[galaxy-dev] Reorder Sam files
Hi there, we are running a local instant of galaxy and when running Picard tools Reorder Sam files I get following error message: An error occurred with this dataset: *## exit code=1; stdout= Error: Unable to access jarfile /ReorderSam.jar* Now, I thought that when installing picard-tools via the toolshed the dependency should be added automatically. I am really not sure why it looks for ReorderSam.jar in the top directory /. Any clues? Best wishes, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 ___ 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] Reorder Sam files
Hi Bjoern, thanks for your quick answer. My path to my picard is /home/galaxy/shed_tools/ toolshed.g2.bx.psu.edu/repos/devteam/picard/bf1c3f9f8282/picardunfortunately I cannot find a env.sh in there. The env.sh is in the dependency folder /home/galaxy/shed_tools/dependency/picard/1.56.0/devteam/package_picard_1_56_0/61e41d21cb6f The env.sh points to the right folder JAVA_JAR_PATH=/home/galaxy/shed_tools/dependency/picard/1.56.0/devteam/package_picard_1_56_0/61e41d21cb6f/jars; export JAVA_JAR_PATH Any suggestions? Alex On Mon, Mar 17, 2014 at 3:31 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Alex, can you check if all dependencies are installed. Afaik Galaxy sets an env variable to point to the actual jar file. That env variable is missing and the constructed path to your picard executable is looking like $SOME_NOT_SET_ENV_VAR/ReorderSam.jar. Hope that helps, Bjoern Am 17.03.2014 15:48, schrieb Alexander Kurze: Hi there, we are running a local instant of galaxy and when running Picard tools Reorder Sam files I get following error message: An error occurred with this dataset: *## exit code=1; stdout= Error: Unable to access jarfile /ReorderSam.jar* Now, I thought that when installing picard-tools via the toolshed the dependency should be added automatically. I am really not sure why it looks for ReorderSam.jar in the top directory /. Any clues? Best wishes, Alex ___ 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/ -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 ___ 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] Quota History not getting purged
Hi there, We have installed a local copy of galaxy but there seems to be a strange behavior with deleting data sets in the history panel. A few users complain that they have deleted their data sets (I can confirm that) but somehow the quota limit still doesn't show the appropriate freed space. Looking at their saved histories and adding up their data the quota limit should have changed. Any clues why this happens? I have also tried to run the clean up script but this didn't do anything on their quota limits. Best, Alex ___ 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] Quota History not getting purged
Perfect! This solved my problem. Alex On Fri, Mar 14, 2014 at 1:23 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Fri, Mar 14, 2014 at 12:28 PM, Alexander Kurze alexander.ku...@gmail.com wrote: Hi there, We have installed a local copy of galaxy but there seems to be a strange behavior with deleting data sets in the history panel. A few users complain that they have deleted their data sets (I can confirm that) but somehow the quota limit still doesn't show the appropriate freed space. Looking at their saved histories and adding up their data the quota limit should have changed. Any clues why this happens? I have also tried to run the clean up script but this didn't do anything on their quota limits. Best, Alex Does this help, or make no difference? $ cd scripts $ python set_user_disk_usage.py It will recalculate and update the user disk totals, and prints this to the terminal too. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] bowtie2 toolshed installation
Hi there, I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto the system via the toolshed. However it just doesn't work. I always get a Server Error message. I have checked if the dependencies are installed and they are all installed in the toolshed depenencies folders. However, the actual repos only contains the tool_dependency.xml. (eg galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml ) I thought that there should be a bowtie2.xml file in the repos of package_bowtie_2_1_0 but there isn't... Also, looking at the shed_tool_config.xml I cannot see any entry for bowtie2. Is there a way to add bowtie2 manually? Best wishes, Alex ___ 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] bowtie2 toolshed installation
Thanks for your quick answers. I actually have installed the dependencies first and then I have tried to add bowtie2 http://toolshed.g2.bx.psu.edu/view/devteam/bowtie2. But this is where the problem lies: I get following error message: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Meanwhile, I have downloaded the bowtie2.xml and added it to the ./tools/sr_mapping/ folder and added it to the tool_config.xml and it now works. Any clue why I get the error message? Is there something wrong with my server or do is it the repository? Cheers, Alex On Fri, Jan 31, 2014 at 1:18 PM, bjoern.gruen...@googlemail.com bjoern.gruen...@gmail.com wrote: Hi Alex, there is a difference in http://toolshed.g2.bx.psu.edu/view/devteam/package_bowtie2_2_1_0 and http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers The package_* is installing the binary for you and can be used by other programs as well. bowtie_wrappers contains the actual wrappers and is depending on package_*. To make it short. You need to install http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers and both packages will be installed and you should see your wrapper. Ciao, Bjoern 2014-01-31 Alexander Kurze alexander.ku...@bioch.ox.ac.uk: Hi there, I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto the system via the toolshed. However it just doesn't work. I always get a Server Error message. I have checked if the dependencies are installed and they are all installed in the toolshed depenencies folders. However, the actual repos only contains the tool_dependency.xml. (eg galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml ) I thought that there should be a bowtie2.xml file in the repos of package_bowtie_2_1_0 but there isn't... Also, looking at the shed_tool_config.xml I cannot see any entry for bowtie2. Is there a way to add bowtie2 manually? Best wishes, Alex ___ 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/ -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 ___ 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] bowtie2 toolshed installation
Here we go changeset: 8796:961ae35ba612 branch: stable tag: tip parent: 8794:1c7174911392 user:Nate Coraor n...@bx.psu.edu date:Fri Feb 08 11:23:04 2013 -0500 summary: Added tag release_2013.02.08 for changeset 1c7174911392 changeset: 8795:9fd7fe0c5712 parent: 8785:25bd9d387135 parent: 8794:1c7174911392 user:Nate Coraor n...@bx.psu.edu date:Fri Feb 08 11:22:54 2013 -0500 summary: merge from stable 961ae35ba612+ (stable) tip Alex On Fri, Jan 31, 2014 at 2:09 PM, Dave Bouvier d...@bx.psu.edu wrote: Alex, To help determine the cause of this, could you paste the output of the following commands run from the root of your Galaxy installation? hg heads hg id --Dave B. On 01/31/2014 09:05 AM, Alexander Kurze wrote: Thanks for your quick answers. I actually have installed the dependencies first and then I have tried to add bowtie2 http://toolshed.g2.bx.psu.edu/view/devteam/bowtie2. But this is where the problem lies: I get following error message: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Meanwhile, I have downloaded the bowtie2.xml and added it to the ./tools/sr_mapping/ folder and added it to the tool_config.xml and it now works. Any clue why I get the error message? Is there something wrong with my server or do is it the repository? Cheers, Alex On Fri, Jan 31, 2014 at 1:18 PM, bjoern.gruen...@googlemail.com mailto:bjoern.gruen...@googlemail.com bjoern.gruen...@gmail.com mailto:bjoern.gruen...@gmail.com wrote: Hi Alex, there is a difference in http://toolshed.g2.bx.psu.edu/view/devteam/package_bowtie2_2_1_0 and http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers The package_* is installing the binary for you and can be used by other programs as well. bowtie_wrappers contains the actual wrappers and is depending on package_*. To make it short. You need to install http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers and both packages will be installed and you should see your wrapper. Ciao, Bjoern 2014-01-31 Alexander Kurze alexander.ku...@bioch.ox.ac.uk mailto:alexander.ku...@bioch.ox.ac.uk: Hi there, I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto the system via the toolshed. However it just doesn't work. I always get a Server Error message. I have checked if the dependencies are installed and they are all installed in the toolshed depenencies folders. However, the actual repos only contains the tool_dependency.xml. (eg galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/jjohnson/ package_bowtie_2_1_0/38652b57e057/package_bowtie_2_ 1_0/tool_dependencies.xml http://testtoolshed.g2.bx.psu.edu/repos/jjohnson/ package_bowtie_2_1_0/38652b57e057/package_bowtie_2_ 1_0/tool_dependencies.xml) I thought that there should be a bowtie2.xml file in the repos of package_bowtie_2_1_0 but there isn't... Also, looking at the shed_tool_config.xml I cannot see any entry for bowtie2. Is there a way to add bowtie2 manually? Best wishes, Alex ___ 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/ -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 -- Alexander Kurze 70 Sunningwell Road Oxford, OX1 4SX Tel: +44 1865-243-609 Mobile: +44 7962-425-865 ___ 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] Active Directory
Hi there, I have a server set up of galaxy. I would like to have a system setup where people can login via their active directory name and then use their mounted share drive to download processed data from the galaxy server. I saw that it is possible via apache to login through the AD, but will the AD also mount the share drives? If yes, is there a wrapper that allows to download Galaxy Histories onto the shared drive? Alex -- Alexander Kurze 70 Sunningwell Road Oxford, OX1 4SX Tel: +44 1865-243-609 Mobile: +44 7962-425-865 ___ 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] Active Directory
Hi there, I have a server set up of galaxy. I would like to have a system setup where people can login via their active directory name and then use their mounted share drive to download processed data from the galaxy server. I saw that it is possible via apache to login through the AD, but will the AD also mount the share drives? If yes, is there a wrapper that allows to download Galaxy Histories onto the shared drive? Alex ___ 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] Active Directory
Hi there, I have a server set up of galaxy. I would like to have a system setup where people can login via their active directory name and then use their mounted share drive to download processed data from the galaxy server. I saw that it is possible via apache to login through the AD, but will the AD also mount the share drives? If yes, is there a wrapper that allows to download Galaxy Histories onto the shared drive? ___ 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] Blank History
Hi there, I am running my own instance of galaxy (April 2013 version) and I have problems with saved histories. Sometimes the histories do NOT show up at all at the right hand side (panel remains white with no error message). I then have make a clone of the history and then I can use it again. I haven't figured out what the problem could be. Does anyone have a similar problem? Best wishes, Alex ___ 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] Downsampling of SAM/BAM files
Hello, I am running a local galaxy server and tried to add the downsampling script for SAM/BAM files from Brad Longhorst which I found on Github. It uses a modified picard_wrapper.py. I get everything running except that the end file shows up empty. I realised when looking at the log file that the Input directory differs from the output directory also instead of adding a .data file it produces a .metrics.txt file. Does anyone know how to fix this, or does anyone have another script which can be used on Galaxy for downsampling SAM/BAM files? Thanks a lot, Alex ___ 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] Fwd: Intersect Tool
Dear All, I am running my own galaxy instance and I have been using the tool intersect (under the tab operate on genomic intervals) a few times successfully. However, recently I get following error message: /home/galaxy/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/local/lib/python2.7/dist-packages/markupsafe/__init__.pyc, but /home/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() I googled it and there was never a straight answer. Could anyon explain how to fix it or at least tell me what it means. Thank you for your help in advance. Keep up the great work! Best wishes, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 ___ 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] Dataset diskspace useage
Hello, I am running a local galaxy server where I have restricted the amount of data for each user to a 100gb. Users are able to delete their own history to regain diskspace. However, for some users deleting the histories (all saved histories and datasets) only frees ~80% of their allowance. As an admin I ran the clean-up scripts which were recommended on the galaxy homepage. But this still didn't increase their data limit. Anyone knows what is going on? Best wishes, Alex ___ 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] Multicore
Hi there, we have a 32 core server but I realised that a lot of programs are only using a fraction of that. I was able to adjust bowtie, bowtie2 and Tophat to use all of the cores but couldn't find an thread/core option for Macs14, Macs2 or PeakRanger. Does anyone know if these programs are capable of multi threading? If yes, where do I adjust it? Would be nice to have some global parameter set in the universewgsi.ini file. Thanks, Alex ___ 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] Multicore
Thanks a lot for your answers. I tried to set the -t value to 32 in peakranger but nothing really happens...it still runs on 1 thread even so it says -t 32 in the execution line I guess I need to contact the author. Thanks for your help! Alex On Tue, Mar 26, 2013 at 2:01 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Tue, Mar 26, 2013 at 10:15 AM, Alexander Kurze alexander.ku...@gmail.com wrote: Hi there, we have a 32 core server but I realised that a lot of programs are only using a fraction of that. I was able to adjust bowtie, bowtie2 and Tophat to use all of the cores but couldn't find an thread/core option for Macs14, Macs2 or PeakRanger. Does anyone know if these programs are capable of multi threading? If yes, where do I adjust it? Would be nice to have some global parameter set in the universewgsi.ini file. Thanks, Alex A more configurable thread setting has come up several times - something that could integrate nicely with cluster back ends for scheduling would be ideal. Some of my wrappers use $NSLOTS if set, and if not default to four threads. This works very nicely under SGE where you can set the thread count via the runner settings in universewgsi.ini - but this is not really general enough. For now however, you do generally have to tweak the wrappers as you have done to edit any hard coded thread setting :( Peter -- Alexander Kurze 70 Sunningwell Road Oxford, OX1 4SX Tel: +44 1865-243-609 Mobile: +44 7962-425-865 ___ 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] bowtie-wrapper
Thanks it is working now. Best wishes, Alex On Wed, Feb 27, 2013 at 9:35 AM, Peter Briggs peter.bri...@manchester.ac.uk wrote: Hello Alexander I've made some changes to our local copy of the bowtie tool files (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing bowtie's stderr output and adding it as an additional history item (here the statistics in this output is used as input to a local tool). I've attached patches to the tool in case they're any use to you. (As an aside and more generally: I'm not sure how to manage these local customisations in the longer term - what do other people on this list do?) HTH, best wishes, Peter On 25/02/13 11:29, Alexander Kurze wrote: Hello, I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads? If I use bowtie vi comman line I get following output: bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s) The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy. Any idea how I can still access the stats? Thanks, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 __**_ 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/ -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 -- Alexander Kurze 70 Sunningwell Road Oxford, OX1 4SX Tel: +44 1865-243-609 Mobile: +44 7962-425-865 ___ 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] bowtie-wrapper
Hello, I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads? If I use bowtie vi comman line I get following output: bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s) The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy. Any idea how I can still access the stats? Thanks, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 ___ 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] Problem with saving workflows
Hello, I am running a local server of Galaxy. I have a problem with editing and then saving already created workflows. The saving workflow bar just does not disappear anymore. I can hit the save on an unaltered workflow, the saving workflow bar appears for 2 secs and then it disappears how it should do. Does anyone now how I can fix it? Thanks, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 ___ 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/
