Tool Installation from Tool Shed

Question: Tool Installation from Tool Shed

2.7 years ago by

hortowe • 10 wrote:

Hi all,

I recently downloaded and installed a local version of Galaxy and am following some basic tutorials. I'm currently attempting to install a tool from the toolshed (https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial).

I checked the tool_sheds_conf.xml file and the main tool shed is there.

I also created a tool dependencies directory: /config/tool_dependencies and edited my galaxy.ini file: (line 173) tool_dependency_dir = config/tool_dependencies

I follow the rest of the instructions to search for and install the tool (I'm attempting to install PEAR, but I receive the same error regardless of the tool I attempt to install)

On my galaxy interface, in the "monitor installing tool shed repositories," the status goes from "new" to "error" and in my terminal output, I get:

galaxy.tools.toolbox.base DEBUG 2016-03-25 11:19:04,590 Appending to tool panel section: Preprocess tool_shed.util.hg_util DEBUG 2016-03-25 11:19:04,779 Error cloning repository: can't clear options before OpenSSL 0.9.8m

I appreciate any help/suggestions on how to go about figuring this out!

galaxy • 1.1k views

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modified 2.7 years ago by Martin Čech ♦♦ 4.9k • written 2.7 years ago by hortowe • 10

2.7 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

You might be experiencing this Python bug:

http://bugs.python.org/issue12440

In which case I would start with confirming your Python version and then following the steps from the link above.

ADD COMMENT • link modified 2.7 years ago • written 2.7 years ago by Martin Čech ♦♦ 4.9k

Thanks for the reply Martin. I don't think that python bug applies to me, my python version is Python 2.7.10 and I'm running OS X Yosemite 10.10.5. I followed the instructions in the final answer on that stack overflow link and have this: ~$ which python /usr/local/bin/python

~$ ls -la /usr/local/bin/python /usr/local/bin/python@ -> /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python

But still received the same error. I also edited my .bash_profile to contain: export DYLD_LIBRARY_PATH=/usr/bin/openssl:$DYLD_LIBRARY_PATH

As well as checked shared libraries with: ~$ otool -L /usr/bin/openssl /usr/bin/openssl: /usr/lib/libcrypto.0.9.8.dylib (compatibility version 0.9.8, current version 0.9.8) /usr/lib/libssl.0.9.8.dylib (compatibility version 0.9.8, current version 0.9.8) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)

Still getting the same error. Should I be setting something differently with the DYLD_LIBRARY_PATH?

ADD REPLY • link written 2.7 years ago by hortowe • 10

I am afraid I cannot help you more here as I am far from being a sysadmin and this feels like a sysadmin problem. I have a very similar system to yours and never seen this problem. Maybe somebody else will respond.

ADD REPLY • link written 2.6 years ago by Martin Čech ♦♦ 4.9k

I ended up just switching to a new computer...not much of a solution but at least I don't have to worry about it anymore! Thanks for your help.

ADD REPLY • link written 2.6 years ago by hortowe • 10

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