Question: Tool htseq_count installation on a local Galaxy
1
gravatar for qyuan
7 months ago by
qyuan30
qyuan30 wrote:

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.

ADD COMMENTlink modified 7 months ago • written 7 months ago by qyuan30
1

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).

ADD REPLYlink written 7 months ago by Devon Ryan1.5k

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".

ADD REPLYlink written 7 months ago by qyuan30
1
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson22k wrote:

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

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson22k

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

Activity on a post you are following on Galaxy Biostarhttp://biostar.usegalaxy.org

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

ADD REPLYlink written 7 months ago by qyuan30
1
gravatar for qyuan
7 months ago by
qyuan30
qyuan30 wrote:

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.

ADD COMMENTlink written 7 months ago by qyuan30

Glad that worked! Jen

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson22k
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