013-12-05 11:53:16,026 Adding new row (or updating an existing row) for repository 's_mart' in the tool_shed_repository table, status set to 'New'. > tool_shed.util.tool_util DEBUG 2013-12-05 11:53:16,039 Appending to tool panel section: S-MART > 127.0.0.1 - - [05/Dec/2013:11:53:15 -0400] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?tool_shed_url=http…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:19 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:22 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:25 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:28 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:31 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:34 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:37 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:40 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:43 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:46 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:49 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:52 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:55 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:58 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > tool_shed.util.shed_util_common DEBUG 2013-12-05 11:54:00,240 Error cloning repository: case-folding collision between SMART/Java/Python/compareOverlapping.py and SMART/Java/Python/CompareOverlapping.py > tool_shed.galaxy_install.repository_util DEBUG 2013-12-05 11:54:00,624 Removed repository installation directory: /Users/vrparreira/shed_tools/toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/b6481845eb0d > 127.0.0.1 - - [05/Dec/2013:11:53:16 -0400] "POST /admin_toolshed/manage_repositories HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:00 -0400] "GET /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:01 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:04 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:07 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:08 -0400] "GET /admin_toolshed/manage_repository?id=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:17 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:23 -0400] "GET /admin/review_tool_migration_stages HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:35 -0400] "GET /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:44 -0400] "GET /admin/reload_tool HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:51 -0400] "GET /forms/browse_form_definitions HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:54 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > > If you could help me it would be great. Thanks in advance, > Valeria > _____________________________________________ > Valeria Parreira, Ph.D > Adjunct Faculty > Department of Pathobiology > OVC, University of Guelph, > Guelph, Ontario, N1G 2W1, Canada > Tel: +1 (519) 824-4120 - Ext. 54717(lab) and 54679 (office) > vparreir(a)uoguelph.ca > > From: "Greg Von Kuster" <greg(a)bx.psu.edu> > To: "Valeria Parreira Pinto" <vparreir(a)uoguelph.ca> > Cc: galaxy-dev(a)bx.psu.edu > Sent: Wednesday, December 4, 2013 3:54:26 PM > Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local > > Hello Valeria, > > The setting for tool_dependency_dir must be an actual path on your local file system, something like: > > tool_dependency_dir = ../tool_dependencies > > Make sure that you set the location to a place that is safe for installing files. > > Greg Von Kuster > > On Dec 4, 2013, at 3:09 PM, Valeria Parreira Pinto <vparreir(a)uoguelph.ca> wrote: > > Hi > > I am having problems to install a tool from tool shed named S_MART (attached paper) on my local Galaxy. > The reason to install S_MART is to use DETR'PROK (attached paper) in Galaxy. > The first time, I got a warning before installing S-MART saying: > " set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing" > > In the universe_wsgi_ini: > > Path to the directory in which managed tool dependencies are placed. To use > # the dependency system, see the documentation at: > # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies > #tool_dependency_dir = None > tool_dependency_dir = tool_dependency_dir > > I have follow the instructions of the Matthias Zytnicki (paper's author). I did not work, still with error, however now it does not mention where or what to do!! > > Could you please let me know what would be the problem? and How to fix it? > Thanks in advance, > Valeria > > > _____________________________________________ > Valeria Parreira, Ph.D > Adjunct Faculty > Department of Pathobiology > OVC, University of Guelph, > Guelph, Ontario, N1G 2W1, Canada > Tel: +1 (519) 824-4120 - Ext. 54717(lab) and 54679 (office) > vparreir(a)uoguelph.ca > > <DETR_PROK.pdf><SMART.pdf>___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/

2 4

Per-tool overrides for environment variables (non-tool shed)?
by Daniel Patrick Sullivan 05 Dec '13

05 Dec '13

Hi, Galaxy-Developers, I apologize if this question has been answered before; I'm trying to override a couple of environment variables on a per-tool level, for a tool that is not installed in the toolshed. I've read a post on the mailing list that suggests this is possible for tools installed from the toolshed ( http://dev.list.galaxyproject.org/environment-variables-and-paths-for-tools…) however I am interested in doing this for a tool not installed from the toolshed, for example, the draw histogram tool. Basically, it appears at this point in time that I have to have multiple versions of R compiled to support our Galaxy instance. This stems from fragmented version support of different software components (for example the new version of the Bioconductor suite (used for CummeRbund) requires R 3.x, but the draw histogram function requires rpy, which isn't supported with R 3.x). For what it is worth, I did read about somebody who released a version of the draw histogram function that supports rpy2 ( http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html) however I am asking this question regardless as I do not want to go through the exercise of testing the rpy2 core tools right now if it is not necessary. So, my question is this; is there a preferred way to handle per-tool overrides for environment variables such as $PATH or $RPATH, for tools *not* included in the tool shed, for example the draw histogram tool? It does not appear that these tools have a tool_dependencies.xml. I appreciate you taking the time to answer my question and wish you a wonderful day. Thank you, Dan Sullivan

1 0

RFC: GALAXY_MEMORY similar to GALAXY_SLOTS
by Bjoern Gruening 05 Dec '13

05 Dec '13

Hi, if we want to include JAVA programs into Galaxy we are usually forced to hardcode -Xmx4g -Xms3g or similar into the wrapper. Would it make sense to have something like GALAXY_MEMORY, similar to GALAXY_SLOTS, to obtain the maximum of allowed memory from the scheduler. With some cheetah magic we would be able to create dynamic "-Xmx4g -Xms3g" entries. Ciao, Bjoern

2 1

Problem installing tool_ Galaxy local
by Valeria Parreira Pinto 04 Dec '13

04 Dec '13

Hi I am having problems to install a tool from tool shed named S_MART (attached paper) on my local Galaxy. The reason to install S_MART is to use DETR'PROK (attached paper) in Galaxy. The first time, I got a warning before installing S-MART saying: " set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing" In the universe_wsgi_ini: Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies #tool_dependency_dir = None tool_dependency_dir = tool_dependency_dir I have follow the instructions of the Matthias Zytnicki (paper's author). I did not work, still with error, however now it does not mention where or what to do!! Could you please let me know what would be the problem? and How to fix it? Thanks in advance, Valeria _____________________________________________ Valeria Parreira, Ph.D Adjunct Faculty Department of Pathobiology OVC, University of Guelph, Guelph, Ontario, N1G 2W1, Canada Tel: +1 (519) 824-4120 - Ext. 54717(lab) and 54679 (office) vparreir(a)uoguelph.ca

2 1

Interacting with output views in Galaxy
by Stephen Taylor 04 Dec '13

04 Dec '13

Hi, I was wondering, if anyone could point me to any resources and that allow the user to interact with the view of the output of a tool in Galaxy. So for example, I would like to load an image, draw a region of interest (ROI) (probably via some js routine) and then store that information in a file, generating an input in the History view. This input could then be used for further analysis. I guess Trackster does something like this, but I don't know if its routines are generic enough to handle this type of interaction. Thanks for any info! Steve

2 2

Installing DeepTools on Cloudman 2.0
by Mohammad Heydarian 04 Dec '13

04 Dec '13

Hello, I recently discovered the DeepTools program and have been looking forward to using it with Galaxy Cloudman. Today I attempted to load DeepTools from the Galaxy tool shed on my freshly started Galaxy Cloudman 2.0 instance and got the following error: Internal Server ErrorGalaxy was unable to sucessfully complete your request URL: http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for… Module galaxy.web.framework.middleware.error:*149* in __call__ >> <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for…> app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.recursive:*84* in __call__ >> <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for…> *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ >> <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for…> *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ >> <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for…> *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*190* in handle_request >> <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for…> body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*221* in decorator >> <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for…> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.webapps.galaxy.controllers.admin_toolshed:*896* in prepare_for_install >> <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for…> common_install_util*.*get_dependencies_for_repository*(* trans*,* tool_shed_url*,* repo_info_dict*,*includes_tool_dependencies *)* Module tool_shed.util.common_install_util:*84* in get_dependencies_for_repository >> <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for…> installed_rd*,* missing_rd *=* get_installed_and_missing_repository_dependencies_for_new_install*(*trans*,* repo_info_tuple *)* Module tool_shed.util.common_install_util:*190* in get_installed_and_missing_repository_dependencies_for_new_install >> <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for…> tool_shed*,* name*,* owner*,* changeset_revision*,* prior_installation_required *=*suc*.*parse_repository_dependency_tuple*(* rd_tup *)* Module tool_shed.util.shed_util_common:*1106* in parse_repository_dependency_tuple >> <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for…> prior_installation_required *=* str*(* prior_installation_required *)* *UnboundLocalError: local variable 'prior_installation_required' referenced before assignment* I got this error when I tried to install either of the three revisions of the tool. Am I doing something wrong? Any guidance is appreciated! Thanks in advance! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205

2 4

how to viz. gff file on fasta file from history in trackster?
by Eric Rasche 03 Dec '13

03 Dec '13

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I'm at a bit of a loss here, I've found that when I have a GFF file, it offers to be visualized, but I cannot figure out how to visualize on a Fasta file in my history. I've done the following 1. GFF3 output file -> trackster 2. New viz 3. Build not listed -> click to add build from a fasta file (my genome) 4. Back to new viz, reference genome selected as the one I created. Now I'm faced with this error: Error: The requested genome file (/home/galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len) could not be opened. Exiting! sort: write failed: standard output: Broken pipe sort: write error Couldn't open /home/galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len , No such file or directory Am I *only* able to viz. gff files on UCSC chromosomes? It seems a bit obtuse when I have GFF data sets related to fasta phage genomes that I'm working with, all of which were uploaded/generated in galaxy. Is there any (preferrably easy) way to accomplish this? Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu rasche.eric(a)yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJSnmjSAAoJEMqDXdrsMcpV2B4QALzzEkR1TgoqjFExTFQQkJZg /K06M5C5Kc4E2jFlfkIcRYpXIDv6KYxahTPCSD5w7FzoTI6cfVe9erhjv2VbLJP0 gwRmM+LW4g+oeO5/zpxgu3z4bWEN9Th19/WXMeD1KOvDkhA+Yrd6ExLqT+NOvn5a MJjSLzrKCh4PMbSP4YAhCmweBAFTCA/Xix+E8E5dPNHJt4xM3NICILFafmK/HYuj vqMV7yDJq0AJhAM6eNzv/b/uJRirNXXeAEqQSfihNPTANeKvKDHr4UAI5vMPPfIB 7PTzdB0Qqlr/6qqfy8vtm4kTzYZHyoT6QtQ7WkytKlWWY9qTNu30eeR1r8uxn6R3 XNJ9SNfOCmOVv9S87phHG5RkJoj217JpnhiH6Kyn9aFhuQEyp/URaJhxn/gJFAuk rYLUvz2F6gwOZNVz6X2l6t2w7jMLDG41wdflBrcDHnvLWcjBZRU/8TRyoqQB8Oop uLkweGF2RdDCGSvZXV8ubCRs7dEl2t6N+iNLS1+5TJmFk9KKg3LNiRR/I2YK73IE cZ1Yzpfb5FpQ72a6B2Mb74rso9b/9zQNNODJejQ4Zbd8mhOZgWnrraTd+dmhlLG/ e190CzpFiag1b3oNRvMy/rcUNnCIbHR44SZiW+KfeEreRNBk3H0iPJT+PynDQ5oz om/wT9z9PhhcaMmBPwoy =0VEm -----END PGP SIGNATURE-----

1 0

Announcing the Galaxy Deployment Catalog!
by Dave Clements 03 Dec '13

03 Dec '13

Hello all, *I am pleased to formally announce the Galaxy Deployment Catalog <http://wiki.galaxyproject.org/Community/Deployments>*, a place to describe individual Galaxy deployments, and to learn how others in the community are implementing Galaxy in production environments. If you have a Galaxy deployment then please take a few minutes to describe your instance to the community. There are two ways to do this. *Use the Wiki Template* Go to the "Using the Wiki" section of the catalog home page<http://wiki.galaxyproject.org/Community/Deployments#Using_the_Wiki>, enter a CamelCase name for your deplloyment, click "Create ...," and then edit, preview, and save the page. Voilà, an entry for your deployment now exists in the catalog. *Use the Google Form* Fill out this Google Form <http://bit.ly/gxydeployform>. In a week or two, a deployment catalog page will be programmatically created and you will receive an email. The wiki method requires a wiki login, but gives you control over how the page appears. The Google form is easier. Thanks a bunch, and please let me know if you have any questions. Dave C. PS: The form submission method was inspired by (stolen from?) Philip Moncuquet's post <http://dev.list.galaxyproject.org/survey-td4662749.html> earlier this week. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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tiff files in galaxy
by Robert Baertsch 03 Dec '13

03 Dec '13

Do you know a fast way to open large tiff files in galaxy ? The sniffer recognizes the type, but clicking on the eyeball on a large 82mb file just hangs. Downloading the file and opening in preview does work but it is clunky. Perhaps storing a low res version that would be display when clicking the eyeball would speed access.

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hierarchical ObjectStore - noatime
by Bjoern Gruening 03 Dec '13

03 Dec '13

Hi, we want to put some more hard drives into your Galaxy Server. And we plan to use the hierarchical ObjectStore for that purpose. The new discs will be type="distributed" id="primary" and the old disc will become type="disk" id="secondary". If I understood correctly the old disc is them in some read-only state and will not touched until the primary discs are full or not working ... Is it save to mount the old discs or all discs with noatime, to get a small performance gain? Is Galaxy using noatime? Thanks, Bjoern

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