[galaxy-dev] questions about uploading and working with directories
Dear all, I have installed a Galaxy instance on my local server and it runs well. However I have some problems with directories. I want to create a workflow that takes a directory of files (e.g. 10) and repeatedly working on all files and then output another set of files (10) which are piped into the next tool. I searched over this forum, but couldn't find the solution (maybe I missed something). Does Galaxy directly support tools which work on a whole directory? Any suggestions/comments on this would be much appreciated! Regards, Jemma ___ 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] Error when installing galaxy - Email found in subject
Hi Dave, Thank you very much for your reply! The problem has been fixed after I installed python-boto. Regards, Jemma -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Emil Bouvier Sent: Wednesday, 28 March 2012 11:55 PM To: Jemma Wu Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Error when installing galaxy - Email found in subject Jemma, It looks like the boto package is not installed on your system. Try: sudo apt-get install python-boto Dave B. On 3/18/12 8:19 PM, Jemma Wu wrote: > Dear Galaxy developers, > > This is the first time that I installed Galaxy on a Debian Lenny 64 > bit server. I got an error of "ImportError: No module named boto" when > I ran %sh run.sh. Please see the error message of the installation output below: > > File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, > in app_factory > > add_ui_controllers( webapp, app ) > > File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, > in add_ui_controllers > > module = __import__( module_name ) > > File "/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/cloud.py", > line 9, in > > import boto > > ImportError: No module named boto > > Does anyone know how to fix this error? Thanks in advance! > > Regards, > > Jemma > > > > ___ > 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/ This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. ___ 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] Import error when running galaxy on Debian Lenny 64bit
Dear galaxy, I'm trying to install galaxy on a 64bit Debian (5.0) Lenny server with python2.5.2. When running %sh run.sh, the fetch_eggs completed successfully. However, I have problem with running galaxy instance. I've posted the error messages below. Traceback (most recent call last): File "./scripts/paster.py", line 34, in command.run() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/ command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/ command.py", line 123, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/ command.py", line 218, in run result = self.command() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/ serve.py", line 276, in command relative_to=base, global_conf=vars) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/ serve.py", line 313, in loadapp **kw) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/ loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/ loadwsgi.py", line 225, in loadobj return context.create() File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/ loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/ loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/ util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_ui_controllers( webapp, app ) File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_ui_controllers module = __import__( module_name ) File "/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/cloud.py", line 9, in import boto ImportError: No module named boto We have another Debian (6.0) Squeeze 32 bit server with python 2.6.6, and I did the same installation of galaxy. Everything went smoothly and galaxy server instance can run successfully on it. Do you know why this importError happens on our 64bit Debian 5.0 server and how I could fix it? Many thanks. Jemma Wu Australian Proteome Analysis Facility (APAF) Level 4, Building F7B, Research Park Drive Macquarie University Sydney NSW 2109 Australia ___ 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] Error when installing galaxy
Dear Galaxy developers, This is the first time that I installed Galaxy on a Debian Lenny 64 bit server. I got an error of "ImportError: No module named boto" when I ran %sh run.sh. Please see the error message of the installation output below: File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_ui_controllers( webapp, app ) File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_ui_controllers module = __import__( module_name ) File "/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/cloud.py", line 9, in import boto ImportError: No module named boto Does anyone know how to fix this error? Thanks in advance! Regards, Jemma ___ 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/
