[galaxy-dev] GATK2 is unable to find reference genomes
Dear All, I installed gatk2 from tool_shed, and see below for my gatk2_picard_index.loc Anyone can tell me what the mistake is? Old gatk can use this file to find all reference genomes, but gatk2 cannot. Fenglou gatk2_picard_index.loc Description: Binary data ___ 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] GATK2 is unable to find reference genomes
Thanks, edited the wrong file. Fenglou On 26 February 2014 16:40, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Fenglou, which file have you edited? Under tool-data or tool-data/ toolshed.g2.bx.psu.edu/repos/iuc/gatk2/340633249b3d/gatk2_picard_index.loc? Cheers, Bjoern Am 26.02.2014 22:37, schrieb Fenglou Mao: Dear All, I installed gatk2 from tool_shed, and see below for my gatk2_picard_index.loc Anyone can tell me what the mistake is? Old gatk can use this file to find all reference genomes, but gatk2 cannot. Fenglou ___ 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] ImportError: No module named json
I just upgraded our galaxy server to the latest version, and I got this error in many of the tools: Traceback (most recent call last): File ./scripts/set_metadata.py, line 14, in ? import json ImportError: No module named json And a find command below give many a few json eggs, please help. Why Galaxy is not pickung up this json module? (galaxy-env)[galaxy@galaxy galaxy-dist]$ find eggs -name *json* eggs/psycopg2-2.5.1_9.2.4_static-py2.6-linux-x86_64-ucs4.egg/psycopg2/_json.py eggs/psycopg2-2.5.1_9.2.4_static-py2.6-linux-x86_64-ucs4.egg/psycopg2/_json.pyc eggs/simplejson-2.1.1-py2.4-linux-x86_64-ucs4.egg eggs/raven-3.1.8-py2.6.egg/raven/utils/json.py eggs/raven-3.1.8-py2.6.egg/raven/utils/json.pyc eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg eggs/boto-2.5.2-py2.6.egg/boto/jsonresponse.py eggs/boto-2.5.2-py2.6.egg/boto/jsonresponse.pyc eggs/boto-2.5.2-py2.6.egg/boto/sqs/jsonmessage.pyc eggs/boto-2.5.2-py2.6.egg/boto/sqs/jsonmessage.py ___ 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] ImportError: No module named json
It is a little complicated here, The Galaxy server itself is running CentOS 6 with python 2.6, but the cluster nodes are running CentOS 5 with python 2.4. Mose jobs are running in the cluster nodes. My questions is: if there is a json module in galaxy-dist/eggs, why Galaxy is not picking it up? If we can do this, then we don't need to upgrade the cluster nodes, which is very difficult here. Fenglou On 20 February 2014 13:47, Dannon Baker dannon.ba...@gmail.com wrote: The json module is included in python's standard library since python 2.6, which is the minimum version of python Galaxy currently supports. Are you using a python version older than that? ___ 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] ImportError: No module named json
Thanks for the answer. I am talking to our sysadmin to upgrade cluster nodes from CentOS 5 to CentOS 6. Fenglou On Feb 20, 2014, at 2:18 PM, Dannon Baker dannon.ba...@gmail.com wrote: Got it. We dropped the simplejson egg during the last release (and any you find are holdovers from previous versions of galaxy) in favor of the stdlib module. The relevant module from your find would have been simplejson-2.1.1, and the rest are unrelated. If possible, I'd *really* recommend updating the python version on those nodes as future galaxy developments and tools may count on python 2.6+ (and not just for json, but syntax changes) being available. Other than that, for those affected tools, you may want to manually revert the changes in revision 11967:0c5e20558f6b and add simplejson back into your galaxy. That said, I'm working on adding the anyjson dependency that will allow json to fail through to any installed json library (whether stdlib, simplejson, etc), and that'll be available in galaxy-central reasonably soon. On Thu, Feb 20, 2014 at 2:51 PM, Fenglou Mao feng...@gmail.com wrote: It is a little complicated here, The Galaxy server itself is running CentOS 6 with python 2.6, but the cluster nodes are running CentOS 5 with python 2.4. Mose jobs are running in the cluster nodes. My questions is: if there is a json module in galaxy-dist/eggs, why Galaxy is not picking it up? If we can do this, then we don't need to upgrade the cluster nodes, which is very difficult here. Fenglou On 20 February 2014 13:47, Dannon Baker dannon.ba...@gmail.com wrote: The json module is included in python's standard library since python 2.6, which is the minimum version of python Galaxy currently supports. Are you using a python version older than that? ___ 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] ImportError: No module named json
Thanks, I will try this tomorrow. Fenglou On 20 February 2014 22:32, Nate Coraor n...@bx.psu.edu wrote: Hi Fenglou, In similar instances, I've simply compiled my own version of Python 2.7 and placed it in a cluster-wide filesystem, then used the environment_setup_file option in universe_wsgi.ini to ensure this version is used when jobs run. --nate On Thu, Feb 20, 2014 at 3:31 PM, Fenglou Mao feng...@gmail.com wrote: Thanks for the answer. I am talking to our sysadmin to upgrade cluster nodes from CentOS 5 to CentOS 6. Fenglou On Feb 20, 2014, at 2:18 PM, Dannon Baker dannon.ba...@gmail.com wrote: Got it. We dropped the simplejson egg during the last release (and any you find are holdovers from previous versions of galaxy) in favor of the stdlib module. The relevant module from your find would have been simplejson-2.1.1, and the rest are unrelated. If possible, I'd *really* recommend updating the python version on those nodes as future galaxy developments and tools may count on python 2.6+ (and not just for json, but syntax changes) being available. Other than that, for those affected tools, you may want to manually revert the changes in revision 11967:0c5e20558f6b and add simplejson back into your galaxy. That said, I'm working on adding the anyjson dependency that will allow json to fail through to any installed json library (whether stdlib, simplejson, etc), and that'll be available in galaxy-central reasonably soon. On Thu, Feb 20, 2014 at 2:51 PM, Fenglou Mao feng...@gmail.com wrote: It is a little complicated here, The Galaxy server itself is running CentOS 6 with python 2.6, but the cluster nodes are running CentOS 5 with python 2.4. Mose jobs are running in the cluster nodes. My questions is: if there is a json module in galaxy-dist/eggs, why Galaxy is not picking it up? If we can do this, then we don't need to upgrade the cluster nodes, which is very difficult here. Fenglou On 20 February 2014 13:47, Dannon Baker dannon.ba...@gmail.com wrote: The json module is included in python's standard library since python 2.6, which is the minimum version of python Galaxy currently supports. Are you using a python version older than that? ___ 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 server user activity
Dear All, We installed a galaxy server here locally, is there any way to generate a report of the user activity? Thanks, Fenglou ___ 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] Working with compressed files
Is Galaxy capable of working with compressed files such as *.fastq.gz? Thanks, Fenglou ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cannot Delete Permanently
Thanks a lot. One more question: once I Delete Permanently, it is marked as Delete Permanently, how do I remove this entry? Thanks, Fenglou On Dec 14, 2012, at 11:31 AM, Dannon Baker dannonba...@me.com wrote: Check the setting 'allow_user_dataset_purge' in your universe_wsgi.ini -- this is false by default to prevent errors, but changing that should allow users of your instance to purge datasets permanently. -Dannon On Dec 14, 2012, at 12:18 PM, Fenglou Mao feng...@gmail.com wrote: I installed a local galaxy server, did some calculation. Now I want to clean datasets for some space. I tried Delete Permanently on both datasets and histories, none of them worked. The datasets and histories will be marked as deleted, but it will not be really deleted even I am using Delete Permanently. They will not be really removed, and space are not released. Sometimes it will give me a message this feature is not enabled, sometimes it won't. Any one know how to enable Delete Permanently feature? Thanks, Fenglou ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Job is waiting to run
I have a local galaxy server, and I built a workflow, it got stuck in one step in the middle. The computer is a 64 cores server, and no other jobs running in this server. Any idea how to trouble shooting? Thanks, Fenglou ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] use multiple cores in BWA
That will be a pain since so many tools can use multiple cores, and if I edit tool XML file, what will happen is I update Galaxy? Will those edited XML be replaced by the files in Galaxy-dist? Thanks, Frank On Nov 30, 2012, at 3:01 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thursday, November 29, 2012, Fenglou Mao wrote: I can use aln -t n to ask BWA to use multiple cores if I run it in command line, in Galaxy, I did not find this option even i tried Full Parameter List, anyone know how to do it? (I installed a local Galaxy server with 64 cores, I want to use multiple cores to run my jobs.) Thanks, Frank The number of cores isn't exposed to the end user (although in some cases it might make sense to do so), but is rather down to the Galaxy administrators (in some cases by editing the defaults in the tool XML or wrapper scripts). There was a discussion about this on the list recently. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Which version of GATK work with Galaxy?
When I use an old version of GATK, it failed with a report -nt option was not supported, I guess old GATK does not support multi-threading. If I use a new version of GATK, it failed with a report -et NO_ET need a key file to work since new GATK force users to report usage unless we obtain a key file, but it seems no place for galaxy to specify the key file. Any help? Thanks, Frank ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] use multiple cores in BWA
I can use aln -t n to ask BWA to use multiple cores if I run it in command line, in Galaxy, I did not find this option even i tried Full Parameter List, anyone know how to do it? (I installed a local Galaxy server with 64 cores, I want to use multiple cores to run my jobs.) Thanks, Frank ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Direct access the fastq files stored in galaxy server local storage
We have a local galaxy server. I know I can get data by ftp, upload directly from browser, or by a URL. If I have some fastq files in the Galaxy server local storage, is it possible to let Galaxy use it directly? Thanks, Fenglou ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] markupsafe module confliction problem
Galaxy imported a library which already existed in the python system folder. See the error message below. Is that because RedHat 6 used a python-marksafe, but Galaxy installation program did not recognize it? Or Galaxy require a higher version of markupsafe module? /home/x/work/galaxy-dist/ lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib64/python2.6/site-packages/markupsafe/__init__.pyc, but /home/x/work/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() The system package is python-markupsafe-0.9.2-4.el6.x86_64 Galaxy has a newer version, it is MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg Any idea how to resolve this problem? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] markupsafe module conflicts
Galaxy imported a library which already existed in the python system folder. See the error message below. /home/x/work/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib64/python2.6/site-packages/markupsafe/__init__.pyc, but /home/x/work/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() The system package is python-markupsafe-0.9.2-4.el6.x86_64 Galaxy has a newer version, it is MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg Any idea how to resolve this problem? Thanks, Fenglou ___ 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/
