upload error in the local instance of galaxy
Hi, I have just installed a local instance of galaxy. Though I am not too familiar with unix, I preferred a local instance because of large amount of data I have to process. However, I am unable to upload a file more that 2 GB in size, the error log is pased below 127.0.0.1 - - [19/Oct/2011:15:06:08 +0800] "POST /tool_runner/index HTTP/1.1" 500 - "http://127.0.0.1:8080/tool_runner?tool_id=upload1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:6.0.2) Gecko/20100101 Firefox/6.0.2" Debug at: http://127.0.0.1:8080/_debug/view/1319007854 ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 61099) Traceback (most recent call last): File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 617, in __init__ self.handle() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py", line 202, in __call__ return app(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/Users/amit/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/config.py", line 164, in __call__ app_iter = self.application(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 226, in __call__ return self.respond(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 399, in respond if self.xmlhttp_key in req.params: File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 900, in params params = self.str_params File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 892, in str_params return NestedMultiDict(self.str_GET, self.str_POST) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 818, in str_POST keep_blank_values=True) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 508, in __init__ self.read_multi(environ, keep_blank_values, strict_parsing) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 632, in read_multi environ, keep_blank_values, strict_parsing) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 510, in __init__ self.read_single() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 647, in read_single self.read_lines() File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/base.py", line 253, in read_lines self.read_lines_to_outerboundary() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 697, in read_lines_to_outerboundary line = self.fp.readline(1<<16) File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 467, in readline data = self.file.readline(self.length - self._consumed) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/socket.py", line 409, in readline bline = buf.readline(size) OverflowError: long int too large to convert to int Please help me to fix this, the python version is 2.6.6. Thank you. Sincerely, Amit, Germline biology group Temasek Life Sciences Laboratory Singapore -- Amit Anand Germ Line Biology Group Temasek Life Sciences Laboratory 1, Research Link National University of Singapore Singapore, 117604 Information in this email is confidential and may also be privileged. It is intended solely for the person to whom it is addressed. If you are not the intended recipient, please notify the sender, and please delete the message and any other record of it from your system immediately.
On 10/19/11 3:09 AM, "Amit Anand" <amit@tll.org.sg> wrote:
Hi,
I have just installed a local instance of galaxy. Though I am not too familiar with unix, I preferred a local instance because of large amount of data I have to process. However, I am unable to upload a file more that 2 GB in size, the error log is pased below
Hi anand: It¹s not possible to upoad such big files. You need to use FTP or local file import methods to do that. See: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files ?highlight=%28import%29 Brad
127.0.0.1 - - [19/Oct/2011:15:06:08 +0800] "POST /tool_runner/index HTTP/1.1" 500 - "http://127.0.0.1:8080/tool_runner?tool_id=upload1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:6.0.2) Gecko/20100101 Firefox/6.0.2" Debug at: http://127.0.0.1:8080/_debug/view/1319007854 ----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 61099) Traceback (most recent call last): File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer. py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer. py", line 617, in __init__ self.handle() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServe r.py", line 329, in handle self.handle_one_request() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 427, in handle_one_request self.wsgi_execute() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 287, in wsgi_execute self.wsgi_start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.p y", line 202, in __call__ return app(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/xfo rwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/Users/amit/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/ deploy/config.py", line 164, in __call__ app_iter = self.application(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/tra nslogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/e valexception/middleware.py", line 226, in __call__ return self.respond(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/e valexception/middleware.py", line 399, in respond if self.xmlhttp_key in req.params: File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init __.py", line 900, in params params = self.str_params File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init __.py", line 892, in str_params return NestedMultiDict(self.str_GET, self.str_POST) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init __.py", line 818, in str_POST keep_blank_values=True) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 508, in __init__ self.read_multi(environ, keep_blank_values, strict_parsing) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 632, in read_multi environ, keep_blank_values, strict_parsing) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 510, in __init__ self.read_single() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 647, in read_single self.read_lines() File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/base.py", line 253, in read_lines self.read_lines_to_outerboundary() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 697, in read_lines_to_outerboundary line = self.fp.readline(1<<16) File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 467, in readline data = self.file.readline(self.length - self._consumed) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/socket.py", line 409, in readline bline = buf.readline(size) OverflowError: long int too large to convert to int
Please help me to fix this, the python version is 2.6.6. Thank you.
Sincerely,
Amit,
Germline biology group Temasek Life Sciences Laboratory Singapore
-- Brad Langhorst Postdoctoral Fellow New England Biolabs langhorst@neb.com
Hi all, I am setting up our own galaxy instance here. We'd like to use fastqc, but I have run into a problem implementing it. Any suggestions would be most welcome, as to what might be wrong. 1. fastqc runs fine outside of galaxy. But when I try the same file inside galaxy, I get errors. 2. I can look to the shell script generated by galaxy inside ~/galaxy-dist/database/pbs/ . When I run that python command inside the sh script, generated by galaxy, to execute fastqc -- it works fine, without errors. Therefore, it seems as if there is some sort of permission or path problem when galaxy runs fastqc. I have fastqc in the main path, and also installed it in the "jars" directory where the fastqc tool looks for it. However, I still can't understand this, since when outside of galaxy, I can run the python command generated by galaxy successfully. The output/error inside galaxy is here: Exception in thread "main" java.lang.NoClassDefFoundError: uk.ac.bbsrc.babraham.FastQC.Sequence.FastQFile at java.lang.Class.initializeClass(libgcj.so.7rh) at uk.ac.bbsrc.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:83) at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:113) at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:84) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308) Caused by: java.lang.ClassFormatError: org.itadaki.bzip2.BZip2InputStream (unrecognized class file version) at java.lang.VMClassLoader.defineClass(libgcj.so.7rh) at java.lang.ClassLoader.defineClass(libgcj.so.7rh) at java.security.SecureClassLoader.defineClass(libgcj.so.7rh) at java.net.URLClassLoader.findClass(libgcj.so.7rh) at java.lang.ClassLoader.loadClass(libgcj.so.7rh) at java.lang.ClassLoader.loadClass(libgcj.so.7rh) at java.lang.Class.forName(libgcj.so.7rh) at java.lang.Class.initializeClass(libgcj.so.7rh) ...4 more Any clues/advice most appreciated! Todd -- ************************************* Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA NEWLY UPDATED LAB WEBSITE: http://labs.eemb.ucsb.edu/oakley/todd/ **************************************
Hi all, I am setting up our own galaxy instance here (or trying to). We'd like to use fastqc, but I have run into a problem implementing it. Any suggestions would be most welcome, as to what might be wrong. 1. fastqc runs fine outside of galaxy. But when I try the same file inside galaxy, I get errors. 2. I can look to the shell script generated by galaxy inside ~/galaxy-dist/database/pbs/ . When I run that python command inside the sh script, generated by galaxy, to execute fastqc -- it works fine, without errors. Therefore, it seems as if there is some sort of permission or path problem when galaxy runs fastqc. I have fastqc in the main path, and also installed it in the "jars" directory where the fastqc tool looks for it. However, I still can't understand this, since when outside of galaxy, I can run the python command generated by galaxy successfully. The output/error inside galaxy is here: Exception in thread "main" java.lang.NoClassDefFoundError: uk.ac.bbsrc.babraham.FastQC.Sequence.FastQFile at java.lang.Class.initializeClass(libgcj.so.7rh) at uk.ac.bbsrc.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:83) at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:113) at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:84) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308) Caused by: java.lang.ClassFormatError: org.itadaki.bzip2.BZip2InputStream (unrecognized class file version) at java.lang.VMClassLoader.defineClass(libgcj.so.7rh) at java.lang.ClassLoader.defineClass(libgcj.so.7rh) at java.security.SecureClassLoader.defineClass(libgcj.so.7rh) at java.net.URLClassLoader.findClass(libgcj.so.7rh) at java.lang.ClassLoader.loadClass(libgcj.so.7rh) at java.lang.ClassLoader.loadClass(libgcj.so.7rh) at java.lang.Class.forName(libgcj.so.7rh) at java.lang.Class.initializeClass(libgcj.so.7rh) ...4 more Any clues/advice most appreciated! Todd -- ************************************* Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA NEWLY UPDATED LAB WEBSITE:http://labs.eemb.ucsb.edu/oakley/todd/ **************************************
Exception in thread "main" java.lang.NoClassDefFoundError: uk.ac.bbsrc.babraham.FastQC.Sequence.FastQFile makes me guess that the fastqc perl script is not being executed from
Hi, Todd. The error message: the root of a complete FastQC distribution directory substructure by the Galaxy tool wrapper. The FastQC Galaxy tool has very specific installation requirements - a system install won't work - even though FastQC works from the command line. The FastQC java applications use a perl wrapper to set up the classpaths, and it expects to be executed from inside the root of the complex FastQC distribution folder structure. Having a system wide installation will allow the various phenomena you describe, but won't work when the Galaxy tool tries to run, because the tool expects to find the entire FastQC distribution layout in the [galaxy root]/tool-data/shared/jars/FastQC directory. Please run the following command from your [galaxy-root]/tool-data/shared/jars/ directory: ls -l FastQC/uk/ac/bbsrc/babraham/FastQC I'm guessing you'll see " No such file or directory" - but if you untar the distribution to where the tool expects it, you should see something like: (vgalaxy)galaxy@omics:~/tool-data/shared$ ls -l jars/FastQC/uk/ac/bbsrc/babraham/FastQC total 68 drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Analysis drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Dialogs -rwxr-xr-x 1 galaxy galaxy 1080 2011-09-19 14:13 FastQCApplication$1.class -rwxr-xr-x 1 galaxy galaxy 1080 2011-09-19 14:13 FastQCApplication$2.class -rwxr-xr-x 1 galaxy galaxy 9366 2011-09-19 14:13 FastQCApplication.class -rwxr-xr-x 1 galaxy galaxy 3661 2011-09-19 14:13 FastQCMenuBar.class drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 FileFilters drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Graphs drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Help drwxr-xr-x 3 galaxy galaxy 4096 2011-09-19 14:13 Modules drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Report drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Resources drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Results drwxr-xr-x 3 galaxy galaxy 4096 2011-09-19 14:13 Sequence drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Statistics Note that it would be possible to change the xml wrapper to expect to find the distribution on the path if there is community preference for requiring the FastQC distribution to be on the execution host path but having it the way it is allows explicit control of the version the tool uses within the layout of the Galaxy installation root, as is done for other fussy java packages. Suggestions welcomed. On Thu, Oct 20, 2011 at 6:03 AM, Todd Oakley <todd.oakley@lifesci.ucsb.edu> wrote:
Hi all, I am setting up our own galaxy instance here. We'd like to use fastqc, but I have run into a problem implementing it. Any suggestions would be most welcome, as to what might be wrong.
1. fastqc runs fine outside of galaxy. But when I try the same file inside galaxy, I get errors.
2. I can look to the shell script generated by galaxy inside ~/galaxy-dist/database/pbs/ . When I run that python command inside the sh script, generated by galaxy, to execute fastqc -- it works fine, without errors.
Therefore, it seems as if there is some sort of permission or path problem when galaxy runs fastqc. I have fastqc in the main path, and also installed it in the "jars" directory where the fastqc tool looks for it. However, I still can't understand this, since when outside of galaxy, I can run the python command generated by galaxy successfully.
The output/error inside galaxy is here:
Exception in thread "main" java.lang.NoClassDefFoundError: uk.ac.bbsrc.babraham.FastQC.Sequence.FastQFile at java.lang.Class.initializeClass(libgcj.so.7rh) at uk.ac.bbsrc.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:83) at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:113) at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:84) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308) Caused by: java.lang.ClassFormatError: org.itadaki.bzip2.BZip2InputStream (unrecognized class file version) at java.lang.VMClassLoader.defineClass(libgcj.so.7rh) at java.lang.ClassLoader.defineClass(libgcj.so.7rh) at java.security.SecureClassLoader.defineClass(libgcj.so.7rh) at java.net.URLClassLoader.findClass(libgcj.so.7rh) at java.lang.ClassLoader.loadClass(libgcj.so.7rh) at java.lang.ClassLoader.loadClass(libgcj.so.7rh) at java.lang.Class.forName(libgcj.so.7rh) at java.lang.Class.initializeClass(libgcj.so.7rh) ...4 more
Any clues/advice most appreciated!
Todd
-- ************************************* Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA
NEWLY UPDATED LAB WEBSITE: http://labs.eemb.ucsb.edu/oakley/todd/ **************************************
___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
Hi Ross, Thanks for your advice. Yes, something like this seems logical. However, after I installed system-wide before, I noticed that galaxy was expecting fastqc in the 'jars' directory. So, I copied the full directory structure over there. As such, when I look at the directory you suggest, I do indeed see files there: [galaxy@node95 jars]$ ls -l FastQC/uk/ac/bbsrc/babraham/FastQC/ total 68 drwxr-xr-x 2 galaxy hpuser 4096 Oct 18 20:18 Analysis drwxr-xr-x 2 galaxy hpuser 4096 Oct 18 20:18 Dialogs -rw-r--r-- 1 galaxy hpuser 1054 Oct 18 20:18 FastQCApplication$1.class -rw-r--r-- 1 galaxy hpuser 10075 Oct 18 20:18 FastQCApplication.class -rw-r--r-- 1 galaxy hpuser 3624 Oct 18 20:18 FastQCMenuBar.class drwxr-xr-x 2 galaxy hpuser 4096 Oct 18 20:18 FileFilters drwxr-xr-x 2 galaxy hpuser 4096 Oct 18 20:18 Graphs drwxr-xr-x 2 galaxy hpuser 4096 Oct 18 20:18 Help drwxr-xr-x 3 galaxy hpuser 4096 Oct 18 20:18 Modules drwxr-xr-x 2 galaxy hpuser 4096 Oct 18 20:18 Report drwxr-xr-x 2 galaxy hpuser 4096 Oct 18 20:18 Resources drwxr-xr-x 2 galaxy hpuser 4096 Oct 18 20:18 Results drwxr-xr-x 4 galaxy hpuser 4096 Oct 18 20:18 Sequence drwxr-xr-x 2 galaxy hpuser 4096 Oct 18 20:18 Statistics drwxr-xr-x 2 galaxy hpuser 4096 Oct 18 20:18 Utilities Perhaps I will remove my system installation, and also try untaring fastqc anew in the jars file, in case something didn't copy. But at first glance, it seems to be something else... Todd On 10/19/2011 2:51 PM, Ross wrote:
Exception in thread "main" java.lang.NoClassDefFoundError: uk.ac.bbsrc.babraham.FastQC.Sequence.FastQFile makes me guess that the fastqc perl script is not being executed from
Hi, Todd. The error message: the root of a complete FastQC distribution directory substructure by the Galaxy tool wrapper.
The FastQC Galaxy tool has very specific installation requirements - a system install won't work - even though FastQC works from the command line. The FastQC java applications use a perl wrapper to set up the classpaths, and it expects to be executed from inside the root of the complex FastQC distribution folder structure. Having a system wide installation will allow the various phenomena you describe, but won't work when the Galaxy tool tries to run, because the tool expects to find the entire FastQC distribution layout in the [galaxy root]/tool-data/shared/jars/FastQC directory.
Please run the following command from your [galaxy-root]/tool-data/shared/jars/ directory: ls -l FastQC/uk/ac/bbsrc/babraham/FastQC
I'm guessing you'll see " No such file or directory" - but if you untar the distribution to where the tool expects it, you should see something like: (vgalaxy)galaxy@omics:~/tool-data/shared$ ls -l jars/FastQC/uk/ac/bbsrc/babraham/FastQC total 68 drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Analysis drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Dialogs -rwxr-xr-x 1 galaxy galaxy 1080 2011-09-19 14:13 FastQCApplication$1.class -rwxr-xr-x 1 galaxy galaxy 1080 2011-09-19 14:13 FastQCApplication$2.class -rwxr-xr-x 1 galaxy galaxy 9366 2011-09-19 14:13 FastQCApplication.class -rwxr-xr-x 1 galaxy galaxy 3661 2011-09-19 14:13 FastQCMenuBar.class drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 FileFilters drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Graphs drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Help drwxr-xr-x 3 galaxy galaxy 4096 2011-09-19 14:13 Modules drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Report drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Resources drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Results drwxr-xr-x 3 galaxy galaxy 4096 2011-09-19 14:13 Sequence drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Statistics
Note that it would be possible to change the xml wrapper to expect to find the distribution on the path if there is community preference for requiring the FastQC distribution to be on the execution host path but having it the way it is allows explicit control of the version the tool uses within the layout of the Galaxy installation root, as is done for other fussy java packages. Suggestions welcomed.
On Thu, Oct 20, 2011 at 6:03 AM, Todd Oakley <todd.oakley@lifesci.ucsb.edu> wrote:
Hi all, I am setting up our own galaxy instance here. We'd like to use fastqc, but I have run into a problem implementing it. Any suggestions would be most welcome, as to what might be wrong.
1. fastqc runs fine outside of galaxy. But when I try the same file inside galaxy, I get errors.
2. I can look to the shell script generated by galaxy inside ~/galaxy-dist/database/pbs/ . When I run that python command inside the sh script, generated by galaxy, to execute fastqc -- it works fine, without errors.
Therefore, it seems as if there is some sort of permission or path problem when galaxy runs fastqc. I have fastqc in the main path, and also installed it in the "jars" directory where the fastqc tool looks for it. However, I still can't understand this, since when outside of galaxy, I can run the python command generated by galaxy successfully.
The output/error inside galaxy is here:
Exception in thread "main" java.lang.NoClassDefFoundError: uk.ac.bbsrc.babraham.FastQC.Sequence.FastQFile at java.lang.Class.initializeClass(libgcj.so.7rh) at uk.ac.bbsrc.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:83) at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:113) at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:84) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308) Caused by: java.lang.ClassFormatError: org.itadaki.bzip2.BZip2InputStream (unrecognized class file version) at java.lang.VMClassLoader.defineClass(libgcj.so.7rh) at java.lang.ClassLoader.defineClass(libgcj.so.7rh) at java.security.SecureClassLoader.defineClass(libgcj.so.7rh) at java.net.URLClassLoader.findClass(libgcj.so.7rh) at java.lang.ClassLoader.loadClass(libgcj.so.7rh) at java.lang.ClassLoader.loadClass(libgcj.so.7rh) at java.lang.Class.forName(libgcj.so.7rh) at java.lang.Class.initializeClass(libgcj.so.7rh) ...4 more
Any clues/advice most appreciated!
Todd
-- ************************************* Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA
NEWLY UPDATED LAB WEBSITE: http://labs.eemb.ucsb.edu/oakley/todd/ **************************************
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-- ************************************* Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA NEWLY UPDATED LAB WEBSITE: http://labs.eemb.ucsb.edu/oakley/todd/ **************************************
Brad Langhorst wrote:
On 10/19/11 3:09 AM, "Amit Anand" <amit@tll.org.sg> wrote:
Hi,
I have just installed a local instance of galaxy. Though I am not too familiar with unix, I preferred a local instance because of large amount of data I have to process. However, I am unable to upload a file more that 2 GB in size, the error log is pased below
Hi anand: It¹s not possible to upoad such big files. You need to use FTP or local file import methods to do that.
See: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files ?highlight=%28import%29
Brad
You probably also need to set: debug = False use_interactive = False In universe_wsgi.ini
127.0.0.1 - - [19/Oct/2011:15:06:08 +0800] "POST /tool_runner/index HTTP/1.1" 500 - "http://127.0.0.1:8080/tool_runner?tool_id=upload1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:6.0.2) Gecko/20100101 Firefox/6.0.2" Debug at: http://127.0.0.1:8080/_debug/view/1319007854 ----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 61099) Traceback (most recent call last): File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer. py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer. py", line 617, in __init__ self.handle() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServe r.py", line 329, in handle self.handle_one_request() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 427, in handle_one_request self.wsgi_execute() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 287, in wsgi_execute self.wsgi_start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.p y", line 202, in __call__ return app(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/xfo rwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/Users/amit/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/ deploy/config.py", line 164, in __call__ app_iter = self.application(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/tra nslogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/e valexception/middleware.py", line 226, in __call__ return self.respond(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/e valexception/middleware.py", line 399, in respond if self.xmlhttp_key in req.params: File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init __.py", line 900, in params params = self.str_params File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init __.py", line 892, in str_params return NestedMultiDict(self.str_GET, self.str_POST) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init __.py", line 818, in str_POST keep_blank_values=True) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 508, in __init__ self.read_multi(environ, keep_blank_values, strict_parsing) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 632, in read_multi environ, keep_blank_values, strict_parsing) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 510, in __init__ self.read_single() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 647, in read_single self.read_lines() File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/base.py", line 253, in read_lines self.read_lines_to_outerboundary() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 697, in read_lines_to_outerboundary line = self.fp.readline(1<<16) File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 467, in readline data = self.file.readline(self.length - self._consumed) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/socket.py", line 409, in readline bline = buf.readline(size) OverflowError: long int too large to convert to int
Please help me to fix this, the python version is 2.6.6. Thank you.
Sincerely,
Amit,
Germline biology group Temasek Life Sciences Laboratory Singapore
-- Brad Langhorst Postdoctoral Fellow New England Biolabs langhorst@neb.com
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participants (5)
-
Amit Anand -
Brad Langhorst -
Nate Coraor -
Ross -
Todd Oakley