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=" 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"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>macs</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>ae2ec275332a</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1 </id> <version>1.0.1</version> </tool> </section> 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: <?xml version="1.0"?> <tool_dependency> <package name="macs" version="1.3.7.1"> <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> <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" /> </package> </tool_dependency> 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: <requirements> <requirement type="package" version="1.3.7.1">macs</requirement> <requirement type="package" version="2.15.0">R</requirement> </requirements> 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? Thanks, Rui