Fail to start galaxy
by colin
Hi,
I launched a big job on my local galaxy server (for which I am admin). The job was to put local dir in the datalist.
It took too long and i wanted to stop it .... but how?? i failed to find a solution.
To stop the job i thought that stopping the galaxy running instance could make it. (AM I RIGHT?)
Unfortunately, i failed to restart galaxy. I have the following error:
galaxy.web.framework.base DEBUG 2011-06-28 14:51:49,031 Enabling 'tracks' controller, class: TracksController
galaxy.web.buildapp DEBUG 2011-06-28 14:51:49,046 Enabling 'httpexceptions' middleware
galaxy.web.buildapp DEBUG 2011-06-28 14:51:49,047 Enabling 'recursive' middleware
galaxy.web.buildapp DEBUG 2011-06-28 14:51:49,048 Enabling 'print debug' middleware
galaxy.web.buildapp DEBUG 2011-06-28 14:51:49,104 Enabling 'eval exceptions' middleware
galaxy.web.buildapp DEBUG 2011-06-28 14:51:49,104 Enabling 'trans logger' middleware
galaxy.web.buildapp DEBUG 2011-06-28 14:51:49,104 Enabling 'config' middleware
galaxy.web.buildapp DEBUG 2011-06-28 14:51:49,104 Enabling 'x-forwarded-host' middleware
Starting server in PID 12394.
Traceback (most recent call last):
File "./scripts/paster.py", line 34, in ?
command.run()
File "/opt/galaxy-central/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 84, in run
invoke(command, command_name, options, args[1:])
File "/opt/galaxy-central/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 123, in invoke
exit_code = runner.run(args)
File "/opt/galaxy-central/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 218, in run
result = self.command()
File "/opt/galaxy-central/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 303, in command
serve()
File "/opt/galaxy-central/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 287, in serve
server(app)
File "/opt/galaxy-central/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 150, in server_wrapper
wsgi_app, context.global_conf,
File "/opt/galaxy-central/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call
val = callable(*args, **kw)
File "/opt/galaxy-central/eggs/Paste-1.6-py2.4.egg/paste/httpserver.py", line 1314, in server_runner
serve(wsgi_app, **kwargs)
File "/opt/galaxy-central/eggs/Paste-1.6-py2.4.egg/paste/httpserver.py", line 1264, in serve
threadpool_options=threadpool_options)
File "/opt/galaxy-central/eggs/Paste-1.6-py2.4.egg/paste/httpserver.py", line 1114, in __init__
RequestHandlerClass, ssl_context)
File "/opt/galaxy-central/eggs/Paste-1.6-py2.4.egg/paste/httpserver.py", line 1094, in __init__
RequestHandlerClass, ssl_context)
File "/opt/galaxy-central/eggs/Paste-1.6-py2.4.egg/paste/httpserver.py", line 328, in __init__
HTTPServer.__init__(self, server_address, RequestHandlerClass)
File "/usr/lib64/python2.4/SocketServer.py", line 330, in __init__
self.server_bind()
File "/usr/lib64/python2.4/BaseHTTPServer.py", line 101, in server_bind
SocketServer.TCPServer.server_bind(self)
File "/usr/lib64/python2.4/SocketServer.py", line 341, in server_bind
self.socket.bind(self.server_address)
File "<string>", line 1, in bind
socket.error: (98, 'Address already in use')
galaxy.jobs INFO 2011-06-28 14:51:49,108 sending stop signal to worker thread
galaxy.jobs INFO 2011-06-28 14:51:49,109 job queue stopped
galaxy.jobs.runners.local INFO 2011-06-28 14:51:49,109 sending stop signal to worker threads
galaxy.jobs.runners.local INFO 2011-06-28 14:51:49,109 local job runner stopped
galaxy.jobs INFO 2011-06-28 14:51:49,109 sending stop signal to worker thread
galaxy.jobs INFO 2011-06-28 14:51:49,109 job stopper stopped
ANY IDEAS to restart galaxy ???
(i have a normal install with no custom stuffs).
thank you
Colin
11 years, 7 months
Regarding output file name in download option
by shashi shekhar
Hi All,
it's possible to give output file name in tool xml .while
downloading same output file name should come. i don't want to change the
extension .
Regards
shashi shekhar
11 years, 7 months
How to set java heap size in Galaxy?
by liu bo
Dear all,
I have added an application to Galaxy's Tools.
Now there occurs an error "java.lang.OutOfMemoryError: Java heap space".
Do you know how to set java heap size in Galaxy?
Thank you very much.
Best regards,
Bo
11 years, 7 months
picard / srma index .loc
by Holger Klein
Dear all,
I have a problem setting up the reference genomes for picard. They
simply do not show up. I used revision 8c11dd28a3cf of galaxy-dist and
just today switched to 720455407d1c, problem still exists.
My picard_index.loc contains the following lines:
hg19full hg19 hg19 Full
/home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.fa
hg18full hg18 hg18 Full
/home/galaxy/galaxy-data/index_files/hg18/picard_index/hg18.fa
mm9full mm9 mm9 Full
/home/galaxy/galaxy-data/index_files/mm9/picard_index/mm9.fa
The respective files are also there (fa and fa.fai are links to the
respective files in other dirs):
/home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.dict
/home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.fa
/home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.fa.fai
Now, using e.g. the SAM/BAM Alignment Summary Metrics module from
Picard, I can't choose a reference genome (no matter if it's "use
assigned ref genome" or "select a different built-in genome").
It doesn't seem to be a problem of formatting or file permissions - the
srma module needs the picard generated indices as well, the entries are
exactly the same and there it works.
Does anyone have a hint on how to get this working?
Regards,
Holger
--
Dr. Holger Klein
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
http://www.imb-mainz.de/
11 years, 7 months
Can't find Samtools binary
by Amirhossein Kiani
Hey there,
I'm not an advanced python developer and have an issue setting up my own galaxy server. I followed the steps on getgalaxy.org and have added ~./galaxy-pyhon to my path.
The server comes up and I can see stuff but when I try to import a BAM file I get the following error in the history:
Traceback (most recent call last):
File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 382, in
__main__()
File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 374, in __main__
add_file( dataset, registry, json_file, output_path )
File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 314, in add_file
if datatype.dataset_content_needs_grooming( output_path ):
File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming
version = self._get_samtools_version()
File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version
output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 594, in __init__
errread, errwrite)
File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 1097, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
I tried it on my RedHat server as well and get the same error:
Traceback (most recent call last):
File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 382, in
__main__()
File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 374, in __main__
add_file( dataset, registry, json_file, output_path )
File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 314, in add_file
if datatype.dataset_content_needs_grooming( output_path ):
File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming
version = self._get_samtools_version()
File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version
output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
File "/usr/lib64/python2.6/subprocess.py", line 633, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
It's worth mentioning that I was able to import a FASTA file.
I also checked the server logs and I see:
galaxy.tools DEBUG 2011-06-24 12:21:34,430 Loaded tool: t_test_two_samples 1.0.0
galaxy.tools DEBUG 2011-06-24 12:21:37,993 Loaded tool: sam_indel_filter 1.0.0
galaxy.tools DEBUG 2011-06-24 12:21:38,015 Loaded tool: indel_sam2interval 1.0.0
galaxy.tools DEBUG 2011-06-24 12:21:38,287 Loaded tool: sam_bw_filter 1.0.0
galaxy.tools DEBUG 2011-06-24 12:21:38,304 Loaded tool: sam2interval 1.0.1
galaxy.tools DEBUG 2011-06-24 12:21:38,319 Loaded tool: sam_to_bam 1.1.2
galaxy.tools DEBUG 2011-06-24 12:21:38,331 Loaded tool: bam_to_sam 1.0.3
galaxy.tools DEBUG 2011-06-24 12:21:38,343 Loaded tool: sam_merge 1.1.1
galaxy.tools DEBUG 2011-06-24 12:21:38,371 Loaded tool: sam_pileup 1.1.1
galaxy.tools DEBUG 2011-06-24 12:21:38,497 Loaded tool: samtools_flagstat 1.0.0
So I'm not sure what the issue is...
Many thanks in advance for your help!
Amir
11 years, 7 months
Can't find Samtools binary
by Amirhossein Kiani
Hey there,
I'm not an advanced python developer and have an issue setting up my own galaxy server. I followed the steps on getgalaxy.org and have added ~./galaxy-pyhon to my path.
The server comes up and I can see stuff but when I try to import a BAM file I get the following error in the history:
Traceback (most recent call last):
File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 382, in
__main__()
File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 374, in __main__
add_file( dataset, registry, json_file, output_path )
File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 314, in add_file
if datatype.dataset_content_needs_grooming( output_path ):
File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming
version = self._get_samtools_version()
File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version
output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 594, in __init__
errread, errwrite)
File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 1097, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
I tried it on my RedHat server as well and get the same error:
Traceback (most recent call last):
File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 382, in
__main__()
File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 374, in __main__
add_file( dataset, registry, json_file, output_path )
File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py", line 314, in add_file
if datatype.dataset_content_needs_grooming( output_path ):
File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming
version = self._get_samtools_version()
File "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version
output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
File "/usr/lib64/python2.6/subprocess.py", line 633, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
It's worth mentioning that I was able to import a FASTA file.
I also checked the server logs and I see:
galaxy.tools DEBUG 2011-06-24 12:21:34,430 Loaded tool: t_test_two_samples 1.0.0
galaxy.tools DEBUG 2011-06-24 12:21:37,993 Loaded tool: sam_indel_filter 1.0.0
galaxy.tools DEBUG 2011-06-24 12:21:38,015 Loaded tool: indel_sam2interval 1.0.0
galaxy.tools DEBUG 2011-06-24 12:21:38,287 Loaded tool: sam_bw_filter 1.0.0
galaxy.tools DEBUG 2011-06-24 12:21:38,304 Loaded tool: sam2interval 1.0.1
galaxy.tools DEBUG 2011-06-24 12:21:38,319 Loaded tool: sam_to_bam 1.1.2
galaxy.tools DEBUG 2011-06-24 12:21:38,331 Loaded tool: bam_to_sam 1.0.3
galaxy.tools DEBUG 2011-06-24 12:21:38,343 Loaded tool: sam_merge 1.1.1
galaxy.tools DEBUG 2011-06-24 12:21:38,371 Loaded tool: sam_pileup 1.1.1
galaxy.tools DEBUG 2011-06-24 12:21:38,497 Loaded tool: samtools_flagstat 1.0.0
So I'm not sure what the issue is...
Many thanks in advance for your help!
Amir
11 years, 7 months
Regadind output file name
by shashi shekhar
Hi All,
it's possible to give output file name in tool xml .while
downloading same output file name should come. i don't want to change the
extension .
Regards
shashi shekhar
11 years, 7 months
bfast_wrapper.xml can't read data from tab-delimited bfast_indexes.loc?
by Peter Briggs
Hello
I'm configuring a personal Galaxy instance with NGS tools (precursor to
setting up a local production version) and had some difficulty getting
the Bfast mapper (NGS Mapping -> Map with BFAST) to pick up the
reference genomes from the bfast_indexes.loc file.
I'm using a hg clone of galaxy-dist, and declared the reference indexes
in tab-delimited format, as indicated by the comments in
bfast_indexes.loc.sample. However the bfast_wrapper.xml seems to expect
some kind of comma-separated value? Anyway patching bfast_wrapper.xml
thusly fixed the problem for me:
--- bfast_wrapper.xml.orig 2011-06-23 09:56:54.008898765 +0100
+++ bfast_wrapper.xml 2011-06-23 10:01:30.048840835 +0100
@@ -62,8 +62,6 @@
<when value="indexed">
<param name="indices" type="select" label="Select a reference
genome index set">
<options from_data_table="bfast_indexes">
- <filter type="multiple_splitter" column="2" separator=","/>
- <filter type="param_value" column="2" ref="input1"
ref_attribute="extension"/>
<filter type="sort_by" column="3"/>
<validator type="no_options" message="No indexes are
available for the selected input dataset"/>
</options>
I can imagine that using a different format in bfast_indexes.loc should
also work, but tab-delimited seems more consistent with the other loc files.
Apologies if this is a known issue (I couldn't find anything in the GMOD
archive, and neither bfast_wrapper.xml or bfast_indexes.loc.sample seem
to have changed wrt this issue in Galaxy Central), or if I've missed
something really obvious.
Thanks for your help, best wishes
Peter
--
Peter Briggs peter.briggs(a)manchester.ac.uk
11 years, 7 months
