August 2013 - galaxy-dev - lists.galaxyproject.org

how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini
by Jennifer Jackson 19 Aug '13

19 Aug '13

Hi Tin, I am going to move this over to the galaxy-dev(a)bx.psu.edu mailing list (good for local install questions) to give it better viability. I am by no means the best person to help with this, so hopefully others will jump in, but just from looking at this I am wondering if you shouldn't be instead looking at the " job_conf.xml.sample_advanced" file. There is the default version as well, but it is probably not what you are looking for if you want to add custom logging scripts. For universe_wsgi.ini, it seems like maybe the problem with the syntax is most likely the unknown "default_cluster_job_runner" variable and the double "=" in the line. Slashes should be fine unescaped here. But as I said, I think the other file is the place for the changes anyway, or maybe both, but using known variables and a single "=" per path. But let's see what the developers think! Jen Galaxy team On 8/12/13 3:49 PM, tin h wrote: > > Hello galaxy gurus,Â > > I am trying to configure a local galaxy server to submit to SGE using > DRMAA,Â > it works, but I would like to specify the equivalent of "-v > TMPDIR=/scratch" for qsub. > > I tried updating universe_wsgi.ini with something like: > Â default_cluster_job_runner = Â drmaa://-q default.q -V -v > TMPDIR=/scratch/ > but that doesn't work because "/" is a delimiter, and I have not been > able to find way to escape it. Â Is there any tricks for this? > > > Much thanks in advance for your help in this matter. > -Tin > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org

3 7

Tool Shed error: AttributeError: 'NoneType' object has no attribute 'status'
by Bjoern Gruening 19 Aug '13

19 Aug '13

Hi, back for testing and migrating to the tool shed. Sorry in advance! During installation via the API I'm usually watching the status with 'Manage installed tool shed repositories'. Installation is still running but I now get these error: URL: http://localhost:8080/admin_toolshed/browse_repositories File '/home/gruening/projects/code/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/usr/lib/python2.7/site-packages/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/lib/python2.7/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/home/gruening/projects/code/galaxy-central/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 151 in browse_repositories return self.installed_repository_grid( trans, **kwd ) File '/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/helpers/grids.py', line 288 in __call__ kwargs=kwargs ) File '/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py', line 990 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py', line 1005 in fill_template_mako return template.render( **data ) File '/home/gruening/projects/code/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/home/gruening/projects/code/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/home/gruening/projects/code/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/gruening/projects/code/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/home/gruening/projects/code/galaxy-central/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py', line 127 in render_body __M_writer(unicode(self.grid_body( grid ))) File '/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py', line 747 in render_grid_body __M_writer(unicode(self.make_grid( grid ))) File '/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py', line 777 in render_make_grid __M_writer(unicode(self.render_grid_table( grid, show_item_checkboxes ))) File '/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py', line 724 in render_render_grid_table __M_writer(unicode(render_grid_table_body_contents( grid, show_item_checkboxes ))) File '/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py', line 627 in render_grid_table_body_contents return render_render_grid_table_body_contents(context,grid,show_item_checkboxes) File '/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py', line 335 in render_render_grid_table_body_contents value = column.get_value( trans, grid, item ) File '/home/gruening/projects/code/galaxy-central/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py', line 58 in get_value if tool_shed_repository.missing_repository_dependencies: File '/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py', line 3566 in missing_repository_dependencies if required_repository.status not in [ self.installation_status.INSTALLED ]: AttributeError: 'NoneType' object has no attribute 'status' Cheers, Bjoern

2 1

functional test changing datasets
by Berner, Thomas 19 Aug '13

19 Aug '13

Hey guys, In our local galaxy instance (10200:fd4113962c32) it seems that we have a problem with the functional test. Every time we run the testscript for a complete test, datasets of existing histories are changed into something like this: chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + Normaly it should be this: PICq_b125 Bacteria domain 1.0 "Actinobacteria" phylum 1.0 Actinobacteria class 1.0 Actinomycetales order 1.0 Nocardiaceae family 0.64 Rhodococcus genus 0.64 PIBS_a1851 Bacteria domain 1.0 "Actinobacteria" phylum 0.89 Actinobacteria class 0.89 Rubrobacterales order 0.22 Rubrobacteraceae family 0.22 Rubrobacter genus 0.22 PICq_a24 Bacteria domain 1.0 "Bacteroidetes" phylum 1.0 Flavobacteria class 1.0 "Flavobacteriales" order 1.0 Flavobacteriaceae family 1.0 Chryseobacterium genus 0.55 BDa_a679 Bacteria domain 1.0 "Actinobacteria" phylum 1.0 Actinobacteria class 1.0 Actinomycetales order 1.0 Nocardiaceae family 0.98 Smaragdicoccus genus 0.97 BBS_a2145 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Alphaproteobacteria class 1.0 Sphingomonadales order 1.0 Sphingomonadaceae family 0.98 Sphingomonas genus 0.89 BCq_b582 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Betaproteobacteria class 1.0 Burkholderiales order 0.97 Burkholderiales_incertae_sedis family 0.77 Methylibium genus 0.48 BBS_a778 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Betaproteobacteria class 1.0 Burkholderiales order 1.0 Comamonadaceae family 0.99 Rhodoferax genus 0.92 BCq_a234 Bacteria domain 1.0 "Actinobacteria" phylum 1.0 Actinobacteria class 1.0 Acidimicrobiales order 0.93 Iamiaceae family 0.92 Iamia genus 0.92 PIBS_b2663 Bacteria domain 1.0 "Actinobacteria" phylum 1.0 Actinobacteria class 1.0 Actinomycetales order 1.0 Micrococcaceae family 1.0 Arthrobacter genus 0.86 PIBS_b1742 Bacteria domain 1.0 "Bacteroidetes" phylum 1.0 Flavobacteria class 1.0 "Flavobacteriales" order 1.0 Flavobacteriaceae family 1.0 Flavobacterium genus 1.0 PIBS_a2353 Bacteria domain 1.0 "Planctomycetes" phylum 1.0 "Planctomycetacia" class 1.0 Planctomycetales order 1.0 Planctomycetaceae family 1.0 Singulisphaera genus 0.86 PIBS_b4367 Bacteria domain 1.0 "Bacteroidetes" phylum 1.0 "Sphingobacteria" class 1.0 "Sphingobacteriales" order 1.0 "Chitinophagaceae" family 0.99 Ferruginibacter genus 0.35 PICq_b2500 Bacteria domain 1.0 "Acidobacteria" phylum 1.0 Acidobacteria_Gp7 class 1.0 Gp7 genus 1.0 BBS_a2200 Bacteria domain 1.0 "Bacteroidetes" phylum 1.0 "Sphingobacteria" class 1.0 "Sphingobacteriales" order 1.0 "Chitinophagaceae" family 0.99 Chitinophaga genus 0.37 PIBS_a1924 Bacteria domain 1.0 "Bacteroidetes" phylum 1.0 "Sphingobacteria" class 1.0 "Sphingobacteriales" order 1.0 Cytophagaceae family 1.0 Spirosoma genus 0.97 PICq_b388 Bacteria domain 1.0 "Acidobacteria" phylum 0.98 Acidobacteria_Gp6 class 0.98 Gp6 genus 0.98 PIBS_b2523 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Alphaproteobacteria class 1.0 Rhodobacterales order 1.0 Rhodobacteraceae family 1.0 Pseudorhodobacter genus 0.79 PVBS_a1261 Bacteria domain 1.0 "Bacteroidetes" phylum 1.0 "Sphingobacteria" class 1.0 "Sphingobacteriales" order 1.0 "Chitinophagaceae" family 1.0 Chitinophaga genus 0.53 PICq_b4776 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Alphaproteobacteria class 1.0 Sphingomonadales order 1.0 Sphingomonadaceae family 0.99 Sphingomonas genus 0.94 PICq_a537 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Betaproteobacteria class 1.0 Rhodocyclales order 0.58 Rhodocyclaceae family 0.58 Ferribacterium genus 0.4 BCq_a2398 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Alphaproteobacteria class 1.0 Sphingomonadales order 1.0 Sphingomonadaceae family 1.0 Sphingomonas genus 0.95 PVBS_b1685 Bacteria domain 1.0 "Firmicutes" phylum 1.0 "Bacilli" class 1.0 Bacillales order 1.0 Planococcaceae family 0.94 Sporosarcina genus 0.72 BCq_a3186 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 0.98 Xanthomonadales order 0.22 Sinobacteraceae family 0.22 Steroidobacter genus 0.22 PIBS_b585 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 Pseudomonadales order 0.92 Pseudomonadaceae family 0.91 Azomonas genus 0.43 BBS_b2423 Bacteria domain 1.0 "Acidobacteria" phylum 1.0 Acidobacteria_Gp4 class 1.0 Gp4 genus 1.0 BCq_b1962 Bacteria domain 1.0 "Gemmatimonadetes" phylum 0.99 Gemmatimonadetes class 0.99 Gemmatimonadales order 0.99 Gemmatimonadaceae family 0.99 Gemmatimonas genus 0.99 This happens to different datasets generated with different tools. The preview shown in the history is still the original but the content of the dataset is changed. There is no entry in the paster.log for this. Can somebody give me a hint? Greetings, Thomas

3 2

disable PBKDF2, revert to SHA1
by Ulf Schaefer 19 Aug '13

19 Aug '13

Hello all It was indicated in several recent posts (e.g. there http://dev.list.galaxyproject.org/support-pbkdf2-in-proftpd-1-3-5rc3-td4660…) that for Galaxy to reliably work with ProFTPD, it is recommended to disable the new PBKDF2 encryption of passwords and revert back to SHA1. Unfortunately it appears to be beyond me to figure out how to do this. Could somebody point me in the right direction, please? Thanks a lot Ulf ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

2 1

upload file not functioning in local installation galaxy
by Yinan Wan 19 Aug '13

19 Aug '13

Hi, I have installed galaxy on our local server, when I was trying to upload data from: Get Data -> Upload File -> choose file. It is not uploading at all; but it works fine when using the URL option. I wonder do you have any suggestions about this problem? The output from the command line is pasted below: ====> 128.118.200.158 - - [15/Aug/2013:14:15:41 -0400] "GET /api/histories/5969b1f7201f12ae/contents?ids=f09437b8822035f7 HTTP/1.1" 200 - "http://128.118.201.68:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/histories/5969b1f7201f12ae HTTP/1.1" 200 - " http://128.118.201.68:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/histories/5969b1f7201f12ae/contents?ids=f09437b8822035f7 HTTP/1.1" 200 - "http://128.118.201.68:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:16:49 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:03 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - " http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:04 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - " http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:08 -0400] "GET /history HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" ==============> Thanks, Yinan -- Yinan Wan, graduate student Bioinformatics and Genomics program Huck Institutes of Life Sciences the Pennsylvania State University

2 3

Exporting Tool Shed revision does not work anymore
by Bjoern Gruening 19 Aug '13

19 Aug '13

Hi Greg, I tried to export the chemicaltoolbox but I only got one tarball called: capsule_with_dependencies_testtoolshed.g2.bx.psu.edu_chemicaltoolbox_bgruening_4133dbf7ff4d.tar.gz with only one dependency and no manifest file. Cheers, Bjoern

2 2

Sample & test-data in tools & workflows
by Peter Cock 19 Aug '13

19 Aug '13

Hi all, This is something I was recently talking to Bjoern about, and which I'm pretty sure came up at the GCC2013 too, perhaps in the Tool Developer's BoF chat?: http://wiki.galaxyproject.org/Events/GCC2013/BoF/ToolDevelopers Currently Galaxy Tools should have test data for their functional tests, included in the Tool Shed repository under a test-data folder. That is good. Currently Galaxy Workflows do NOT support similar functional tests and they should (i.e. they need something very similar with a test-data folder and configuration file giving the input/output files and other input parameters). This might make sense as part of any ongoing work to present a workflow within Galaxy as a Tool? Trello issue filed: https://trello.com/c/S5CZGOb3/1061-workflows-need-functional-tests-like-we-… Neither Galaxy Tools nor Galaxy Workflows yet have any support for "sample data", which might just be larger examples then we already have for the tool's functional tests. This could even be implemented as and extension to the existing <test> markup where a test can be marked as also being sample data? I am imaging that each tool (and workflow) should have at least one sample input dataset (files and parameters) with a description. These would be shown via new GUI element in the Galaxy interface to auto-populate the Galaxy Tool interface with those sample input files (imported into the current history?) and the associated parameter values - ready for the user to modify if desired and then execute. Ross brought this up sample data for tools back in May 2010, and there is a relevant Trello issue filed: https://trello.com/c/GTLNlcwH/298-308-demystifying-the-first-ever-galaxy-lo… In the short term, we can just resort to documenting examples in the Tool's <help> text using URLs to public datasets. Here it would be nice if the workflows also supported a similar <help> field to be shown to the user when running a workflow: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014479.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016132.html https://trello.com/c/HaQnZGvW/1060-embedding-help-text-in-workflows-ideally… Unless enhancing the workflow annotation with a tool <help> like field is imminent, then for workflows we are probably for the short term restricted to documenting sample data in a README file which would be visible on the Tool Shed, but not available once the workflow is actually installed into a Galaxy instance. The current situation is clearly not ideal - what is realistic to hope/aim for in the next Galaxy release? Thanks, Peter

1 0

Is there a way to install a tool from toolshed in cloudman without using commands?
by Anto Praveen Rajkumar Rajamani 19 Aug '13

19 Aug '13

Hello, I launched a new Cloudman instance last week to analyse my RNA-seq data. I uploaded and cleaned my data, but could not run Tophat and Cufflinks due to the "Broken symbolic links" problem (https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-t…) I have completed running Tophat2 on the public server. Now, I like to install edgeR (http://toolshed.g2.bx.psu.edu/repository?repository_id=0c447003da85ae19) from the toolshed for further analyses. I cannot find a way to install that tool in my cloudman instance. My background is in psychiatry and I do not have any knowledge of Linux commands. Is there a way to install a tool (edgeR) from the toolshed without using command lines? Any help is greatly appreciated. Thank you. Best wishes, Anto Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. Ph (office) : 045- 87167292 E-mail: APR(a)hum-gen.au.dk

2 7

Tool Shed repository install directory
by Jeanré Smit 19 Aug '13

19 Aug '13

Hi We are in the process of creating a Galaxy Tool Shed repo and we need to know what the absolute path of the local installation of the repo is, inside a Python wrapper, since it's unique for every instance of Galaxy. We need this path in order to run an R script. The only possible way we found on Google is by using the galaxy.tool_shed.tool_dependencies.install_util.get_tool_shed_repository_install_dir(app, tool_shed_repository) command, but as I understand it this command is only usable during the installation of a repository. Is there any way to get the absolute path of the installation directory when a wrapper is executed? Thanks in advance -- Jeanré Smit Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria 0002 Cell +27 72 073 6011 Office +27 12 420 5802 Fax +27 12 420 5800

2 1

OSError: [Errno 5] Input/output error
by Richard Kuo 19 Aug '13

19 Aug '13

Hello, I tried restarting my local Galaxy instance today bit it won't start up properly. I keep getting this message when I run "sh run.sh": Traceback (most recent call last): File "/mnt/ris-fas1a/linux_users/avnglxy/ris-lx10/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/mnt/ris-fas1a/linux_users/avnglxy/ris-lx10/galaxy-dist/lib/galaxy/app.py", line 79, in __init__ self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) File "/mnt/ris-fas1a/linux_users/avnglxy/ris-lx10/galaxy-dist/lib/galaxy/datatypes/registry.py", line 273, in load_datatypes self.to_xml_file() File "/mnt/ris-fas1a/linux_users/avnglxy/ris-lx10/galaxy-dist/lib/galaxy/datatypes/registry.py", line 681, in to_xml_file os.close( fd ) OSError: [Errno 5] Input/output error The reason for my restart was dur to a users complaint about upload speeds. Any help is much appreciated! Richard

2 1