[galaxy-dev] Error running Clustalw and HyPhy on Cloudman
Hello - I am running to errors when trying to run Clustalw and HyPhy on our cloudman instance. (1) Clustalw: The program completes without error and produces an empty file and a log file that states "/bin/sh: 1: clustalw2: not found" Searching around a bit I am not seeing clustalw2 previously installed. I am happy to do it if need be, however, I wanted to check in and see if I am overlooking the directory or an easy fix. If I do need to install clustalw, I would prefer to use clustalw-omega, but was not sure if I needed to script a brand new wrapper or if I could use the previous one that came with galaxy image. (2) HyPhy: The cloud the link was initially broken. I changed it to the correct path: sudo ln -sfn /mnt/galaxy/tools/hyphy/default /mnt/galaxy/galaxy-app/tool-data/HYPHY I am using a fasta alignment file of 6 protein sequences (566 AA each) as a test case (*also fails with nucleotide alignments). It runs briefly and then issues an error statement "Single Alignment Analyses Segmentation fault (core dumped)". Thank you in advance, Karen ___ 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] Error running Clustalw and HyPhy on Cloudman
Hi Ross, Thanks for your email. I have clustalw2 working now - I installed the clustal repository (as suggested) from toolshed and then installed the clustalw2 binaries in our mnt/galaxy/tools/bin. Thanks again! Karen On Wed, Nov 27, 2013 at 12:46 AM, Ross wrote: > Hi, Karen - how did you install clustalw? > If not already done, can you please try installing the clustal > repository owned by fubar from the test toolshed through your Galaxy admin > interface - search/browse toolsheds? Please let me know how you go and if > there's a problem I'll try to fix it for you. I think there's a clustal > omega tool too but it's not one of mine. As far as I know my clustal > repository should install cleanly on a CloudMan instance. > > Sorry but we'll have to wait to from someone who knows about HyPhy. > > Hello - I am running to errors when trying to run Clustalw and HyPhy on > our cloudman instance. > > (1) Clustalw: The program completes without error and produces an empty > file and a log file that states "/bin/sh: 1: clustalw2: not found" > > Searching around a bit I am not seeing clustalw2 previously installed. I > am happy to do it if need be, however, I wanted to check in and see if I am > overlooking the directory or an easy fix. > > If I do need to install clustalw, I would prefer to use clustalw-omega, > but was not sure if I needed to script a brand new wrapper or if I could > use the previous one that came with galaxy image. > > (2) HyPhy: The cloud the link was initially broken. I changed it to the > correct path: > > sudo ln -sfn /mnt/galaxy/tools/hyphy/default > /mnt/galaxy/galaxy-app/tool-data/HYPHY > > I am using a fasta alignment file of 6 protein sequences (566 AA each) as > a test case (*also fails with nucleotide alignments). > > It runs briefly and then issues an error statement "Single Alignment > Analyses Segmentation fault (core dumped)". > > Thank you in advance, > > Karen > > > > ___ > 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/ > -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232 ___ 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] hmmer install
Hello, I would like to use hmmer on our cloudman instance. However, when I install I am only finding a wrapper for hmmpress. There was some conversation about this back in 2012 ( http://gmod.827538.n3.nabble.com/Missing-tool-previews-in-tool-shed-e-g-hmmer-xml-td3838635.html). I installed the hmmer package 3.0 and 3.1 from the toolshed as well, however, I am not seeing a wrapper for these tools - perhaps I am missing something? Best wishes, Karen ___ 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] Error running Clustalw and HyPhy on Cloudman
Hi Ross, I did not detect any type of auto-install (?) After installing from toolshed I did not find the binary under the /mnt/galaxy/shed_tools/ toolshed.g2.bx.psu.edu/repos/ (or /mnt/galaxy/tools or /mnt/galaxy/tools/bin for that matter). Am I looking in the wrong place? Karen On Sun, Dec 1, 2013 at 2:00 PM, Ross wrote: > Hi Karen, > Glad to hear it worked for you. It the tool auto-installs correctly, it > downloads and unpacks the binary under > [tool_dependency_directory]/clustalw/2.1/fubar/clustalw/76de6971a0de/ so > the binary you installed manually should not ever be needed by the toolshed > version - try moving it off your path - the tool should continue to work > correctly? Apologies - I should have suggested removing any manual > installations and their corresponding tool_conf.xml entries before using > the automated installation - the tool shed installation doesn't prevent you > from having 2 versions of the same tool in your tool menu - until those > manually installed ones (which may depend on clustalw2 being on the path) > are removed? > > > On Mon, Dec 2, 2013 at 8:36 AM, Karen Miga wrote: > >> Hi Ross, >> >> Thanks for your email. I have clustalw2 working now - I installed the >> clustal repository (as suggested) from toolshed and then installed the >> clustalw2 binaries in our mnt/galaxy/tools/bin. >> >> Thanks again! >> Karen >> >> >> On Wed, Nov 27, 2013 at 12:46 AM, Ross wrote: >> >>> Hi, Karen - how did you install clustalw? >>> If not already done, can you please try installing the clustal >>> repository owned by fubar from the test toolshed through your Galaxy admin >>> interface - search/browse toolsheds? Please let me know how you go and if >>> there's a problem I'll try to fix it for you. I think there's a clustal >>> omega tool too but it's not one of mine. As far as I know my clustal >>> repository should install cleanly on a CloudMan instance. >>> >>> Sorry but we'll have to wait to from someone who knows about HyPhy. >>> >>> Hello - I am running to errors when trying to run Clustalw and HyPhy on >>> our cloudman instance. >>> >>> (1) Clustalw: The program completes without error and produces an empty >>> file and a log file that states "/bin/sh: 1: clustalw2: not found" >>> >>> Searching around a bit I am not seeing clustalw2 previously installed. >>> I am happy to do it if need be, however, I wanted to check in and see if I >>> am overlooking the directory or an easy fix. >>> >>> If I do need to install clustalw, I would prefer to use clustalw-omega, >>> but was not sure if I needed to script a brand new wrapper or if I could >>> use the previous one that came with galaxy image. >>> >>> (2) HyPhy: The cloud the link was initially broken. I changed it to >>> the correct path: >>> >>> sudo ln -sfn /mnt/galaxy/tools/hyphy/default >>> /mnt/galaxy/galaxy-app/tool-data/HYPHY >>> >>> I am using a fasta alignment file of 6 protein sequences (566 AA each) >>> as a test case (*also fails with nucleotide alignments). >>> >>> It runs briefly and then issues an error statement "Single Alignment >>> Analyses Segmentation fault (core dumped)". >>> >>> Thank you in advance, >>> >>> Karen >>> >>> >>> > -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232 ___ 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] Error running Clustalw and HyPhy on Cloudman
Hi Ross, That is listed as "tool_dependency_dir = /mnt/galaxy/tools" in my universe_wsgi.ini file, and that did not contain a clustalw directory either before or after the toolshed install. Karen On Sun, Dec 1, 2013 at 2:10 PM, Ross wrote: > yes. In universe_wsgi_ini you have a definition for tool_dependency_dir - > that's why I wrote: > [tool_dependency_directory]/clustalw/2.1/fubar/clustalw/76de6971a0de/ as > the path - the funny numbers are the repository revision number - that's > where the toolshed installs the binary and the env.sh file needed for the > tool to find it. > > > > On Mon, Dec 2, 2013 at 9:08 AM, Karen Miga wrote: > >> Hi Ross, >> >>I did not detect any type of auto-install (?) After installing from >> toolshed I did not find the binary under the /mnt/galaxy/shed_tools/ >> toolshed.g2.bx.psu.edu/repos/ (or /mnt/galaxy/tools or >> /mnt/galaxy/tools/bin for that matter). Am I looking in the wrong place? >> >> Karen >> >> >> On Sun, Dec 1, 2013 at 2:00 PM, Ross wrote: >> >>> Hi Karen, >>> Glad to hear it worked for you. It the tool auto-installs correctly, it >>> downloads and unpacks the binary under >>> [tool_dependency_directory]/clustalw/2.1/fubar/clustalw/76de6971a0de/ so >>> the binary you installed manually should not ever be needed by the toolshed >>> version - try moving it off your path - the tool should continue to work >>> correctly? Apologies - I should have suggested removing any manual >>> installations and their corresponding tool_conf.xml entries before using >>> the automated installation - the tool shed installation doesn't prevent you >>> from having 2 versions of the same tool in your tool menu - until those >>> manually installed ones (which may depend on clustalw2 being on the path) >>> are removed? >>> >>> >>> On Mon, Dec 2, 2013 at 8:36 AM, Karen Miga wrote: >>> >>>> Hi Ross, >>>> >>>> Thanks for your email. I have clustalw2 working now - I installed >>>> the clustal repository (as suggested) from toolshed and then installed the >>>> clustalw2 binaries in our mnt/galaxy/tools/bin. >>>> >>>> Thanks again! >>>> Karen >>>> >>>> >>>> On Wed, Nov 27, 2013 at 12:46 AM, Ross wrote: >>>> >>>>> Hi, Karen - how did you install clustalw? >>>>> If not already done, can you please try installing the clustal >>>>> repository owned by fubar from the test toolshed through your Galaxy admin >>>>> interface - search/browse toolsheds? Please let me know how you go and if >>>>> there's a problem I'll try to fix it for you. I think there's a clustal >>>>> omega tool too but it's not one of mine. As far as I know my clustal >>>>> repository should install cleanly on a CloudMan instance. >>>>> >>>>> Sorry but we'll have to wait to from someone who knows about HyPhy. >>>>> >>>>> Hello - I am running to errors when trying to run Clustalw and HyPhy >>>>> on our cloudman instance. >>>>> >>>>> (1) Clustalw: The program completes without error and produces an >>>>> empty file and a log file that states "/bin/sh: 1: clustalw2: not found" >>>>> >>>>> Searching around a bit I am not seeing clustalw2 previously installed. >>>>> I am happy to do it if need be, however, I wanted to check in and see if >>>>> I >>>>> am overlooking the directory or an easy fix. >>>>> >>>>> If I do need to install clustalw, I would prefer to use >>>>> clustalw-omega, but was not sure if I needed to script a brand new wrapper >>>>> or if I could use the previous one that came with galaxy image. >>>>> >>>>> (2) HyPhy: The cloud the link was initially broken. I changed it to >>>>> the correct path: >>>>> >>>>> sudo ln -sfn /mnt/galaxy/tools/hyphy/default >>>>> /mnt/galaxy/galaxy-app/tool-data/HYPHY >>>>> >>>>> I am using a fasta alignment file of 6 protein sequences (566 AA each) >>>>> as a test case (*also fails with nucleotide alignments). >>>>> >>>>> It runs briefly and then issues an error statement "Single Alignment >>>>> Analyses Segmentation fault (core dumped)". >>>>> >>>>> Thank you in advance, >>>>> >>>>> Karen >>>>> >>>>> >>>>> >>> >> >> >> -- >> Karen H. Miga, PhD >> >> Postdoctoral Scholar >> University of California, Santa Cruz >> (831)459-5232 >> > > > > -- > Ross Lazarus MBBS MPH; > Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 > http://scholar.google.com/citations?hl=en&user=UCUuEM4J > -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232 ___ 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] Error running Clustalw and HyPhy on Cloudman
Yes, I do all of my installs from the toolshed through the admin menu, however I did not use the "test toolshed..." I used the main. Ah ha - maybe that was the issue? Karen On Sun, Dec 1, 2013 at 2:23 PM, Ross wrote: > Just to confirm, you used automated installation via the admin menu -> > search and browse toolsheds -> test toolshed -> etc ? > If you installed manually by downloading and unpacking the archive under > your tools/ directory, then yes, there is no automation and you need to > install the binary on your path. I believe the documentation explains this > - if it's not clear please suggest some revisions ? > > > On Mon, Dec 2, 2013 at 9:18 AM, Karen Miga wrote: > >> Hi Ross, >> >> That is listed as "tool_dependency_dir = /mnt/galaxy/tools" in my >> universe_wsgi.ini file, and that did not contain a clustalw directory >> either before or after the toolshed install. >> >> Karen >> >> >> On Sun, Dec 1, 2013 at 2:10 PM, Ross wrote: >> >>> yes. In universe_wsgi_ini you have a definition for tool_dependency_dir >>> - that's why I wrote: >>> [tool_dependency_directory]/clustalw/2.1/fubar/clustalw/76de6971a0de/ as >>> the path - the funny numbers are the repository revision number - that's >>> where the toolshed installs the binary and the env.sh file needed for the >>> tool to find it. >>> >>> >>> >>> On Mon, Dec 2, 2013 at 9:08 AM, Karen Miga wrote: >>> >>>> Hi Ross, >>>> >>>>I did not detect any type of auto-install (?) After installing from >>>> toolshed I did not find the binary under the /mnt/galaxy/shed_tools/ >>>> toolshed.g2.bx.psu.edu/repos/ (or /mnt/galaxy/tools or >>>> /mnt/galaxy/tools/bin for that matter). Am I looking in the wrong place? >>>> >>>> Karen >>>> >>>> >>>> On Sun, Dec 1, 2013 at 2:00 PM, Ross wrote: >>>> >>>>> Hi Karen, >>>>> Glad to hear it worked for you. It the tool auto-installs correctly, >>>>> it downloads and unpacks the binary under >>>>> [tool_dependency_directory]/clustalw/2.1/fubar/clustalw/76de6971a0de/ so >>>>> the binary you installed manually should not ever be needed by the >>>>> toolshed >>>>> version - try moving it off your path - the tool should continue to work >>>>> correctly? Apologies - I should have suggested removing any manual >>>>> installations and their corresponding tool_conf.xml entries before using >>>>> the automated installation - the tool shed installation doesn't prevent >>>>> you >>>>> from having 2 versions of the same tool in your tool menu - until those >>>>> manually installed ones (which may depend on clustalw2 being on the path) >>>>> are removed? >>>>> >>>>> >>>>> On Mon, Dec 2, 2013 at 8:36 AM, Karen Miga wrote: >>>>> >>>>>> Hi Ross, >>>>>> >>>>>> Thanks for your email. I have clustalw2 working now - I installed >>>>>> the clustal repository (as suggested) from toolshed and then installed >>>>>> the >>>>>> clustalw2 binaries in our mnt/galaxy/tools/bin. >>>>>> >>>>>> Thanks again! >>>>>> Karen >>>>>> >>>>>> >>>>>> On Wed, Nov 27, 2013 at 12:46 AM, Ross wrote: >>>>>> >>>>>>> Hi, Karen - how did you install clustalw? >>>>>>> If not already done, can you please try installing the clustal >>>>>>> repository owned by fubar from the test toolshed through your Galaxy >>>>>>> admin >>>>>>> interface - search/browse toolsheds? Please let me know how you go and >>>>>>> if >>>>>>> there's a problem I'll try to fix it for you. I think there's a clustal >>>>>>> omega tool too but it's not one of mine. As far as I know my clustal >>>>>>> repository should install cleanly on a CloudMan instance. >>>>>>> >>>>>>> Sorry but we'll have to wait to from someone who knows about HyPhy. >>>>>>> >>>>>>> Hello - I am running to errors when trying to run Clustalw and HyPhy >>>>>>> on our cloudman i
Re: [galaxy-dev] hmmer install
Hi Greg, Thanks for the feedback. I cannot seem to find information for hmmdb.loc. When I look in the associated xml file it looks like it could be removed completely (does one need a precompiled HMM Database? I do not remember using anything like this when I run hmmer on the commandline). I have less experience with changing wrappers, etc. Have you tried just commenting this part out? And do I need to start the instance over to test it? Thanks in advance! - Karen Precompiled HMM Database HMM Database in your History On Sun, Dec 1, 2013 at 5:32 PM, Greg Von Kuster wrote: > Hello Karen, > > You are undoubtedly seeing only the hmmpress tool because the other tool > in that repository is not valid: > > Contents of this repository > > Valid tools* - click the name to preview the tool and use the pop-up menu > to inspect all > metadata*<http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&operation=view_or_manage_repository&id=e7e502574a48abf0&async=false&show_item_checkboxes=false&f-free-text-search=hmmer&page=1> > NameDescriptionVersion > hmmpress<http://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=e7e502574a48abf0&render_repository_actions_for=tool_shed&tool_config=database%2Fcommunity_files%2F000%2Frepo_148%2Fhmmpress.xml&changeset_revision=c0fb858f44a2> > Compress profile db1.0.0 > > Invalid tools* - click the tool config file name to see why the tool is > invalid*<http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&operation=view_or_manage_repository&id=e7e502574a48abf0&async=false&show_item_checkboxes=false&f-free-text-search=hmmer&page=1> > hmmer.xml<http://toolshed.g2.bx.psu.edu/repository/load_invalid_tool?repository_id=e7e502574a48abf0&render_repository_actions_for=tool_shed&tool_config=hmmer.xml&changeset_revision=c0fb858f44a2> > > > If you click on the invalid tool in the tool shed, you'll see the reason > that it is invalid: > > > *hmmer.xml* - This file refers to a file named *hmmdb.loc*. Upload a file > named *hmmdb.loc.sample* to the repository to correct this error. > You should also see an exception thrown in your paster when you start your > Galaxy instance telling you why the tool is not being loaded into Galaxy. > > It look like this repository is missing a file named hmmdb.loc.sample that > should provide sample entries for the Galaxy data tables that this tool > must use. I'm not sure of the layout of this table for this particular > tool, but if you discover what it should be, you can manually add them into > a file named hmmdb.loc in the ~/tool-data directory in your Galaxy > environment. > > Greg Von Kuster > > > On Dec 1, 2013, at 4:44 PM, Karen Miga wrote: > > Hello, > >I would like to use hmmer on our cloudman instance. However, when I > install I am only finding a wrapper for hmmpress. There was some > conversation about this back in 2012 ( > http://gmod.827538.n3.nabble.com/Missing-tool-previews-in-tool-shed-e-g-hmmer-xml-td3838635.html). > > > I installed the hmmer package 3.0 and 3.1 from the toolshed as well, > however, I am not seeing a wrapper for these tools - perhaps I am missing > something? > > Best wishes, > Karen > ___ > 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/ > > > -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232 ___ 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] phyloviz: save visualization error
Hello, I am trying to use phyloviz on the cloud/Galaxy cloudman. Unfortunately, I am unable to save the visualization using the save/disk icon on the right hand side of the banner. Any help would be appreciated. Karen ___ 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] hmmer install
Thank you, Peter and Greg, for your feedback. Unfortunately, I am still hitting a wall with the hmmer install - even after creating a dummy hmmer.loc file and a hmmer.loc.sample file in my tool-data dir. All of my paths seem to be ok. Has anyone gotten hmmer to work on galaxy? Do I need to restart my cloud instance? Should I get instant feedback with the invalid hmmer.xml is valid, do I need to reinstall? Karen On Mon, Dec 2, 2013 at 3:51 AM, Peter Cock wrote: > > > > On Mon, Dec 2, 2013 at 4:50 AM, Karen Miga wrote: > >> Hi Greg, >> >>Thanks for the feedback. I cannot seem to find information for >> hmmdb.loc. When I look in the associated xml file it looks like it could >> be removed completely (does one need a precompiled HMM Database? I do not >> remember using anything like this when I run hmmer on the commandline). I >> have less experience with changing wrappers, etc. Have you tried just >> commenting this part out? And do I need to start the instance over to test >> it? >> >> Thanks in advance! >> - Karen >> >> >> >> Precompiled HMM >> Database >> HMM Database in your History >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > This lets the Galaxy HMMER wrapper either be used with system level > HMM databases (listed in hmmer.loc, e.g. PFAM) or with the user's own > HMM databases in their current history. > > [This is very similar to how the BLAST+ wrappers work.] > > If you don't have or need any standard HMM databases (e.g. PFAM) > then an empty hmmer.loc file should work fine. Try that first. > > However, the tool author ought to provide an example named > hmmer.loc.sample which explains how to set this up - it looks > like two columns, description and filename. > > Peter > > -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232 ___ 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] toolshed error on cloudman
Hello, I am currently unable to install a number of tools from toolshed to our cloud instance. Unfortunately, this pops up for quite a few tools (I am currently trying to install cuffmerge, but I see this again and again). Any help would be appreciated! I am seeing the following error: URL: http://ec2-54-204-115-185.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&repository_ids=1a0e2ec172f34c67&changeset_revisions=a29a35968ddb File '/mnt/galaxy/galaxy-app/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/mnt/galaxy/galaxy-app/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/mnt/galaxy/galaxy-app/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/mnt/galaxy/galaxy-app/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/mnt/galaxy/galaxy-app/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/mnt/galaxy/galaxy-app/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/mnt/galaxy/galaxy-app/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 896 in prepare_for_install common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) File '/mnt/galaxy/galaxy-app/lib/tool_shed/util/common_install_util.py', line 84 in get_dependencies_for_repository installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ) File '/mnt/galaxy/galaxy-app/lib/tool_shed/util/common_install_util.py', line 190 in get_installed_and_missing_repository_dependencies_for_new_install tool_shed, name, owner, changeset_revision, prior_installation_required = suc.parse_repository_dependency_tuple( rd_tup ) File '/mnt/galaxy/galaxy-app/lib/tool_shed/util/shed_util_common.py', line 1106 in parse_repository_dependency_tuple prior_installation_required = str( prior_installation_required ) UnboundLocalError: local variable 'prior_installation_required' referenced before assignment -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232 ___ 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] cloudman console error
Hello, I am unable to reach my cloudman console. I was trying to reboot the master. The instance is running on AWS console with no error, I just have no way of access the admin console to terminate or figure out the error through cloud launch. Further, I am now unable to launch a new instance. When attempting to start a new instance I am unable to attach my existing volume-id. Error message below: - 19:14:14 - Error processing filesystems in existing cluster configuration: 'Volume' object has no attribute 'volume_id' Any help would be extremely appreciated. Karen ___ 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/
