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 <nate@bx.psu.edu <mailto:nate@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.lazarus@gmail.com <mailto:ross.lazarus@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 <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
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