Hi Guys,

Sorry for the duplicate posting...nobody saw my original one seems and I'm
still wondering what the proper way is. I searched around the wiki but
didn't find much.

Originally, I installed macs dependency for galaxy myself. The version is
1.4.2. It worked well.

Now, after galaxy upgrading removed it, and I installed it back from
tool_shed, things broke. In the galaxy tool panel, it looks the same like
before(as expected), but when I click on macs, it will show an option of
MACS 'version 1.0.0' and 'version 1.0.1'. Be default it is 1.0.1, which is
defined in migrated_tools_conf.xml:

<section id="peak_calling" name="NGS: Peak Calling" version="">
  <tool file="


if we dive in this file
we could see that in this dir /home/bioinfoadmin/app/shed_tools/
toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs, there is a
tool_dependency xml file that has following content:

<?xml version="1.0"?>
  <package name="macs" version="">
      <repository changeset_revision="a7ea583a35d2"
name="package_macs_1_3_7_1" owner="devteam"
prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu";
    <package name="R" version="2.15.0">
      <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0"
owner="devteam" prior_installation_required="False" toolshed="
http://toolshed.g2.bx.psu.edu"; />

These versions are both older than what we installed before(1.4.2 and
3.0.2). could we manually modify that to use our own? wouldn't that be a
bad practice?

while in the same dir, macs_wrapper.xml has:

    <requirement type="package" version="">macs</requirement>
    <requirement type="package" version="2.15.0">R</requirement>

Seems that this is the tool_shed version of macs(which is identical to the
one on main galaxy server, I think?). However this one does not work with
our input data. Additionally, when I click to switch from 1.0.1 to 1.0.0 of
macs, it immediately reports error.

So, what if I want to keep using the one I installed myself? I know that
tool_shed is a cleaner way to manage tools, but in our situation the
upgrade and elimination actually broke the thing that worked before. I want
to ask the proper way to handle this kind of situation. could I simply drop
the entry from migrated_tools_conf.xml about macs, and restore the old
tools_conf.xml entry? in that way we could continue using the 1.4.2 we
have. However next time when we do the upgrade, things will break again I

I think that I shouldn't be the only person that has this concern? how to
handle multiple version/dependency version for a tool? is there an option
to not use the tool_shed but keep own version?

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