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.
Hello,
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
Hi, Jen,
Should I install an earlier version of Galaxy or an earlier version of htseq_count? Thanks.
From: Jennifer Hillman Jackson on Galaxy Biostar [notifications@biostars.org] Sent: Friday, November 18, 2016 4:13 PM To: Yuan, Qiaoping (NIH/NIAAA) [E] Subject: [galaxy-biostar] Tool htseq_count installation on a local Galaxy
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User Jennifer Hillman Jacksonhttp://biostar.usegalaxy.org/u/254/ wrote Answer: Tool htseq_count installation on a local Galaxyhttp://biostar.usegalaxy.org/p/20588/#20593:
Hello,
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
Following Jen's suggestion, I have re-installed htseq_count with an earlier version: 0.6.1galaxy1, 21 (2015-07-28). This earlier version of htseq_count works now in my local Galaxy. Thanks to all of you.
What version of Galaxy are you using? There was a change after 16.01 that normally fixed stuff like this (i.e., it allowed using more recent releases of the same package in the toolshed if a given release is no longer available). At least if you have 16.01, then there's a patch that can be applied (let me know if that's what you need, then I or someone else can find it for you).
I don't know where I can find the exact version of my local installed Galaxy. But from the "Makefile" under the Galaxy installation dir, I saw "RELEASE_CURR:=16.01" and "RELEASE_NEXT:=16.04". However, lib/galaxy/version.py has VERSION_MAJOR = "16.07".