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Problem when I submit 'gatk_wrapper.py' task with my job scheduling system arranged on my sever.
by Wei Liu 20 Aug '13

20 Aug '13

Dear everyone, These days I want to localize Galaxy on our server. When I tried to arrange gatk, I met a problem as follow. Firstly, I run the script 'gatk_wrapper.py' like this: python /bio-db/apps/api/galaxy-galaxy-dist-e6444e7a1685/tools/gatk/gatk_wrapper.py -d -I /share/home/wuyilei/bioc/test/111/test1.bbioc/test/111/test1.bam .bam test1 -p /bio-db/apps/pool/java1.6/jre1.6.0_24/bin/java -jar /bio-db/apps/api/galaxy-galaxy-dist-e6444e7a1685/shared/jars/gatk/GenomeAnalysisTK.jar -R /bio-db/reference-genome/hg19.fa -T DepthOfCoverage But I got an error message like this: gatk_wrapper.py: error: no such option: -j Then I tried to add a couple of single quotes on the parameters behind of -d and -p, just like the following: python /bio-db/apps/api/galaxy-galaxy-dist-e6444e7a1685/tools/gatk/gatk_wrapper.py -d '-I' /share/home/wuyilei/bioc/test/111/test1.bbioc/test/111/test1.bam .bam test1 -p '/bio-db/apps/pool/java1.6/jre1.6.0_24/bin/java -jar /bio-db/apps/api/galaxy-galaxy-dist-e6444e7a1685/shared/jars/gatk/GenomeAnalysisTK.jar -R /bio-db/reference-genome/hg19.fa -T DepthOfCoverage ' Then 'gatk_wrapper.py' can work well! But if I use the ob scheduling system which was arranged on my server, I can not run the 'gatk_wrapper.py' script any more. After a long time research, I found the problem, all because of the single quotes behind of -d and -p. Can anyone help me, for example, rewrite the script 'gatk_wrapper.py' for me, then I can delete the single quotes! Or give me some other advice. Looking forward your reply! Best, Wei Liu.

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Re: [galaxy-dev] OSError: [Errno 5] Input/output error
by Hans-Rudolf Hotz 20 Aug '13

20 Aug '13

Please keep all replies on the list by using "reply all" I am not really a tool shed expert, hence I can only direct you to the wiki pages: http://wiki.galaxyproject.org/Tool%20Shed Hans-Rudolf On 08/20/2013 12:12 PM, Richard Kuo wrote: > Hello Hans-Rudolf, > > I am wondering if the issue could have been caused by the tool shed? I > had been playing around with adding new tools via the tool shed just > before this happened. The sys admin has restored our Galaxy instance to > a previous time point before I did all this and it seems to be working > alright now. Is there any documentation of how the tool shed interacts > with the conf files within the galaxy folder? > > Thank you! > Richard > > > On Mon, Aug 19, 2013 at 12:32 PM, Hans-Rudolf Hotz <hrh(a)fmi.ch > <mailto:hrh@fmi.ch>> wrote: > > Hi Richard > > this looks like a system error to me (and has nothing to do with the > galaxy server itself). Something is wrong with your disk? which > might also be the original reason why you got complaints about the > upload speed. > > Sorry, I can't help you any further. I suggest you contact your sys > admin. > > > Regards, Hans-Rudolf > > > > On 08/19/2013 01:07 PM, Richard Kuo wrote: > > 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 > > > _____________________________________________________________ > 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/ > <http://galaxyproject.org/search/mailinglists/> > >

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Showing images in README.rst on Tool Shed
by Peter Cock 20 Aug '13

20 Aug '13

Hi all, Thanks to Bjoern's recent enhancement, most of the Tool Shed pages now render a repository's README file as reStructuredText if the filename ends *.rst [I've noticed a bug where during repository installation the README file is just shown as plain test - I'm not sure if this a Galaxy bug or a Tool Shed bug though.] What I wanted to ask today is can we include images in the rendered README file? For instance a small PNG showing sample output, or any other kind of documentation: http://docutils.sourceforge.net/docs/ref/rst/directives.html#image I've tried it here but it fails: http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow/2dfe8b788… Assuming I want to show a local image included within the Tool Shed repository, I presume this would require tweaks to get the image served by the Tool Shed at the appropriate relative URL? I can work-around this by using a full http URL to a publicly hosted image, but that may raise privacy concerns: http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow/d89313312… Thoughts? Peter

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Note about running functional tests.
by Dave Bouvier 20 Aug '13

20 Aug '13

Dear Galaxy admins, As of 10408:6822f41bc9bb stable/10409:2ca0b65d5005 default, a bug has been fixed where running functional tests could overwrite some files in your Galaxy path. If you intend to run functional tests, it is recommended to update to the relevant revision on the branch you are running. Additionally, it is not recommended to run functional tests on a production instance, since the test suite alters a number of configuration settings on the fly, with the result being that it is not a reliable test of the exact production environment, which may give misleading results. -- --Dave B.

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Apache authentication UCSC error
by Shane Sturrock 20 Aug '13

20 Aug '13

I've followed the instructions on setting up Apache Authentication (have to authenticate against an Active Directory server) here http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy and it doesn't work for external display sites unfortunately. The section on display sites suggests the following: <Location "/root/display_as"> Satisfy Any Order deny,allow Deny from all Allow from hgw1.cse.ucsc.edu Allow from hgw2.cse.ucsc.edu Allow from hgw3.cse.ucsc.edu Allow from hgw4.cse.ucsc.edu Allow from hgw5.cse.ucsc.edu Allow from hgw6.cse.ucsc.edu Allow from hgw7.cse.ucsc.edu Allow from hgw8.cse.ucsc.edu </Location> but that doesn't stop Apache requiring authentication. Only putting the Allow from hgw1.csc.ucsc.edu lines in the Location "/" directive gets past that but then I hit another issue which didn't previously exist where I get an error "redirected to non-http(s): /static/user_disabled.html" which is new since I have had it work with this current install. It is possible that CentOS has pushed an update onto my server that has changed some subtle behaviour I guess but it is eluding me entirely and Google isn't doing me much good (Samsung, why did you have to exist?!) For the moment I've disabled the UCSC sites but that isn't a long term solution and I'm stuck because I have to use Apache and AD authentication so I would appreciate hearing from anyone who has figured out how to get this to work. Shane -- For urgent cases, contact support(a)biomatters.com Dr Shane Sturrock shane.sturrock(a)biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand

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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

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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

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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

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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 **************************************************************************

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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

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