Question: Installed tools not appearing in list of tools
0
ablanchetcohen • 10 wrote:
Hi,
This is a new installation of Galaxy. I'm able to install tools, but they never appear in the list of installed tools.
These are what I believe to be the essential configuration files in galaxy.ini tool_sheds_config_file = config/tool_sheds_conf.xml tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
The tools do appear in the list of installed tools in the administration panel. I have restarted Galaxy several times.
tool_conf.xml never appears to get updated.
The installed tools do appear in the tools dependency directory specified in galaxy.ini. tool_dependency_dir = /stockage/galaxy/dependency_dir
Thank you for your help,
Alexis
ADD COMMENT
• link
•
modified 2.2 years ago
by
Aris Adam • 10
•
written
2.2 years ago by
ablanchetcohen • 10
is the tool listed in config/shed_tool_conf.xml ?
try removing the file 'integrated_tool_panel.xml' and then restart......though this bug has been fixed several releases ago
Hans-Rudolf
No, the installed tool, hisat2, does not appear in shed_tool_conf.xml.
[galaxy@gen01 config]$ grep hisat shed_tool_conf.xml [galaxy@gen01 config]$
I don't have a file called integrated_tool_panel.xml.
[galaxy@gen01 config]$ pwd /home/galaxy/galaxy/config [galaxy@gen01 config]$ ls ntegrated_tool_panel.xml ls: cannot access ntegrated_tool_panel.xml: No such file or directory [galaxy@gen01 config]$
The file shed_tool_conf.xml does contain an entry for bwa, that I tried to install previously, and then uninstalled. bwa does not appear in the list of available tools either though.
Thank you for your help.
It's probably in
/home/galaxy/galaxy(at least that'd be the equivalent of where mine ended up).I've tried restarting Galaxy yet again. I just don't see any changes.
hisat appears in the list of installed tools in the Admin panel, but a search of hisat in "Search tools" returns nothing, and there is no entry for hisat in tool_conf.xml.
Is tool_conf.xml supposed to get updated?
Am I supposed to uncomment this line in galaxy.ini, and then restart Galaxy?
# File that contains the XML section and tool tags from all tool panel config
# files integrated into a single file that defines the tool panel layout. This
# file can be changed by the Galaxy administrator to alter the layout of the
# tool panel. If not present, Galaxy will create it.
#integrated_tool_panel_config = integrated_tool_panel.xml
Sorry, this should not be a reply, but I clicked on the wrong button, and there is no delete option.
I did try uncommenting this line, and restarting Galaxy. No integrated_tool_panel.xml file appeared.
Still, none of the installed tools appear in the list of tools. :(
Has this issue been resolved? Just checking in. You can create a reply yourself that includes the solution and moderate this issue as accepted/resolved. Thanks, Jen, Galaxy team
No, I wish it had. :( I'll try do some more troubleshooting, and report the results here, but I'm still looking for an answer if anyone has one.
Have you been able to solve this? I'm currently experiencing similar issues.