I have just installed Galaxy locally in a Linux server (Fedora 14). I tried to install htseq (htseq_count, package_htseq_0_6) from "Search Tool Shed". package_htseq_0_6 showed "Installed, missing tool dependencies" from "Manage installed tools". The missing dependency is matplotlib 1.2.1 with the error message "Error installing tool dependency matplotlib version 1.2.1: Unable to locate the repository directory for revision 48020985e28c of installed repository package_matplotlib_1_2 owned by iuc". I couldn't find any package with a name "matplotlib". On the "Dependency Resolver Details" for htseq_count, samtools (0.1.19) and htseq (0.6.1.post1) have the Status with red cross symbol. When I tried to run htseq_count, I got error message "Fatal error: The HTSeq python package is not properly installed, contact Galaxy administrators ....". Please help in resovling this problem. Thanks.
I can reproduce this with the lastest version of htseq_count that makes use of Conda dependencies. The prior version (without Conda) installs without issue. Installs were tested on a default 16.07 master Galaxy.
Conda dependencies are still in Beta. I suggest installing the earlier version for now (that is also the version currently installed at Galaxy main http://usegalaxy.org).
I did contact the tool owner and the dev team (internally) to bring their attention to the issue. It is not exactly clear at this time what is causing the install failure for the conda-sourced dependencies. No issues have been created yet.
I will bookmark this for additional feedback as it comes in. Others are welcome to comment and/or add in their experiences installing this tool here as well.
Best, Jen, Galaxy team