Re: [galaxy-dev] Send data to GBrowse
Hi Liisa When setting this up on our own local instance to get bigwig files to display in Gbrowse we edited: 1. universe_wsgi.ini 2. tool-data/shared/gbrowse/gbrowse_build_sites.txt 3. datatypes_conf.xml so that it includes display file=gbrowse/gbrowse_wig.xml / 4. and in display_applications/gbrowse/ make sure you have the relevant xml files eg gbrowse_wig.xml, gbrowse_bigwig.xml Nicki Gray MRC Molecular Haematology Unit On 7 Feb 2011, at 19:03, Liisa Koski wrote: Hi, I have just installed Galaxy and am trying to configure it to allow display of data on my local installation of GBrowse. I have edited tool-data/shared/gbrowse/gbrowse_build_sites.txt (species http://domain.ca/cgi-bin/gbrowse/species species) As well as universe_wsgi.ini (gbrowse_display_sites = species) However I do not see a link in history items after I stop and start the server. Is there something else I'm missing? Thanks in advance for your help, LiisaATT1.txt ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
[galaxy-dev] Hiding a tool via tool_conf.xml
Hi all, I'm aware that in an individual tool's XML wrapper you can add hidden=true to the tool element to hide the tool from the listing shown in Galaxy's left hand panel (but the tool is still loaded and can be called by old workflows etc). Can this be done via the tool_conf.xml file as well? This would seem useful from a system configuration point of view where it seems wrong to edit the tool wrappers themselves. In fact, it might also be nice to add hidden=true support to section as well as tool in tool_conf.xml - although I'm not so sure how useful that would be. Peter ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] Inquiring
Dear Nate, It is great suggestion. I copy my root folder of galaxy as follows, could you please let me know if I need to change them to one user kangtu/admin. I hope we new user register can work today after I restart. - kangtu@dscbc-compute:~/Downloads/galaxy-dist$ ls -la total 1688 drwxr-xr-x 18 junzhu admin 36864 2011-01-28 15:05 . drwxr-xr-x 4 kangtu admin 36864 2011-01-21 21:44 .. -rw-r--r-- 1 root root 2882 2011-01-27 02:38 buildbot_setup.sh -rw-r--r-- 1 root root352 2011-01-27 02:38 community_datatypes_conf.xml.sample -rw-r--r-- 1 root root 2170 2011-01-27 02:38 community_wsgi.ini.sample drwxr-xr-x 2 kangtu admin 36864 2011-01-28 06:08 contrib drwxr-xr-x 2 kangtu admin 36864 2011-01-28 06:09 cron drwxr-xr-x 9 kangtu admin 36864 2011-01-27 02:40 database -rw-r--r-- 1 root root 21698 2011-01-27 02:38 datatypes_conf.xml -rw-r--r-- 1 root root 21698 2011-01-27 02:38 datatypes_conf.xml.sample drwxr-xr-x 5 kangtu admin 36864 2011-01-28 06:07 display_applications -rw-r--r-- 1 root root 7360 2011-01-27 02:38 dist-eggs.ini drwxr-xr-x 20 kangtu admin 36864 2011-01-28 15:04 eggs -rw-r--r-- 1 root root 1602 2011-01-27 02:38 eggs.ini -rwxr-xr-x 1 root root 65 2011-01-27 02:38 export_history.sh drwxr-xr-x 5 kangtu admin 36864 2011-01-24 01:49 galaxy_env drwxr-xr-x 3 kangtu admin 36864 2011-01-28 06:09 .hg -rw-r--r-- 1 root root552 2011-01-27 02:38 .hgignore drwxr-xr-x 4 kangtu admin 36864 2011-02-01 18:22 lib -rw-r--r-- 1 root root 1254 2011-01-27 02:38 LICENSE.txt drwxr-xr-x 4 kangtu admin 36864 2011-01-28 06:08 locale -rw-r--r-- 1 root root303 2011-01-27 02:38 Makefile -rwxr-xr-x 1 root root238 2011-01-27 02:38 manage_db.sh -rw-r--r-- 1 root root507 2011-01-27 02:38 MANIFEST.in -rw-r--r-- 1 root root977 2011-01-27 02:38 README.txt -rw-r--r-- 1 root root 1994 2011-01-27 02:38 reports_wsgi.ini -rw-r--r-- 1 root root 1994 2011-01-27 02:38 reports_wsgi.ini.sample -rw-r--r-- 1 root root146 2011-01-27 02:38 run_community.sh -rwxr-xr-x 1 root root 1946 2011-01-27 02:38 run_functional_tests.sh -rw-r--r-- 1 root root105 2011-01-27 02:38 run_galaxy_listener.sh -rw-r--r-- 1 root root140 2011-01-27 02:38 run_reports.sh -rwxr-xr-x 1 kangtu admin 826 2010-11-01 17:06 run.sh -rwxr-xr-x 1 root root263 2011-01-27 02:38 run_unit_tests.sh drwxr-xr-x 11 kangtu admin 36864 2011-01-28 06:08 scripts -rwxr-xr-x 1 root root 63 2011-01-27 02:38 set_metadata.sh -rw-r--r-- 1 root root 1499 2011-01-27 02:38 setup.sh drwxr-xr-x 16 kangtu admin 36864 2011-01-27 02:39 static drwxr-xr-x 16 kangtu admin 36864 2011-01-27 02:39 templates drwxr-xr-x 5 kangtu admin 36864 2011-01-24 01:49 test drwxr-xr-x 8 kangtu admin 90112 2011-01-28 06:13 test-data -rwxr-xr-x 1 root root 21748 2011-01-27 02:38 tool_conf.xml -rw-r--r-- 1 root root 18242 2011-01-27 02:38 tool_conf.xml.main -rw-r--r-- 1 root root 21300 2011-01-27 02:38 tool_conf.xml.sample lrwxrwxrwx 1 kangtu admin28 2010-11-02 09:44 tool-data - ../galaxy-central/tool-data/ drwxr-xr-x 3 kangtu admin 36864 2011-01-27 02:39 tool-data-bak -rw-r--r-- 1 root root878 2011-01-27 02:38 tool_data_table_conf.xml -rw-r--r-- 1 root root878 2011-01-27 02:38 tool_data_table_conf.xml.sample -rw-r--r-- 1 root root 2556 2011-01-27 02:38 tool_list.py lrwxrwxrwx 1 kangtu admin23 2010-11-01 17:37 tools - ../galaxy-central/tools drwxr-xr-x 37 kangtu admin 36864 2011-01-24 01:49 tools-bak -rw-r--r-- 1 root root438 2011-01-27 02:38 transfer_datasets.ini.sample -rw-r--r-- 1 root root 16421 2011-01-27 02:38 universe_wsgi.ini -rw-r--r-- 1 root root 16367 2011-01-27 02:38 universe_wsgi.ini.sample -rw-r--r-- 1 root root 75592 2011-01-27 02:38 virtualenv.py -rw-r--r-- 1 root root 69811 2011-01-27 02:38 virtualenv.pyc --- I have not checked the subfolder, is it necessary to change all the sub folders and its files. And we also need to reset the all files permission to 777 after I restart galaxy? Thanks, Yan ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] Inquiring
Yan Luo wrote: Dear Nate, Please find the following errors, it is the newest, and our restart is stopped. I hope we can get the solution from you as soon as possible. Hi Yan, Your last 4 messages included 3 different paths to Galaxy. It seems as though there are quite a few copies of Galaxy in use here. To ensure there are no permissions problems, please do the following, all as the same non-root user: 1. Remove the ~/.python-eggs directory and all of its contents. 2. Clone a new copy of Galaxy. 3. Start Galaxy using `./run.sh` And report back any errors which persist. If the numpy error below remains, I suggest setting up a Python virtualenv as described on: http://usegalaxy.org/production --nate Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 218, in run result = self.command() File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 276, in command relative_to=base, global_conf=vars) File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 313, in loadapp **kw) File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 225, in loadobj return context.create() File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 625, in create return self.object_type.invoke(self) File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py, line 57, in fix_call val = callable(*args, **kw) File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/web/buildapp.py, line 90, in app_factory add_controllers( webapp, app ) File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/web/buildapp.py, line 39, in add_controllers module = __import__( module_name ) File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/web/controllers/tracks.py, line 23, in module from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider File /mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/visualization/tracks/data/array_tree.py, line 8, in module from bx.arrays.array_tree import FileArrayTreeDict File numpy.pxd, line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object Looking forward to hearing from you. Best Wishes, Yan ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
