June 2011 - galaxy-dev - lists.galaxyproject.org

Fail to start galaxy
by colin 28 Jun '11

28 Jun '11

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

2 1

manage data libraries -menu upload files from filesystem paths not present
by colin 28 Jun '11

28 Jun '11

Hi, i all, my first post in the mailing list. I started one moth ago galaxy (at the conference) and the tool is really impressive. thx for it. I installed a local version of galaxy (http://ampere.ulb.ac.be) but i am having some trouble when uploading private data on it. Here is the procedure i followed: 1/ I got sra samples from ncbi: http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP000546 2/ i transformed these sra in fastq format using the sratoolkit https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFil… --> this provides me fastq files of 25Gb 3/ PROBLEMS: a/ IF I try to upload the data set using an URL in upload file (I created a controller here: http://insilico.ulb.ac.be/publicutilities/sendonthefly?url=/fs1-ampere/Geno…) then only 155Mb are uploaded to galaxy (and no error) b/ if i try to follow that method: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFil… and i try to get data from the server, the menu "upload files from filesystem paths" and "upload directory of files" are not present. ==> no way to access these files locally any hints for that? thx Colin

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Regarding output file name in download option
by shashi shekhar 28 Jun '11

28 Jun '11

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

1 0

How to set java heap size in Galaxy?
by liu bo 27 Jun '11

27 Jun '11

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

3 3

picard / srma index .loc
by Holger Klein 27 Jun '11

27 Jun '11

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/

2 2

Can't find Samtools binary
by Amirhossein Kiani 24 Jun '11

24 Jun '11

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

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Can't find Samtools binary
by Amirhossein Kiani 24 Jun '11

24 Jun '11

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

1 0

Regadind output file name
by shashi shekhar 24 Jun '11

24 Jun '11

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

1 0

bfast_wrapper.xml can't read data from tab-delimited bfast_indexes.loc?
by Peter Briggs 24 Jun '11

24 Jun '11

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

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change dataset label in exec_after_process()
by Leandro Hermida 24 Jun '11

24 Jun '11

Hi everyone, Is it possible to change dataset labels in exec_after_process() ? best, Leandro

2 3