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="">
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:
<package name="macs" version="18.104.22.168">
<package name="R" version="2.15.0">
<repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0"
owner="devteam" prior_installation_required="False" toolshed="
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
while in the same dir, macs_wrapper.xml has:
<requirement type="package" version="22.214.171.124">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?
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:
To search Galaxy mailing lists use the unified search at: