Hi, Is it possible to embed Galaxy in my own website instead of embed my website into Galaxy framework? Or can I change the look and feel of Galaxy framework, such as header, footer? Thanks
Hi, Any help will be appreciated. I'm following the steps to configure the LIMS system and I'm stuck in step 3. Maybe I'm missing something, I get an SyntaxError. my version of python maybe? Python 2.4.3 (#1, Sep 3 2009, 15:37:37) [GCC 4.1.2 20080704 (Red Hat 4.1.2-46)] on linux2 Thanks, Victor 3. Add configured request types, forms and sample states to the database: $ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini File "scripts/nglims/add_ng_defaults.py", line 51 with open(config["nglims_config_file"]) as in_handle: ^ SyntaxError: invalid syntax http://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims
On Wed, Oct 6, 2010 at 10:05 PM, Victor Ruotti <ruotti@wisc.edu> wrote:
Hi,
Any help will be appreciated. I'm following the steps to configure the LIMS system and I'm stuck in step 3. Maybe I'm missing something, I get an SyntaxError. my version of python maybe? Python 2.4.3 (#1, Sep 3 2009, 15:37:37) [GCC 4.1.2 20080704 (Red Hat 4.1.2-46)] on linux2 Thanks, Victor 3. Add configured request types, forms and sample states to the database:
$ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini
sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini File "scripts/nglims/add_ng_defaults.py", line 51 with open(config["nglims_config_file"]) as in_handle: ^ SyntaxError: invalid syntax
The "with" statement is Python 2.5+ only and you have Python 2.4 Peter
Thanks Peter, I updated to python 2.5 and got the same error. Any ideas? Thanks, Victor sudo python2.5 scripts/nglims/add_ng_defaults.py universe_wsgi.ini galaxy_dev_1 > sudo python2.5 scripts/nglims/add_ng_defaults.py universe_wsgi.ini scripts/nglims/add_ng_defaults.py:51: Warning: 'with' will become a reserved keyword in Python 2.6 File "scripts/nglims/add_ng_defaults.py", line 51 with open(config["nglims_config_file"]) as in_handle: ^ SyntaxError: invalid syntax galaxy_dev_1 > python2.5 Python 2.5.4 (r254:67916, Oct 6 2010, 16:12:31) [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
On Oct 6, 2010, at 4:43 PM, Peter wrote:
On Wed, Oct 6, 2010 at 10:05 PM, Victor Ruotti <ruotti@wisc.edu> wrote:
Hi,
Any help will be appreciated. I'm following the steps to configure the LIMS system and I'm stuck in step 3. Maybe I'm missing something, I get an SyntaxError. my version of python maybe? Python 2.4.3 (#1, Sep 3 2009, 15:37:37) [GCC 4.1.2 20080704 (Red Hat 4.1.2-46)] on linux2 Thanks, Victor 3. Add configured request types, forms and sample states to the database:
$ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini
sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini File "scripts/nglims/add_ng_defaults.py", line 51 with open(config["nglims_config_file"]) as in_handle: ^ SyntaxError: invalid syntax
The "with" statement is Python 2.5+ only and you have Python 2.4
Peter
On Thu, Oct 7, 2010 at 2:33 AM, Victor Ruotti <ruotti@wisc.edu> wrote:
Thanks Peter, I updated to python 2.5 and got the same error. Any ideas? Thanks, Victor
sudo python2.5 scripts/nglims/add_ng_defaults.py universe_wsgi.ini galaxy_dev_1 > sudo python2.5 scripts/nglims/add_ng_defaults.py universe_wsgi.ini scripts/nglims/add_ng_defaults.py:51: Warning: 'with' will become a reserved keyword in Python 2.6 File "scripts/nglims/add_ng_defaults.py", line 51 with open(config["nglims_config_file"]) as in_handle: ^ SyntaxError: invalid syntax
galaxy_dev_1 > python2.5 Python 2.5.4 (r254:67916, Oct 6 2010, 16:12:31) [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
You started Galaxy using Python 2.5, but when Galaxy starts a child process for the python tool it would default to the system python I think, which must still be Python 2.4. One solution I'd try would be to hack the tool's XML file to change <command interpreter="python"> to be explicit, <command interpreter="python2.5"> The better fix would be in scripts/nglims/add_ng_defaults.py to make it Python 2.4 compatible. I think this just means replacing lines 51 and 52, with open(config["nglims_config_file"]) as in_handle: nglims_config = yaml.load(in_handle) with: in_handle = open(config["nglims_config_file"]) nglims_config = yaml.load(in_handle) in_handle.close() Right Brad? ;) Then try again, and hope that is the only thing blocking this from working on Python 2.4. I didn't see any more with statements so fingers crossed. Peter P.S. Current version is here: http://bitbucket.org/chapmanb/galaxy-central/src/tip/scripts/nglims/add_ng_d...
Peter wrote:
You started Galaxy using Python 2.5, but when Galaxy starts a child process for the python tool it would default to the system python I think, which must still be Python 2.4.
One solution I'd try would be to hack the tool's XML file to change <command interpreter="python"> to be explicit, <command interpreter="python2.5">
Although I see that Brad fixed this, it's probably worth pointing out that you wouldn't normally need to go to this much trouble. Rather than having to edit all the tools, you can simply ensure that the first `python` on your $PATH is the version you need. Instructions for this can be found as "Step 0" on http://getgalaxy.org . You can also use a Python virtualenv, the process for which is explained in the production server documentation at: http://usegalaxy.org/production --nate
The better fix would be in scripts/nglims/add_ng_defaults.py to make it Python 2.4 compatible. I think this just means replacing lines 51 and 52,
with open(config["nglims_config_file"]) as in_handle: nglims_config = yaml.load(in_handle)
with:
in_handle = open(config["nglims_config_file"]) nglims_config = yaml.load(in_handle) in_handle.close()
Right Brad? ;)
Then try again, and hope that is the only thing blocking this from working on Python 2.4. I didn't see any more with statements so fingers crossed.
Peter
P.S. Current version is here: http://bitbucket.org/chapmanb/galaxy-central/src/tip/scripts/nglims/add_ng_d...
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Thank you for all your help that was really quick and helpful. Using the central repository with a newer version of python and the virtual env Peter suggested all worked out great. I was able to create a request form and sample form from the admin section. Now I can create a new sequencing request and use it to add samples etc. All this looked very good! I was trying to follow the documentation to now to fully enable glims from here. http://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims Now when I do this 3. Add configured request types, forms and sample states to the database: $ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini I get, galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 363, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 57, in main db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % config["database_file"] KeyError: 'database_file' galaxy-central > python Python 2.5.4 (r254:67916, Oct 7 2010, 12:46:34) [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
also doing this I get galaxy-central > which python python is /usr/local/bin/python python is /usr/bin/python Both are python2.5. Almost there I think, thanks in advance. Victor On Oct 7, 2010, at 8:23 AM, Nate Coraor wrote:
Peter wrote:
You started Galaxy using Python 2.5, but when Galaxy starts a child process for the python tool it would default to the system python I think, which must still be Python 2.4.
One solution I'd try would be to hack the tool's XML file to change <command interpreter="python"> to be explicit, <command interpreter="python2.5">
Although I see that Brad fixed this, it's probably worth pointing out that you wouldn't normally need to go to this much trouble.
Rather than having to edit all the tools, you can simply ensure that the first `python` on your $PATH is the version you need. Instructions for this can be found as "Step 0" on http://getgalaxy.org . You can also use a Python virtualenv, the process for which is explained in the production server documentation at:
http://usegalaxy.org/production
--nate
The better fix would be in scripts/nglims/add_ng_defaults.py to make it Python 2.4 compatible. I think this just means replacing lines 51 and 52,
with open(config["nglims_config_file"]) as in_handle: nglims_config = yaml.load(in_handle)
with:
in_handle = open(config["nglims_config_file"]) nglims_config = yaml.load(in_handle) in_handle.close()
Right Brad? ;)
Then try again, and hope that is the only thing blocking this from working on Python 2.4. I didn't see any more with statements so fingers crossed.
Peter
P.S. Current version is here: http://bitbucket.org/chapmanb/galaxy-central/src/tip/scripts/nglims/add_ng_d...
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Victor;
Using the central repository with a newer version of python and the virtual env Peter suggested all worked out great.
I was able to create a request form and sample form from the admin section. Now I can create a new sequencing request and use it to add samples etc. All this looked very good!
Awesome. Great to hear it.
Now when I do this 3. Add configured request types, forms and sample states to the database:
$ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini I get,
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 363, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 57, in main db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % config["database_file"] KeyError: 'database_file'
It looks like database_connection isn't set in your universe_wsgi.ini. If you update the repository (hg pull; hg update) or grab the latest script I added a fix for this case: http://bitbucket.org/chapmanb/galaxy-central/src/tip/scripts/nglims/add_ng_d... You may also want to explicitly set the connection in the configuration file as a more general solution. Let us know if you run into any other problems. Thanks much, Brad
Thanks Brad. Did an hq pull and hq update. Looks like its looking for the file_path. Do I set this in the universe_wsgi.ini and what should I set to? thanks Victor galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 367, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 62, in main app = SimpleApp(db_con, config['file_path']) KeyError: 'file_path' On Oct 8, 2010, at 6:55 AM, Brad Chapman wrote:
Victor;
Using the central repository with a newer version of python and the virtual env Peter suggested all worked out great.
I was able to create a request form and sample form from the admin section. Now I can create a new sequencing request and use it to add samples etc. All this looked very good!
Awesome. Great to hear it.
Now when I do this 3. Add configured request types, forms and sample states to the database:
$ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini I get,
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 363, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 57, in main db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % config["database_file"] KeyError: 'database_file'
It looks like database_connection isn't set in your universe_wsgi.ini. If you update the repository (hg pull; hg update) or grab the latest script I added a fix for this case:
http://bitbucket.org/chapmanb/galaxy-central/src/tip/scripts/nglims/add_ng_d...
You may also want to explicitly set the connection in the configuration file as a more general solution.
Let us know if you run into any other problems. Thanks much, Brad _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Victor Ruotti wrote:
Thanks Brad. Did an hq pull and hq update.
Looks like its looking for the file_path. Do I set this in the universe_wsgi.ini and what should I set to? thanks Victor
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 367, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 62, in main app = SimpleApp(db_con, config['file_path']) KeyError: 'file_path'
Just a heads up to Brad, I recently changed galaxy.config so that almost everything that was "set" in universe_wsgi.ini was correctly defined as a default in the config, and then I commented out all of those values. The hope is that it makes it easier to maintain your config file against the sample as the sample changes over time. However, it means that a lot of the things your script expects to be defined aren't defined, so you may need to load galaxy.config yourself to access the defaults. --nate
On Oct 8, 2010, at 6:55 AM, Brad Chapman wrote:
Victor;
Using the central repository with a newer version of python and the virtual env Peter suggested all worked out great.
I was able to create a request form and sample form from the admin section. Now I can create a new sequencing request and use it to add samples etc. All this looked very good!
Awesome. Great to hear it.
Now when I do this 3. Add configured request types, forms and sample states to the database:
$ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini I get,
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 363, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 57, in main db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % config["database_file"] KeyError: 'database_file'
It looks like database_connection isn't set in your universe_wsgi.ini. If you update the repository (hg pull; hg update) or grab the latest script I added a fix for this case:
http://bitbucket.org/chapmanb/galaxy-central/src/tip/scripts/nglims/add_ng_d...
You may also want to explicitly set the connection in the configuration file as a more general solution.
Let us know if you run into any other problems. Thanks much, Brad _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Victor and Nate;
Looks like its looking for the file_path. Do I set this in the universe_wsgi.ini and what should I set to?
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 367, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 62, in main app = SimpleApp(db_con, config['file_path']) KeyError: 'file_path'
Just a heads up to Brad,
I recently changed galaxy.config so that almost everything that was "set" in universe_wsgi.ini was correctly defined as a default in the config, and then I commented out all of those values. The hope is that it makes it easier to maintain your config file against the sample as the sample changes over time. However, it means that a lot of the things your script expects to be defined aren't defined, so you may need to load galaxy.config yourself to access the defaults.
Nate, thanks for the details on the change. Victor, sorry to trip you up. I took a full look at this on a clean system with the new universe_wsgi.ini so hopefully have ironed out all of the problems. Could you do one more hg pull/hg update? Hopefully that'll take care of everything but definitely let us know if not. I also updated the documentation to be clearer for future users: http://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims If you have any suggestions about things I missed there, please feel free to add them. Thanks again, Brad
Hey, Getting a fresh copy of the distribution worked! Whatever you did thanks! No more file path error. Things are working good. Victor sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini [sudo] password for victor: Adding standard forms and requests for sequencing Creating potential sample states Adding standard sequencing controls Creating form for sequencing results On Oct 8, 2010, at 9:23 AM, Nate Coraor wrote:
Victor Ruotti wrote:
Thanks Brad. Did an hq pull and hq update.
Looks like its looking for the file_path. Do I set this in the universe_wsgi.ini and what should I set to? thanks Victor
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 367, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 62, in main app = SimpleApp(db_con, config['file_path']) KeyError: 'file_path'
Just a heads up to Brad,
I recently changed galaxy.config so that almost everything that was "set" in universe_wsgi.ini was correctly defined as a default in the config, and then I commented out all of those values. The hope is that it makes it easier to maintain your config file against the sample as the sample changes over time. However, it means that a lot of the things your script expects to be defined aren't defined, so you may need to load galaxy.config yourself to access the defaults.
--nate
On Oct 8, 2010, at 6:55 AM, Brad Chapman wrote:
Victor;
Using the central repository with a newer version of python and the virtual env Peter suggested all worked out great.
I was able to create a request form and sample form from the admin section. Now I can create a new sequencing request and use it to add samples etc. All this looked very good!
Awesome. Great to hear it.
Now when I do this 3. Add configured request types, forms and sample states to the database:
$ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini I get,
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 363, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 57, in main db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % config["database_file"] KeyError: 'database_file'
It looks like database_connection isn't set in your universe_wsgi.ini. If you update the repository (hg pull; hg update) or grab the latest script I added a fix for this case:
http://bitbucket.org/chapmanb/galaxy-central/src/tip/scripts/nglims/add_ng_d...
You may also want to explicitly set the connection in the configuration file as a more general solution.
Let us know if you run into any other problems. Thanks much, Brad _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi, I noticed some chances in the repository which give the following error. sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 43, in <module> import galaxy.model.mapping File "/opt/glims/galaxy-central/lib/galaxy/model/__init__.py", line 10, in <module> from galaxy.util.bunch import Bunch File "/opt/glims/galaxy-central/lib/galaxy/util/__init__.py", line 485, in <module> os.path.join(shared_dir, "ucsc", "top_builds.txt")) File "/opt/glims/galaxy-central/lib/galaxy/util/__init__.py", line 322, in read_dbnames for line in open(filename): IOError: [Errno 2] No such file or directory: '/opt/glims/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/builds.txt' I also see the error below when trying to start galaxy. Thanks in advance. Victor galaxy-central > ./run.sh Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/new/Mako/Mako-0.2.5-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/Babel/Babel-0.9.4-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/Whoosh/Whoosh-0.3.18-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/Tempita/Tempita-0.1-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/Cheetah/Cheetah-2.2.2-py2.5-linux-x86_64-ucs2.... Fetched http://eggs.g2.bx.psu.edu/new/lrucache/lrucache-0.2-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/boto/boto-1.8d-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/NoseHTML/NoseHTML-0.3.1-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/pexpect/pexpect-2.4-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/bx_python/bx_python-0.5.0_dev_f74aec067563-py2... Fetched http://eggs.g2.bx.psu.edu/new/PasteDeploy/PasteDeploy-1.3.3-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/WebHelpers/WebHelpers-0.2-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/numpy/numpy-1.3.0-py2.5-linux-x86_64-ucs2.egg Fetched http://eggs.g2.bx.psu.edu/new/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.5-li... Fetched http://eggs.g2.bx.psu.edu/new/Beaker/Beaker-1.4-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/SVGFig/SVGFig-1.1.6-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/simplejson/simplejson-2.1.1-py2.5-linux-x86_64... Fetched http://eggs.g2.bx.psu.edu/new/WebError/WebError-0.8a-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/python_lzo/python_lzo-1.08_2.03_static-py2.5-l... Fetched http://eggs.g2.bx.psu.edu/new/twill/twill-0.9-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/Routes/Routes-1.12.3-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/decorator/decorator-3.1.2-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/sqlalchemy_migrate/sqlalchemy_migrate-0.5.4-py... Fetched http://eggs.g2.bx.psu.edu/new/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998... Fetched http://eggs.g2.bx.psu.edu/new/pycrypto/pycrypto-2.0.1-py2.5-linux-x86_64-ucs... Fetched http://eggs.g2.bx.psu.edu/new/Paste/Paste-1.6-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/nose/nose-0.11.1-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/amqplib/amqplib-0.6.1-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/WebOb/WebOb-0.8.5-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/PasteScript/PasteScript-1.7.3-py2.5.egg Fetch successful. python path is: /opt/glims/galaxy-central/eggs/Whoosh-0.3.18-py2.5.egg, /opt/glims/galaxy-central/eggs/pycrypto-2.0.1-py2.5-linux-x86_64-ucs2.egg, /opt/glims/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.5-linux-x86_64-ucs2.egg, /opt/glims/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.5-linux-x86_64-ucs2.egg, /opt/glims/galaxy-central/eggs/amqplib-0.6.1-py2.5.egg, /opt/glims/galaxy-central/eggs/pexpect-2.4-py2.5.egg, /opt/glims/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg, /opt/glims/galaxy-central/eggs/Babel-0.9.4-py2.5.egg, /opt/glims/galaxy-central/eggs/Beaker-1.4-py2.5.egg, /opt/glims/galaxy-central/eggs/Mako-0.2.5-py2.5.egg, /opt/glims/galaxy-central/eggs/WebHelpers-0.2-py2.5.egg, /opt/glims/galaxy-central/eggs/simplejson-2.1.1-py2.5-linux-x86_64-ucs2.egg, /opt/glims/galaxy-central/eggs/wchartype-0.1-py2.5.egg, /opt/glims/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.5.egg, /opt/glims/galaxy-central/eggs/docutils-0.4-py2.5.egg, /opt/glims/galaxy-central/eggs/WebOb-0.8.5-py2.5.egg, /opt/glims/galaxy-central/eggs/Routes-1.12.3-py2.5.egg, /opt/glims/galaxy-central/eggs/Cheetah-2.2.2-py2.5-linux-x86_64-ucs2.egg, /opt/glims/galaxy-central/eggs/PasteDeploy-1.3.3-py2.5.egg, /opt/glims/galaxy-central/eggs/PasteScript-1.7.3-py2.5.egg, /opt/glims/galaxy-central/eggs/Paste-1.6-py2.5.egg, /opt/glims/galaxy-central/lib, /usr/local/lib/python2.5/site-packages/setuptools-0.6c11-py2.5.egg, /usr/local/lib/python2.5/site-packages/rpy2-2.1.5_20101007-py2.5-linux-x86_64.egg, /usr/local/lib/python25.zip, /usr/local/lib/python2.5, /usr/local/lib/python2.5/plat-linux2, /usr/local/lib/python2.5/lib-tk, /usr/local/lib/python2.5/lib-dynload, /usr/local/lib/python2.5/site-packages Traceback (most recent call last): File "/opt/glims/galaxy-central/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/opt/glims/galaxy-central/lib/galaxy/app.py", line 19, in __init__ self.config.check() File "/opt/glims/galaxy-central/lib/galaxy/config.py", line 161, in check raise ConfigurationError("Directory does not exist: %s" % path ) ConfigurationError: Directory does not exist: ./database/files On Oct 8, 2010, at 9:23 AM, Nate Coraor wrote:
Victor Ruotti wrote:
Thanks Brad. Did an hq pull and hq update.
Looks like its looking for the file_path. Do I set this in the universe_wsgi.ini and what should I set to? thanks Victor
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 367, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 62, in main app = SimpleApp(db_con, config['file_path']) KeyError: 'file_path'
Just a heads up to Brad,
I recently changed galaxy.config so that almost everything that was "set" in universe_wsgi.ini was correctly defined as a default in the config, and then I commented out all of those values. The hope is that it makes it easier to maintain your config file against the sample as the sample changes over time. However, it means that a lot of the things your script expects to be defined aren't defined, so you may need to load galaxy.config yourself to access the defaults.
--nate
On Oct 8, 2010, at 6:55 AM, Brad Chapman wrote:
Victor;
Using the central repository with a newer version of python and the virtual env Peter suggested all worked out great.
I was able to create a request form and sample form from the admin section. Now I can create a new sequencing request and use it to add samples etc. All this looked very good!
Awesome. Great to hear it.
Now when I do this 3. Add configured request types, forms and sample states to the database:
$ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini I get,
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 363, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 57, in main db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % config["database_file"] KeyError: 'database_file'
It looks like database_connection isn't set in your universe_wsgi.ini. If you update the repository (hg pull; hg update) or grab the latest script I added a fix for this case:
http://bitbucket.org/chapmanb/galaxy-central/src/tip/scripts/nglims/add_ng_d...
You may also want to explicitly set the connection in the configuration file as a more general solution.
Let us know if you run into any other problems. Thanks much, Brad _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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Victor;
I noticed some chances in the repository which give the following error. sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini
This doesn't affect your problem, but you don't need to run this script as root.
Traceback (most recent call last): IOError: [Errno 2] No such file or directory: '/opt/glims/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/builds.txt' [...] I also see the error below when trying to start galaxy. galaxy-central > ./run.sh Traceback (most recent call last): ConfigurationError: Directory does not exist: ./database/files
Have you run the setup script ('sh setup.sh') on this repository? Both the files you are missing will be created by it. You'll want to run setup.sh and run.sh at least once on a brand new repository before running the nglims script: http://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims Hope this helps, Brad
Thank you for pointing that out to me. Ahhh, yes, my fault. I'll be testing the lims part now. I'm hoping to help out with testing and the overall flow. Will keep you posted on things go. Victor On Oct 11, 2010, at 12:40 PM, Brad Chapman wrote:
Victor;
I noticed some chances in the repository which give the following error. sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini
This doesn't affect your problem, but you don't need to run this script as root.
Traceback (most recent call last): IOError: [Errno 2] No such file or directory: '/opt/glims/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/builds.txt' [...] I also see the error below when trying to start galaxy. galaxy-central > ./run.sh Traceback (most recent call last): ConfigurationError: Directory does not exist: ./database/files
Have you run the setup script ('sh setup.sh') on this repository? Both the files you are missing will be created by it.
You'll want to run setup.sh and run.sh at least once on a brand new repository before running the nglims script:
http://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims
Hope this helps, Brad
Victor;
Any help will be appreciated. I'm following the steps to configure the LIMS system and I'm stuck in step 3. Maybe I'm missing something, I get an SyntaxError. my version of python maybe?
Yes, that's right. As Peter mentioned, this add-on code needs a more recent version of Python. Galaxy itself works fine on Python 2.4 but unfortunately I'm not as disciplined as the Galaxy crew, so the LIMS patch uses some more recent syntax features. If you're taking a look at this, you might prefer to use my fork of Galaxy main. The patch is probably a bit out of date with the latest code base, while this is maintained and up to date since it's what we run locally: https://bitbucket.org/chapmanb/galaxy-central Happy to help with any questions. Thanks for checking it out, Brad
Excellent thank you. Makes sense. So I'll do this? hg clone http://bitbucket.org/chapmanb/galaxy-central Along with using a 2.5 version of python to move on? Thanks for the quick response. Will keep you posted on how things go. Victor On Oct 6, 2010, at 8:29 PM, Brad Chapman wrote:
Victor;
Any help will be appreciated. I'm following the steps to configure the LIMS system and I'm stuck in step 3. Maybe I'm missing something, I get an SyntaxError. my version of python maybe?
Yes, that's right. As Peter mentioned, this add-on code needs a more recent version of Python. Galaxy itself works fine on Python 2.4 but unfortunately I'm not as disciplined as the Galaxy crew, so the LIMS patch uses some more recent syntax features.
If you're taking a look at this, you might prefer to use my fork of Galaxy main. The patch is probably a bit out of date with the latest code base, while this is maintained and up to date since it's what we run locally:
https://bitbucket.org/chapmanb/galaxy-central
Happy to help with any questions. Thanks for checking it out, Brad
Victor;
Excellent thank you. Makes sense. So I'll do this? hg clone http://bitbucket.org/chapmanb/galaxy-central
Along with using a 2.5 version of python to move on?
That sounds perfect. If you are upgrading Python, you'll want to go with Python 2.6, which is compatible with the available Galaxy eggs and has lots of the newer language features.
I updated to python 2.5 and got the same error. Any ideas?
The better fix would be in scripts/nglims/add_ng_defaults.py to make it Python 2.4 compatible. I think this just means replacing lines 51 and 52,
Yes, agreed. Apologies I didn't have a chance to do this last night. In addition to the with statement, I am also a big fan of conditional expressions. Victor, if you do 'hg pull' and 'hg update' on the forked repository you'll get a fixed version of the code that will run with python2.4. I tried to fix all of the incompatibility pieces, but if you find any remaining issues let me know. Thanks much, Brad
On Thu, Oct 7, 2010 at 12:52 PM, Brad Chapman <chapmanb@50mail.com> wrote:
The better fix would be in scripts/nglims/add_ng_defaults.py to make it Python 2.4 compatible. I think this just means replacing lines 51 and 52,
Yes, agreed. Apologies I didn't have a chance to do this last night. In addition to the with statement, I am also a big fan of conditional expressions. Victor, if you do 'hg pull' and 'hg update' on the forked repository you'll get a fixed version of the code that will run with python2.4. I tried to fix all of the incompatibility pieces, but if you find any remaining issues let me know.
Looks like I just did the easy bit - I missed the fact that functools was Python 2.5+ only. Is there a plan for when Galaxy will drop Python 2.4 (and support Python 2.7)? See also, http://bitbucket.org/galaxy/galaxy-central/issue/386/python-27-support Peter
participants (5)
-
Brad Chapman -
Nate Coraor -
Peter -
Victor Ruotti -
Zhe Chen