Re: [galaxy-dev] Duplicated entries in Manage installed tool shed repositories table
On Tue, Aug 20, 2013 at 8:34 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter and Ross, I've not been able to reproduce this behavior, most likely because I am not following the precise steps you've used when you see it. Can you clarify what you do when you encounter it? Thanks! Greg Von Kuster If it happens to me again, I'll try to narrow down what triggered it. Meanwhile this sounds like another white ghost tool stuck in the new state: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016193.html 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/
Re: [galaxy-dev] Duplicated entries in Manage installed tool shed repositories table
Thanks Peter, As soon as I can get the steps to produce white ghost, I'll get a fix committed - I've not been able to produce one yet. Greg Von Kuster On Aug 21, 2013, at 5:41 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Aug 20, 2013 at 8:34 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter and Ross, I've not been able to reproduce this behavior, most likely because I am not following the precise steps you've used when you see it. Can you clarify what you do when you encounter it? Thanks! Greg Von Kuster If it happens to me again, I'll try to narrow down what triggered it. Meanwhile this sounds like another white ghost tool stuck in the new state: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016193.html 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/
Re: [galaxy-dev] Duplicated entries in Manage installed tool shed repositories table
Peter and Ross, I've not been able to reproduce this behavior, most likely because I am not following the precise steps you've used when you see it. Can you clarify what you do when you encounter it? Thanks! Greg Von Kuster On Aug 15, 2013, at 4:50 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Aug 14, 2013 at 11:08 PM, Ross ross.laza...@gmail.com wrote: FWIW: I've managed to produce a few of these too - generally arose after futzing with a failed dependency, reaching for the nuke it ( 'completely remove' tool) button, then reinstalling it - sometimes there's a complaint that the same version was previously installed (even though it had been supposedly totally nuked), sometimes not - but occasionally a white 'new' ghost will reappear in the manage installed tools list after reinstallation - AFAIK those white ghosts are impossible to remove... Thanks Ross, It is good to know this isn't an isolated problem - and I too had been nuking failed installs, starting with the July 2013 galaxy-dist but also the August galaxy-dist. Maybe that will help Dave reproduce it? I like your name white ghost for this since the new entry is shown on with a white background (it didn't show up in the HTML email sadly). 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/ ___ 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] Duplicated entries in Manage installed tool shed repositories table
On Wed, Aug 14, 2013 at 11:08 PM, Ross ross.laza...@gmail.com wrote: FWIW: I've managed to produce a few of these too - generally arose after futzing with a failed dependency, reaching for the nuke it ( 'completely remove' tool) button, then reinstalling it - sometimes there's a complaint that the same version was previously installed (even though it had been supposedly totally nuked), sometimes not - but occasionally a white 'new' ghost will reappear in the manage installed tools list after reinstallation - AFAIK those white ghosts are impossible to remove... Thanks Ross, It is good to know this isn't an isolated problem - and I too had been nuking failed installs, starting with the July 2013 galaxy-dist but also the August galaxy-dist. Maybe that will help Dave reproduce it? I like your name white ghost for this since the new entry is shown on with a white background (it didn't show up in the HTML email sadly). 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] Duplicated entries in Manage installed tool shed repositories table
Hi Greg, I'm seeing something strange on a system running the August stable release of galaxy-dist, $ sudo -u galaxy hg head changeset: 10393:d05bf67aefa6 branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Mon Aug 12 11:55:41 2013 -0400 summary: Added tag release_2013.08.12 for changeset 1ae95b3aa98d changeset: 10390:009088d5e76f user:Ross Lazarus ross.laza...@gmail.com date:Sat Aug 10 11:28:28 2013 +1000 summary: Patch for missing options in FromDataTableOutputActionOption when these are used in an output filter 1. Run Galaxy 2. Log in as an administrator 3. Click on Admin (top menu) 4. Click on Manage installed tool shed repositories (left menu) 5. Observe duplicate entries: Names of repositories for which updates are available are highlighted in yellow. Description Owner Revision Installation Status Tool shed Galaxy wrappers for Emboss version 5.0.0 tools devteam c159a6ded912 Installed toolshed.g2.bx.psu.edu Galaxy applicable data formats used by Emboss tools. devteam a89163f31369 Installed toolshed.g2.bx.psu.edu Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. bgruening b1ad88bbc5fa Installed toolshed.g2.bx.psu.edu Gene calling with glimmer and a trainingset of know genes. bgruening 22bfc027a718 Installed toolshed.g2.bx.psu.edu Contains a tool dependency definition that downloads and compiles version 1.61 of the biopython package. biopython b482933a6de5 Installed toolshed.g2.bx.psu.edu NCBI BLAST+ 2.2.26 (binaries only) iuc c85236cd100d Installed testtoolshed.g2.bx.psu.edu NCBI BLAST+ 2.2.26 (binaries only) iuc 9ff9bfdcd04f New testtoolshed.g2.bx.psu.edu NCBI BLAST+ 2.2.26 (binaries only) iuc 0e536576294c New testtoolshed.g2.bx.psu.edu Contains a tool dependency definition that downloads and compiles version 2.4 of the freetype font library. iuc 8761091302c4 Installed toolshed.g2.bx.psu.edu Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package iuc 74c21f9bdc39 Installed toolshed.g2.bx.psu.edu As you can see I have been trying the NCBI BLAST+ package from the TEST tool shed, http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 Why are there these extra entries (older revisions) labelled with an Installation Status of New? Are they relics from failed installation attempts? Thanks, 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/
Re: [galaxy-dev] Duplicated entries in Manage installed tool shed repositories table
Peter, Remnants from previously failed installation attempts seems the most likely explanation, but I'll try to duplicate that situation locally and see if there's any underlying issue. --Dave B. On 8/14/13 09:51:24.000, Peter Cock wrote: Hi Greg, I'm seeing something strange on a system running the August stable release of galaxy-dist, $ sudo -u galaxy hg head changeset: 10393:d05bf67aefa6 branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu mailto:n...@bx.psu.edu date:Mon Aug 12 11:55:41 2013 -0400 summary: Added tag release_2013.08.12 for changeset 1ae95b3aa98d changeset: 10390:009088d5e76f user:Ross Lazarus ross.laza...@gmail.com mailto:ross.laza...@gmail.com date:Sat Aug 10 11:28:28 2013 +1000 summary: Patch for missing options in FromDataTableOutputActionOption when these are used in an output filter 1. Run Galaxy 2. Log in as an administrator 3. Click on Admin (top menu) 4. Click on Manage installed tool shed repositories (left menu) 5. Observe duplicate entries: Names of repositories for which updates are available are highlighted in yellow. Description Owner RevisionInstallation Status Tool shed Galaxy wrappers for Emboss version 5.0.0 tools devteam c159a6ded912 Installed toolshed.g2.bx.psu.edu http://toolshed.g2.bx.psu.edu Galaxy applicable data formats used by Emboss tools. devteam a89163f31369 Installed toolshed.g2.bx.psu.edu http://toolshed.g2.bx.psu.edu Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. bgruening b1ad88bbc5fa Installed toolshed.g2.bx.psu.edu http://toolshed.g2.bx.psu.edu Gene calling with glimmer and a trainingset of know genes. bgruening 22bfc027a718 Installed toolshed.g2.bx.psu.edu http://toolshed.g2.bx.psu.edu Contains a tool dependency definition that downloads and compiles version 1.61 of the biopython package. biopython b482933a6de5 Installed toolshed.g2.bx.psu.edu http://toolshed.g2.bx.psu.edu NCBI BLAST+ 2.2.26 (binaries only) iuc c85236cd100d Installed testtoolshed.g2.bx.psu.edu http://testtoolshed.g2.bx.psu.edu NCBI BLAST+ 2.2.26 (binaries only) iuc 9ff9bfdcd04f New testtoolshed.g2.bx.psu.edu http://testtoolshed.g2.bx.psu.edu NCBI BLAST+ 2.2.26 (binaries only) iuc 0e536576294c New testtoolshed.g2.bx.psu.edu http://testtoolshed.g2.bx.psu.edu Contains a tool dependency definition that downloads and compiles version 2.4 of the freetype font library. iuc 8761091302c4 Installed toolshed.g2.bx.psu.edu http://toolshed.g2.bx.psu.edu Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package iuc 74c21f9bdc39 Installed toolshed.g2.bx.psu.edu http://toolshed.g2.bx.psu.edu As you can see I have been trying the NCBI BLAST+ package from the TEST tool shed, http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 Why are there these extra entries (older revisions) labelled with an Installation Status of New? Are they relics from failed installation attempts? Thanks, 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/ ___ 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/
