[galaxy-dev] Problem with executing newly installed tools (via admin)
Hi,
I have installed the Picard tools using the Tool-shed functionality in
the admin tools.
The tools and requisites have been correctly installed and run correctly.
The insert statement to the event table fails however. I get the
following error on screen:
|OperationalError: (OperationalError) (1241, 'Operand should contain 1
column(s)') 'INSERT INTO event (create_time, update_time, history_id,
user_id, message, session_id, tool_id) VALUES (%s, %s, %s, %s, %s, %s,
%s)' (datetime.datetime(2014, 4, 2, 9, 32, 47, 823142),
datetime.datetime(2014, 4, 2, 9, 32, 47, 823170), 35L, 4L, Tool params:
{'histWidth': u'0', 'deviations': u'10.0', 'malevel': u'ALL_READS',
'input_file': u'5266', 'out_prefix': u'Insertion size metrics',
'refresh': u'refresh', 'minPct': u'0.05', 'tool_state':
u'800254cf01316164663833323133363237333739303833323639353065346362343762393730383966363664313a37623232363836393733373435373639363437343638323233613230323235633232333035633232323232633230323236343635373636393631373436393666366537333232336132303232356332323331333032653330356332323232326332303232363936653730373537343566363636393663363532323361323032323335333233363336323232633230323235663566373036313637363535663566323233613230333032633230323235663566373236353732373536653566373236353664363137303566366136663632356636393634356635663232336132303665373536633663326332303232366436313663363537363635366332323361323032323563323234313463346335663532343534313434353335633232323232633230323236663735373435663730373236353636363937383232336132303232356332323439366537333635373237343639366636653230373336393761363532303664363537343,
1468L,
[u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0',
u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0'])
|The problem seems to be a duplicate entry of the tool_id
|[u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0',
u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0']
|In the shed_tool_conf.xml the tools are generated as follows
tool
file=toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardInsertSize.xml
guid=toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0
If I change this guid to something less complicated like
tool
file=toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardInsertSize.xml
guid=testPicard
and restart galaxy it works ...
for all tools (so not only the one that I've changed).
Does anyone have an idea as to why this is ?
kind regards,
Nicolas
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool
Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009). Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) ?xml version=1.0? repositories description= repository toolshed=http://localhost:9009; name=string_occurrence owner=janakiram-t1 / /repositories I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wikihttps://wiki.galaxyproject.org/SimpleRepositoryDependencies Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] snpEff and FASTQ Summary Statistics errors
Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Can you give us the complete error message. The important part is missing. Here is the whole thing for the error: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/xiaofe I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for FASTQ Summary Statistics or CloundMap? Thanks a lot! From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Hi Xiaofei, To get the complete error message, can you click on the bug icon (left-most icon at the bottom of the expanded history item) of the error’d dataset and copy and paste from the page that loads in the middle pane? Thanks for using Galaxy, Dan On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei xfw...@ku.edu wrote: Can you give us the complete error message. The important part is missing. Here is the whole thing for the error: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/xiaofe I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for FASTQ Summary Statistics or CloundMap? Thanks a lot! From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Oh, yes, here it is: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in module if __name__ == __main__: main() File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 32, in main base_counts = aggregator.get_base_counts_for_column( i ) File /Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy_utils/sequence/fastq.py, line 397, in get_base_counts_for_column return self.nuc_index_base[ column ] IndexError: list index out of range From: Daniel Blankenberg [d...@bx.psu.edu] Sent: Wednesday, April 02, 2014 11:14 AM To: Wang, Xiaofei Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, To get the complete error message, can you click on the bug icon (left-most icon at the bottom of the expanded history item) of the error’d dataset and copy and paste from the page that loads in the middle pane? Thanks for using Galaxy, Dan On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei xfw...@ku.edu wrote: Can you give us the complete error message. The important part is missing. Here is the whole thing for the error: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/xiaofe I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for FASTQ Summary Statistics or CloundMap? Thanks a lot! From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy unhandled exception checking jobs error
Hi guys, I keep getting an error everytime I start up the galaxy server. I am guessing this has to do with a job that galaxy is trying to resume and cannot find. galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception checking active jobs Traceback (most recent call last): File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 366, in monitor self.check_watched_items() File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py, line 363, in check_watched_items ( failures, statuses ) = self.check_all_jobs() File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py, line 452, in check_all_jobs c = pbs.pbs_connect( pbs_server_name ) TypeError: in method 'pbs_connect', argument 1 of type 'char *' Because of this error I cannot get any other jobs to run either. They just sit queued on the cluster. Any ideas? Thanks___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy unhandled exception checking jobs error
This looks very to similar to an issue discussed here: http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-unicode-tt4663616.html. The default branch of Galaxy contains changeset that should address this issue - https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0. Hope this helps. -John On Wed, Apr 2, 2014 at 11:35 AM, Ravi Alla ravi.a...@berkeley.edu wrote: Hi guys, I keep getting an error everytime I start up the galaxy server. I am guessing this has to do with a job that galaxy is trying to resume and cannot find. galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception checking active jobs Traceback (most recent call last): File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 366, in monitor self.check_watched_items() File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py, line 363, in check_watched_items ( failures, statuses ) = self.check_all_jobs() File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py, line 452, in check_all_jobs c = pbs.pbs_connect( pbs_server_name ) TypeError: in method 'pbs_connect', argument 1 of type 'char *' Because of this error I cannot get any other jobs to run either. They just sit queued on the cluster. Any ideas? Thanks ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Problems submitting using PBS Pro 12.1
Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled exception calling queue_job Traceback (most recent call last): File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 62, in run_next method(arg) File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 151, in queue_job external_job_id = self.ds.runJob(jt) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py, line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py, line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py, line 90, in error_check raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value If I do qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/249/galaxy_249.sh however the qsub returns 12345.myserver and the corresponding qstat | grep -i galaxy 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq Is the above error message perhaps related with a) PBS 12.1 b) drmaa-0.7-py2.6.egg I am trying to compile pbs-drmaa-1.0.17 but there are problems ... any advice ? any alternative ? Thanks luca ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy unhandled exception checking jobs error
John, Thanks for this. I am new to managing galaxy, but how do I go about updating my galaxy to reflect these changes? I found directions on https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date about pulling changes from the bitbucket repository. Does this preserve my previous galaxy settings? Do I have to back up before I do this? I spent considerable time to get galaxy to work on the cluster and don't want to ruin it. Thank you Ravi On Apr 2, 2014, at 9:58 AM, John Chilton jmchil...@gmail.com wrote: This looks very to similar to an issue discussed here: http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-unicode-tt4663616.html. The default branch of Galaxy contains changeset that should address this issue - https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0. Hope this helps. -John On Wed, Apr 2, 2014 at 11:35 AM, Ravi Alla ravi.a...@berkeley.edu wrote: Hi guys, I keep getting an error everytime I start up the galaxy server. I am guessing this has to do with a job that galaxy is trying to resume and cannot find. galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception checking active jobs Traceback (most recent call last): File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 366, in monitor self.check_watched_items() File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py, line 363, in check_watched_items ( failures, statuses ) = self.check_all_jobs() File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py, line 452, in check_all_jobs c = pbs.pbs_connect( pbs_server_name ) TypeError: in method 'pbs_connect', argument 1 of type 'char *' Because of this error I cannot get any other jobs to run either. They just sit queued on the cluster. Any ideas? Thanks ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Yes, it is figured, when I changed the java version to 1.7. Thank you so much! But, I got another error for snpEff. java.lang.RuntimeException: Property: 'dm5.30.genome' not found at ca.mcgill.mcb.pcingola.interval.Genome.init(Genome.java:92) at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481) at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444) at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345) at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:96) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply. Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? ) param name=genomeVersion type=select label=Genome option value=hg37Human (hg37)option option value=mm37.61Mouse (mm37.61)option param From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Hi, that means that the snpeff annotation is missing. You can install it with the snpeff datamanager under your Admin panel. Have a look at the wiki page about data-manager and the snpeff wrapper documentation. You do not need to edit xml files. If so that is an bug in the wrapper and we should fix it :) Cheers, Bjoern Am 02.04.2014 19:34, schrieb Wang, Xiaofei: When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Yes, it is figured, when I changed the java version to 1.7. Thank you so much! But, I got another error for snpEff. java.lang.RuntimeException: Property: 'dm5.30.genome' not found at ca.mcgill.mcb.pcingola.interval.Genome.init(Genome.java:92) at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481) at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444) at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345) at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:96) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply. Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? ) param name=genomeVersion type=select label=Genome option value=hg37Human (hg37)option option value=mm37.61Mouse (mm37.61)option param From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problems submitting using PBS Pro 12.1
Hi Luca, Are you passing any params to the runner for inclusion as PBS submit parameters (param id=nativeSpecification in job_conf.xml)? --nate On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo lucato...@gmail.com wrote: Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled exception calling queue_job Traceback (most recent call last): File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 62, in run_next method(arg) File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 151, in queue_job external_job_id = self.ds.runJob(jt) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py, line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py, line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py, line 90, in error_check raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value If I do qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/249/galaxy_249.sh however the qsub returns 12345.myserver and the corresponding qstat | grep -i galaxy 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq Is the above error message perhaps related with a) PBS 12.1 b) drmaa-0.7-py2.6.egg I am trying to compile pbs-drmaa-1.0.17 but there are problems ... any advice ? any alternative ? Thanks luca ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problems submitting using PBS Pro 12.1
Thanks Björn. Luca, what version of pbs-drmaa are you using now? On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Nate, I tried to help Luca today, but I failed totally ... He is not using param id=nativeSpecification at all. Or put it that way if he isn't using it, he gets the same error. Cheers, Bjoern Am 02.04.2014 20:34, schrieb Nate Coraor: Hi Luca, Are you passing any params to the runner for inclusion as PBS submit parameters (param id=nativeSpecification in job_conf.xml)? --nate On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo lucato...@gmail.com wrote: Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled exception calling queue_job Traceback (most recent call last): File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 62, in run_next method(arg) File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 151, in queue_job external_job_id = self.ds.runJob(jt) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py, line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py, line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py, line 90, in error_check raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value If I do qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_ directory/000/249/galaxy_249.sh however the qsub returns 12345.myserver and the corresponding qstat | grep -i galaxy 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq Is the above error message perhaps related with a) PBS 12.1 b) drmaa-0.7-py2.6.egg I am trying to compile pbs-drmaa-1.0.17 but there are problems ... any advice ? any alternative ? Thanks luca ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problems submitting using PBS Pro 12.1
Dear Nate, and Björn thankyou for your help. As Björn said, indeed i get always the same error message regardless if I use the id=nativeSpecification or not. How can one figure out the version of pbs-drmaa that the system is using ? It would be really useful to have a step-by-step tutorial on how to configure this part of the system. I've spent already several days trying to get it working and it constantly fails. Unfortunately I also got serious problem trying to compile the pbs-drmaa-1.0.17 as mentioned in my posting. What can I try next ? I was thinking to modify /jobs/runners/drmaa.py adding more logging ... Thankyou for your advice ! 2014-04-02 20:43 GMT+02:00 Nate Coraor n...@bx.psu.edu: Thanks Björn. Luca, what version of pbs-drmaa are you using now? On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Nate, I tried to help Luca today, but I failed totally ... He is not using param id=nativeSpecification at all. Or put it that way if he isn't using it, he gets the same error. Cheers, Bjoern Am 02.04.2014 20:34, schrieb Nate Coraor: Hi Luca, Are you passing any params to the runner for inclusion as PBS submit parameters (param id=nativeSpecification in job_conf.xml)? --nate On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo lucato...@gmail.com wrote: Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled exception calling queue_job Traceback (most recent call last): File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__. py, line 62, in run_next method(arg) File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 151, in queue_job external_job_id = self.ds.runJob(jt) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py, line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py, line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py, line 90, in error_check raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value If I do qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_ directory/000/249/galaxy_249.sh however the qsub returns 12345.myserver and the corresponding qstat | grep -i galaxy 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq Is the above error message perhaps related with a) PBS 12.1 b) drmaa-0.7-py2.6.egg I am trying to compile pbs-drmaa-1.0.17 but there are problems ... any advice ? any alternative ? Thanks luca ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problems submitting using PBS Pro 12.1
Hi Luca, We generally have not provided detailed documentation on this portion since it's not really within the scope of Galaxy itself, and documentation would be likely to become out of date as these external libraries (like pbs-drmaa) are updated, and cluster configurations are very site-specific. We are happy to help, though. It might be useful to add some debugging about the generated jobTemplate in drmaa.py to see what params are being set. The value you've set as the path to the drmaa library ($DRMAA_LIBRARY_PATH) might provide some insight on the version, or the output of: strings $DRMAA_LIBRARY_PATH | grep 1\.0 What are the problems you're experiencing compiling pbs-drmaa 1.0.17? --nate On Wed, Apr 2, 2014 at 2:52 PM, Luca Toldo lucato...@gmail.com wrote: Dear Nate, and Björn thankyou for your help. As Björn said, indeed i get always the same error message regardless if I use the id=nativeSpecification or not. How can one figure out the version of pbs-drmaa that the system is using ? It would be really useful to have a step-by-step tutorial on how to configure this part of the system. I've spent already several days trying to get it working and it constantly fails. Unfortunately I also got serious problem trying to compile the pbs-drmaa-1.0.17 as mentioned in my posting. What can I try next ? I was thinking to modify /jobs/runners/drmaa.py adding more logging ... Thankyou for your advice ! 2014-04-02 20:43 GMT+02:00 Nate Coraor n...@bx.psu.edu: Thanks Björn. Luca, what version of pbs-drmaa are you using now? On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Nate, I tried to help Luca today, but I failed totally ... He is not using param id=nativeSpecification at all. Or put it that way if he isn't using it, he gets the same error. Cheers, Bjoern Am 02.04.2014 20:34, schrieb Nate Coraor: Hi Luca, Are you passing any params to the runner for inclusion as PBS submit parameters (param id=nativeSpecification in job_conf.xml)? --nate On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo lucato...@gmail.com wrote: Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled exception calling queue_job Traceback (most recent call last): File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__. py, line 62, in run_next method(arg) File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 151, in queue_job external_job_id = self.ds.runJob(jt) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py, line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py, line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py, line 90, in error_check raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value If I do qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_ directory/000/249/galaxy_249.sh however the qsub returns 12345.myserver and the corresponding qstat | grep -i galaxy 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq Is the above error message perhaps related with a) PBS 12.1 b) drmaa-0.7-py2.6.egg I am trying to compile pbs-drmaa-1.0.17 but there are problems ... any advice ? any alternative ? Thanks luca ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problems submitting using PBS Pro 12.1
Thankyou Nate for your prompt and detailed support. Unfortunately I am on a different time zone and I do not have access now to the system. Thankyou for the suggestion you provided me to do the debugging. I will carry that out in about 12 hours from now and let you know. Thankyou again Luca p.s. although I do agree that the problems I am facing are not as challenging as the other aspects of galaxy, I am convinced that a detailed explanation on the methodology to use for debugging this kind of low level aspects will be extremely appreciated by many :-) 2014-04-02 21:05 GMT+02:00 Nate Coraor n...@bx.psu.edu: Hi Luca, We generally have not provided detailed documentation on this portion since it's not really within the scope of Galaxy itself, and documentation would be likely to become out of date as these external libraries (like pbs-drmaa) are updated, and cluster configurations are very site-specific. We are happy to help, though. It might be useful to add some debugging about the generated jobTemplate in drmaa.py to see what params are being set. The value you've set as the path to the drmaa library ($DRMAA_LIBRARY_PATH) might provide some insight on the version, or the output of: strings $DRMAA_LIBRARY_PATH | grep 1\.0 What are the problems you're experiencing compiling pbs-drmaa 1.0.17? --nate On Wed, Apr 2, 2014 at 2:52 PM, Luca Toldo lucato...@gmail.com wrote: Dear Nate, and Björn thankyou for your help. As Björn said, indeed i get always the same error message regardless if I use the id=nativeSpecification or not. How can one figure out the version of pbs-drmaa that the system is using ? It would be really useful to have a step-by-step tutorial on how to configure this part of the system. I've spent already several days trying to get it working and it constantly fails. Unfortunately I also got serious problem trying to compile the pbs-drmaa-1.0.17 as mentioned in my posting. What can I try next ? I was thinking to modify /jobs/runners/drmaa.py adding more logging ... Thankyou for your advice ! 2014-04-02 20:43 GMT+02:00 Nate Coraor n...@bx.psu.edu: Thanks Björn. Luca, what version of pbs-drmaa are you using now? On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Nate, I tried to help Luca today, but I failed totally ... He is not using param id=nativeSpecification at all. Or put it that way if he isn't using it, he gets the same error. Cheers, Bjoern Am 02.04.2014 20:34, schrieb Nate Coraor: Hi Luca, Are you passing any params to the runner for inclusion as PBS submit parameters (param id=nativeSpecification in job_conf.xml)? --nate On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo lucato...@gmail.com wrote: Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled exception calling queue_job Traceback (most recent call last): File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__. py, line 62, in run_next method(arg) File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 151, in queue_job external_job_id = self.ds.runJob(jt) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/ drmaa/__init__.py, line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py, line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py, line 90, in error_check raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value If I do qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_ directory/000/249/galaxy_249.sh however the qsub returns 12345.myserver and the corresponding qstat | grep -i galaxy 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq Is the above error message perhaps related with a) PBS 12.1 b) drmaa-0.7-py2.6.egg I am trying to compile pbs-drmaa-1.0.17 but there are problems ... any advice ? any alternative ? Thanks luca ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the
Re: [galaxy-dev] Problems submitting using PBS Pro 12.1
Hi Nate, I tried to help Luca today, but I failed totally ... He is not using param id=nativeSpecification at all. Or put it that way if he isn't using it, he gets the same error. Cheers, Bjoern Am 02.04.2014 20:34, schrieb Nate Coraor: Hi Luca, Are you passing any params to the runner for inclusion as PBS submit parameters (param id=nativeSpecification in job_conf.xml)? --nate On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo lucato...@gmail.com wrote: Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled exception calling queue_job Traceback (most recent call last): File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 62, in run_next method(arg) File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 151, in queue_job external_job_id = self.ds.runJob(jt) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py, line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py, line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File /opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py, line 90, in error_check raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value If I do qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/249/galaxy_249.sh however the qsub returns 12345.myserver and the corresponding qstat | grep -i galaxy 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq Is the above error message perhaps related with a) PBS 12.1 b) drmaa-0.7-py2.6.egg I am trying to compile pbs-drmaa-1.0.17 but there are problems ... any advice ? any alternative ? Thanks luca ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Dear Bjoern, As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is: Admin Data Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome, I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.) Next, I clicked on SnpEff Databases Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty. Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel? I really appreciate for your help, and thank you so much for your patience! Best, Xiaofei Data Manager Choose your data managing option from below. * Access data managers - get data, build indexes, etc * SnpEff Databaseshttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4 - Download a new database * BWA indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by manager * SnpEff Databaseshttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1 - Download a new database * BWA indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by Tool Data Table * snpeff_databaseshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases * snpeff_genomedbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb * snpeff_regulationdbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb * snpeff_annotationshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations * bwa_indexeshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes * bwa_indexes_colorhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color * all_fastahttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta * * * * * From: Björn Grüning [bjoern.gruen...@gmail.com] * Sent: Wednesday, April 02, 2014 12:55 PM * To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu * Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors * * Hi, * * that means that the snpeff annotation is missing. You can install it * with the snpeff datamanager under your Admin panel. Have a look at the * wiki page about data-manager and the snpeff wrapper documentation. * You do not need to edit xml files. If so that is an bug in the wrapper * and we should fix it :) * * Cheers, * Bjoern * * Am 02.04.2014 19:34, schrieb Wang, Xiaofei: *When I used SnpEff in local galaxy instance, I got an error: *Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j * * * * *Which Java version do you use. Please make sure you are running Java 1.7. * * * * *Yes, it is figured, when I changed the
Re: [galaxy-dev] ENA SRA data retrieval with Cloudman
Hey Mo, Sorry for the super delayed response here. I can't find a decision to remove it documented anywhere, so my guess is that this tool was unintentionally removed when we last updated the volume. It's actually still available on disk, though, and can be re-enabled in your tool_conf.xml by adding the following back to your Get Data section: tool file=data_source/ebi_sra.xml / -Dannon On Mon, Mar 10, 2014 at 11:53 AM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hi Cloudman Development Team, I noticed on the most recent Cloudman release (revision 11219:5c789ab4144ahttp://bitbucket.org/galaxy/galaxy-dist/changesets/5c789ab4144a) that there is no option to Get Data from the ENA SRA. We've found that retrieving large (fastq) data sets from public databases into Galaxy/Cloudman is the most convenient from the ENA SRA option in the Get Data menu. Will this option be coming back, or is the ENA SRA option permanently removed? Cheers, Mo Heydarian ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Hi Xiaofei, Dear Bjoern, As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is: Admin Data Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome, I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.) Next, I clicked on SnpEff Databases Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty. After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. Hope that will help! Bjoern Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel? I really appreciate for your help, and thank you so much for your patience! Best, Xiaofei Data Manager Choose your data managing option from below. * Access data managers - get data, build indexes, etc * SnpEff Databaseshttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4 - Download a new database * BWA indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by manager * SnpEff Databaseshttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1 - Download a new database * BWA indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by Tool Data Table * snpeff_databaseshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases * snpeff_genomedbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb * snpeff_regulationdbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb * snpeff_annotationshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations * bwa_indexeshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes * bwa_indexes_colorhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color * all_fastahttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta * * * * * From: Björn Grüning [bjoern.gruen...@gmail.com] * Sent: Wednesday, April 02, 2014 12:55 PM * To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu * Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors * * Hi, * * that means that the snpeff annotation is missing. You can install it * with the snpeff datamanager under your Admin panel. Have a look at the * wiki page about data-manager and the snpeff wrapper documentation. * You do not need to edit xml files. If so that is an bug in the wrapper * and we should fix it :) * * Cheers, * Bjoern * * Am 02.04.2014 19:34, schrieb Wang, Xiaofei: *When I used SnpEff in local galaxy instance, I got an error: *Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at
Re: [galaxy-dev] ENA SRA data retrieval with Cloudman
Hi Dannon, Thanks for this information. Will the ENA SRA button be enabled on the next update of Cloudman? Is there a protocol (or help page) available for how to re-enable tools in the 'tool_conf.xml'? One of the great things about Galaxy Cloudman is that someone who doesn't know programming (myself and many other biologists and clinicians) can seamlessly use the platform. Unfortunately, when trivial issues arise where the solution is to insert a line or two of code in the universe of Galaxy Cloudman people like me are stymied and really don't even know where to start. I know it requires work at some level, but a tutorial on how to find your 'tool_conf.xml' (or dummies guide to quick Cloudman fixes) would likely be helpful to many end users (including myself). Thanks again, Dannon! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Wed, Apr 2, 2014 at 5:03 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Mo, Sorry for the super delayed response here. I can't find a decision to remove it documented anywhere, so my guess is that this tool was unintentionally removed when we last updated the volume. It's actually still available on disk, though, and can be re-enabled in your tool_conf.xml by adding the following back to your Get Data section: tool file=data_source/ebi_sra.xml / -Dannon On Mon, Mar 10, 2014 at 11:53 AM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hi Cloudman Development Team, I noticed on the most recent Cloudman release (revision 11219:5c789ab4144ahttp://bitbucket.org/galaxy/galaxy-dist/changesets/5c789ab4144a) that there is no option to Get Data from the ENA SRA. We've found that retrieving large (fastq) data sets from public databases into Galaxy/Cloudman is the most convenient from the ENA SRA option in the Get Data menu. Will this option be coming back, or is the ENA SRA option permanently removed? Cheers, Mo Heydarian ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ENA SRA data retrieval with Cloudman
On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hi Dannon, Thanks for this information. Will the ENA SRA button be enabled on the next update of Cloudman? I'll check to make sure there wasn't a good reason to remove it (couldn't find one in my first pass, and it's available on main, so it should be in the cloud), but yes. Is there a protocol (or help page) available for how to re-enable tools in the 'tool_conf.xml'? With everything headed to the toolshed, hopefully this is a thing of the past very soon. The only documentation I found on the wiki is here: https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial In short, you'll need to: 1) ssh to your cloud galaxy instance 2) navigate to /mnt/galaxy/galaxy-app 3) open tool_conf.xml in your favorite editor, and add the line below, exactly, in the Get Data section (the first one, begins on line 3): tool file=data_source/ebi_sra.xml / 4) Close down ssh, 5) In a web browser, go to the cloud admin panel and click restart for the Galaxy service. One of the great things about Galaxy Cloudman is that someone who doesn't know programming (myself and many other biologists and clinicians) can seamlessly use the platform. Unfortunately, when trivial issues arise where the solution is to insert a line or two of code in the universe of Galaxy Cloudman people like me are stymied and really don't even know where to start. I know it requires work at some level, but a tutorial on how to find your 'tool_conf.xml' (or dummies guide to quick Cloudman fixes) would likely be helpful to many end users (including myself). We definitely do try to make it as ready-to-go out of the box as possible, but that's a great idea. I'll try to document this better. Thanks again, Dannon! Anytime, thanks for your patience and for using Galaxy/Cloudman! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] label element
Hi all, It seems that the recent release does not support label element anymore, i.e. no sub-section with the section title displayed in grey. Is there any alternative way to organize the tool under one big section? Best regards! Jun ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] label element
This was kindly fixed by Nicola Soranzo (https://bitbucket.org/galaxy/galaxy-central/pull-request/346/fix-for-https-trellocom-c-8npgym3u-1430/diff) and merged into the latest stable branch of galaxy-central. There are ongoing discussions internally about how to best get these between release fixes out but for now there is are some tips in this e-mail (http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-tp4663719p4663831.html) about upgrading to the latest stable branch. -John On Wed, Apr 2, 2014 at 6:55 PM, Jun Fan j@qmul.ac.uk wrote: Hi all, It seems that the recent release does not support label element anymore, i.e. no sub-section with the section title displayed in grey. Is there any alternative way to organize the tool under one big section? Best regards! Jun ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ENA SRA data retrieval with Cloudman
Hi Dannon, Thanks so much, your protocol was extremely helpful! Thanks for looking into ENA SRA. In our experience, the ENA SRA is the easiest and most reliable way of importing public NGS data into Galaxy. The ENA SRA has an actual button to click that will import your data set of choice into Galaxy, while retaining the data set ID. It is much more straight forward (and reliable) than using any of the NCBI databases. Thanks for your help with all of this, Dannon! Have a great night. Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Wed, Apr 2, 2014 at 6:21 PM, Dannon Baker dannon.ba...@gmail.com wrote: On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hi Dannon, Thanks for this information. Will the ENA SRA button be enabled on the next update of Cloudman? I'll check to make sure there wasn't a good reason to remove it (couldn't find one in my first pass, and it's available on main, so it should be in the cloud), but yes. Is there a protocol (or help page) available for how to re-enable tools in the 'tool_conf.xml'? With everything headed to the toolshed, hopefully this is a thing of the past very soon. The only documentation I found on the wiki is here: https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial In short, you'll need to: 1) ssh to your cloud galaxy instance 2) navigate to /mnt/galaxy/galaxy-app 3) open tool_conf.xml in your favorite editor, and add the line below, exactly, in the Get Data section (the first one, begins on line 3): tool file=data_source/ebi_sra.xml / 4) Close down ssh, 5) In a web browser, go to the cloud admin panel and click restart for the Galaxy service. One of the great things about Galaxy Cloudman is that someone who doesn't know programming (myself and many other biologists and clinicians) can seamlessly use the platform. Unfortunately, when trivial issues arise where the solution is to insert a line or two of code in the universe of Galaxy Cloudman people like me are stymied and really don't even know where to start. I know it requires work at some level, but a tutorial on how to find your 'tool_conf.xml' (or dummies guide to quick Cloudman fixes) would likely be helpful to many end users (including myself). We definitely do try to make it as ready-to-go out of the box as possible, but that's a great idea. I'll try to document this better. Thanks again, Dannon! Anytime, thanks for your patience and for using Galaxy/Cloudman! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. You mean SnpEff Download under Data Manager? But, there is no response when I click on it. Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response. But, when I go to Admin Data Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why? When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time? Thank you so much! Best, Xiaofei From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 4:17 PM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear Bjoern, As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is: Admin Data Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome, I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.) Next, I clicked on SnpEff Databases Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty. After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. Hope that will help! Bjoern Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel? I really appreciate for your help, and thank you so much for your patience! Best, Xiaofei Data Manager Choose your data managing option from below. * Access data managers - get data, build indexes, etc * SnpEff Databaseshttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4 - Download a new database * BWA indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by manager * SnpEff Databaseshttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1 - Download a new database * BWA indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by Tool Data Table * snpeff_databaseshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases * snpeff_genomedbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb * snpeff_regulationdbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb * snpeff_annotationshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations * bwa_indexeshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes * bwa_indexes_colorhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color
Re: [galaxy-dev] Galaxy unhandled exception checking jobs error
This change is very small and was not committed to the stable branch of galaxy-central so I would just modify the your Galaxy's copy of the pbs runner file directly until the next release: % wget https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0/raw -O /tmp/pbs.patch % hg import --no-commit /tmp/pbs.patch When you go to update Galaxy next it will probably warn you that this file has been modified - at that time you can just run the following command to cleanup your Galaxy instance: % hg revert lib/galaxy/jobs/runners/pbs.py Hope this helps. The Galaxy team is actively discussing alternative ways to distribute fixes between large releases - hopefully I can stop e-mailing out random mercurial commands at some point :). Back to your broader question however, the Galaxy release and update process is such that you really shouldn't lose your configuration as a result of updating Galaxy. Galaxy distributes sample tool_conf.xml, universe_wsgi.ini, etc... files but the actual configuration files themselves are not tracked in the Galaxy central repositories so these files should be unaffected by updates. Deviations from this ideal should be rare and I believe will be spelled out the dev news for releases as they occur. Hope this helps. -John On Wed, Apr 2, 2014 at 12:27 PM, Ravi Alla ravi.a...@berkeley.edu wrote: John, Thanks for this. I am new to managing galaxy, but how do I go about updating my galaxy to reflect these changes? I found directions on https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date about pulling changes from the bitbucket repository. Does this preserve my previous galaxy settings? Do I have to back up before I do this? I spent considerable time to get galaxy to work on the cluster and don't want to ruin it. Thank you Ravi On Apr 2, 2014, at 9:58 AM, John Chilton jmchil...@gmail.com wrote: This looks very to similar to an issue discussed here: http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-unicode-tt4663616.html. The default branch of Galaxy contains changeset that should address this issue - https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0. Hope this helps. -John On Wed, Apr 2, 2014 at 11:35 AM, Ravi Alla ravi.a...@berkeley.edu wrote: Hi guys, I keep getting an error everytime I start up the galaxy server. I am guessing this has to do with a job that galaxy is trying to resume and cannot find. galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception checking active jobs Traceback (most recent call last): File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 366, in monitor self.check_watched_items() File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py, line 363, in check_watched_items ( failures, statuses ) = self.check_all_jobs() File /srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py, line 452, in check_all_jobs c = pbs.pbs_connect( pbs_server_name ) TypeError: in method 'pbs_connect', argument 1 of type 'char *' Because of this error I cannot get any other jobs to run either. They just sit queued on the cluster. Any ideas? Thanks ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
