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="toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1">
if we dive in this file toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml, 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="220.127.116.11">
<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="18.104.22.168">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 guess?
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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