Re: [galaxy-dev] rgenetics galaxy
Hi, For information, here is my install script for rpy, because I had to reinstall all of that on CentOS 5.4... : #!/bin/bash # # # echo RPY for R and Python ** cd rpy; export LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64:/lib64:/usr/lib64:/usr/local/lib64:/usr/lib/:/usr/local/lib/ #export R_HOME=/usr/lib64/R/ # remy modifications 17/01/2012 unset R_HOME export RHOME=/usr/lib64/R/ cp -s /usr/lib64/R/lib/* /usr/lib64/R/bin/ # rajout 17/01/2012 mkdir -p /usr/share/R/include cp -s /usr/lib64/R/include/* /usr/share/R/include/ cp -s /usr/lib64/R/include/* /usr/local/include/ cp -s /usr/lib64/R/include/* /usr/include/ cp -s /usr/lib64/R/lib/* /usr/lib/ cp -s /usr/lib64/R/lib/* /lib64/ cp -s /usr/lib64/R/lib/* /usr/local/lib64/ cp -s /usr/lib64/R/lib/* /usr/local/lib/ ldconfig cd trunk/rpy sed -i s/libraries=\['R'\]/libraries=\['R','Rlapack'\]/g setup.py # added 17/01/2012 sed -i s|/usr/share/R/include|/usr/lib64/R/include/|g setup.py # added 17/01/2012 sed -i 's|\[0-9]+\\\.\[0-9]+\\\.\[0-9]+|[0-9]\.[0-9]+\.[0-9]|g' rpy_tools.py python setup.py install If it does not work, try with R_HOME. 2011/11/25 Oleksandr Moskalenko o...@hpc.ufl.edu On Nov 25, 2011, at 6:52 AM, Ivan Merelli wrote: Hi, I'm trying to use rgenetics in galaxy, but I have some problem in installting rpy-1.0.3 with R-2.13.1. I found this guide, which is about the same problem of mine: http://gmod.827538.n3.nabble.com/Rpy-1-0-3-and-R-2-13-1-td3359590.html but didn't work for me (although the part about the modulefile is quite obscure for me). The problem seems to be correlated to an header file (Rdevices.h) which is no more present in the latest R distribution. Any hints to solve this problem? May I use rpy2? Best, Ivan ___ 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/ There is information on solving this available via a web search - http://www.mail-archive.com/rpy-list@lists.sourceforge.net/msg01500.html for instance. In short, - Unpack rpy-1.0.3 and patch the following files: - rpm_tools.py version = re.search( +([0-9]\.[0-9]+\.[0-9]), output) - setup.py include_dirs = [ os.path.join(RHOME.strip(), 'include'), 'src', '/usr/share/R/include', '/apps/R/2.13.1/include' ] * Build rpy with python setup.py install Cheers, Alex ___ 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/
[galaxy-dev] embedded code into Pages
Hi, I would like to modify Pages a lot. For example, I would like to create a galaxy Page with rss-reader written in PHP (or javascript) in it. I found where content is stored for Pages, but not the script who read this content. Is there any possibility to integrate code into Galaxy Page which could be executed ? Thanks, Regards. ___ 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/
[galaxy-dev] Timeout for job submission
Hello, In my configuration, I submit job through SGE. I have a cluster in the backend. If nodes are shutdown job is in state queue wait and I noticed that it disappear sometime. Is there a timeout somewhere in galaxy which is monitoring jobs ? In fact, I whish to use a script in SGE which is halting or booting nodes according to the SGE queue. -Regards Rem. ___ 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/
[galaxy-dev] link file bug in the new version
Hi, We found a little problem in the new galaxy release. When we upload a dataset library from filesystem : Admin Manage data libraries create new data library Add dataset Upload files from filesystem path Link to files without copying If galaxy user is the owner of this file or if he has write permission on it (on the filesystem), the file is deleted !! I do not think it is the normal behaviour... Regards. ___ 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/
Re: [galaxy-dev] DRMAA broken following SGE update. How to fix?
Hi Chris, Take a look at this file : lib/galaxy/jobs/runners/drmaa.py in your galaxy directory. You can export a path for binaries here. For example : export PATH=$PATH:/opt/bin/ before export PYTHONPATH Moreover, do not forget other path values in your service script or in your galaxy user profile. Hope this help. 2011/8/23 Roman Valls brainst...@nopcode.org 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/ ___ 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/
Re: [galaxy-dev] Invalid job runner: drmaa
Hi, I found the error. sh run.sh worked fine. So, I added some lines to my galaxy script service to load environnement variables : . /etc/profile.d/settings.sh . /etc/profile.d/drmaa.sh Now it works, but I still have some warning when I run a megablast : An error occurred running this job: *'num_threads' is currently ignored when 'subject' is specified. WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched *However I can download the result file. Best Regards, Thanks for help, Remy 2011/7/27 remy d1 remy...@gmail.com Hi Ka Ming, Thanks for your answer, but I already checked this for my galaxy user (and for root) on both the galaxy frontend node and on each node all over the cluster. It's the same path as yours for me. If you have any other idea It would be great ! :) Regards, Remy 2011/7/26 Ka Ming Nip km...@bcgsc.ca Hi, You may want to check whether your env variables are exported properly. For example, $ env DRMAA_LIBRARY_PATH=/opt/sge/lib/lx24-amd64/libdrmaa.so.1.0 Hope that helps! Ka Ming From: galaxy-dev-boun...@lists.bx.psu.edu [ galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of remy d1 [ remy...@gmail.com] Sent: July 26, 2011 7:44 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Invalid job runner: drmaa Hi, I try to configure Galaxy with SGE. It works one time yesterday but now I have the following message all the time : galaxy.jobshttp://galaxy.jobs DEBUG 2011-07-26 16:50:54,002 dispatching job 118 to drmaa runner galaxy.jobshttp://galaxy.jobs ERROR 2011-07-26 16:50:54,002 put(): (118) Invalid job runner: drmaa [ An error occurred running this job: Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. ] On the web page. Here is my universe_wsgi.ini file : [server:main] port = 8000 host = X.X.X.X use_threadpool = True [filter:proxy-prefix] prefix = /galaxy [app:main] paste.app_factory = galaxy.web.buildapp:app_factory filter-with = proxy-prefix database_connection = mysql://galaxy:xx@localhost :3306/galaxy?unix_socket=/var/run/mysqld/mysqld.sock file_path = database/files new_file_path = database/tmp job_working_directory = database/users_space/user_galaxy cluster_files_directory = database/users_space/user_galaxy use_nglims = False nglims_config_file = tool-data/nglims.yaml static_enabled = True static_cache_time = 360 static_dir = %(here)s/static/ static_images_dir = %(here)s/static/images static_favicon_dir = %(here)s/static/favicon.ico static_scripts_dir = %(here)s/static/scripts/ static_style_dir = %(here)s/static/june_2007_style/blue log_events = True log_actions = True debug = True use_interactive = True library_import_dir = /home/galaxy/galaxy-dist/tmpdir user_library_import_dir = True allow_library_path_paste = True admin_users = me@... enable_pages = True enable_api = True set_metadata_externally = True retry_metadata_internally = True outputs_to_working_directory = True start_job_runners = drmaa default_cluster_job_runner = drmaa:/// [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = local:/// ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:/// [galaxy_amqp] I checked many things, but it did not change anything... Any help would gracefull. Regards. ___ 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/
Re: [galaxy-dev] Invalid job runner: drmaa
Hi Ka Ming, Thanks for your answer, but I already checked this for my galaxy user (and for root) on both the galaxy frontend node and on each node all over the cluster. It's the same path as yours for me. If you have any other idea It would be great ! :) Regards, Remy 2011/7/26 Ka Ming Nip km...@bcgsc.ca Hi, You may want to check whether your env variables are exported properly. For example, $ env DRMAA_LIBRARY_PATH=/opt/sge/lib/lx24-amd64/libdrmaa.so.1.0 Hope that helps! Ka Ming From: galaxy-dev-boun...@lists.bx.psu.edu [ galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of remy d1 [ remy...@gmail.com] Sent: July 26, 2011 7:44 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Invalid job runner: drmaa Hi, I try to configure Galaxy with SGE. It works one time yesterday but now I have the following message all the time : galaxy.jobshttp://galaxy.jobs DEBUG 2011-07-26 16:50:54,002 dispatching job 118 to drmaa runner galaxy.jobshttp://galaxy.jobs ERROR 2011-07-26 16:50:54,002 put(): (118) Invalid job runner: drmaa [ An error occurred running this job: Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. ] On the web page. Here is my universe_wsgi.ini file : [server:main] port = 8000 host = X.X.X.X use_threadpool = True [filter:proxy-prefix] prefix = /galaxy [app:main] paste.app_factory = galaxy.web.buildapp:app_factory filter-with = proxy-prefix database_connection = mysql://galaxy:xx@localhost :3306/galaxy?unix_socket=/var/run/mysqld/mysqld.sock file_path = database/files new_file_path = database/tmp job_working_directory = database/users_space/user_galaxy cluster_files_directory = database/users_space/user_galaxy use_nglims = False nglims_config_file = tool-data/nglims.yaml static_enabled = True static_cache_time = 360 static_dir = %(here)s/static/ static_images_dir = %(here)s/static/images static_favicon_dir = %(here)s/static/favicon.ico static_scripts_dir = %(here)s/static/scripts/ static_style_dir = %(here)s/static/june_2007_style/blue log_events = True log_actions = True debug = True use_interactive = True library_import_dir = /home/galaxy/galaxy-dist/tmpdir user_library_import_dir = True allow_library_path_paste = True admin_users = me@... enable_pages = True enable_api = True set_metadata_externally = True retry_metadata_internally = True outputs_to_working_directory = True start_job_runners = drmaa default_cluster_job_runner = drmaa:/// [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = local:/// ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:/// [galaxy_amqp] I checked many things, but it did not change anything... Any help would gracefull. Regards. ___ 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/
[galaxy-dev] Invalid job runner: drmaa
Hi, I try to configure Galaxy with SGE. It works one time yesterday but now I have the following message all the time : galaxy.jobs DEBUG 2011-07-26 16:50:54,002 dispatching job 118 to drmaa runner galaxy.jobs ERROR 2011-07-26 16:50:54,002 put(): (118) Invalid job runner: drmaa [ An error occurred running this job: *Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.* ] On the web page.* * Here is my universe_wsgi.ini file : [server:main] port = 8000 host = X.X.X.X use_threadpool = True [filter:proxy-prefix] prefix = /galaxy [app:main] paste.app_factory = galaxy.web.buildapp:app_factory filter-with = proxy-prefix database_connection = mysql://galaxy:xx@localhost :3306/galaxy?unix_socket=/var/run/mysqld/mysqld.sock file_path = database/files new_file_path = database/tmp job_working_directory = database/users_space/user_galaxy cluster_files_directory = database/users_space/user_galaxy use_nglims = False nglims_config_file = tool-data/nglims.yaml static_enabled = True static_cache_time = 360 static_dir = %(here)s/static/ static_images_dir = %(here)s/static/images static_favicon_dir = %(here)s/static/favicon.ico static_scripts_dir = %(here)s/static/scripts/ static_style_dir = %(here)s/static/june_2007_style/blue log_events = True log_actions = True debug = True use_interactive = True library_import_dir = /home/galaxy/galaxy-dist/tmpdir user_library_import_dir = True allow_library_path_paste = True admin_users = me@... enable_pages = True enable_api = True set_metadata_externally = True retry_metadata_internally = True outputs_to_working_directory = True start_job_runners = drmaa default_cluster_job_runner = drmaa:/// [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = local:/// ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:/// [galaxy_amqp] I checked many things, but it did not change anything... Any help would gracefull. Regards. ___ 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/
