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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