That's pretty much what I had to do. Thanks for the full explanation so
others will know!
Philip Mabon
Senior Bioinformatician
National Microbiology Laboratory
Public Health Agency of Canada
On Wed, Aug 29, 2012 at 10:31 AM, Assaf Gordon wrote:
> Hello Philip,
>
> Philip Mabon wrote, On 08/29
Hello Philip,
Philip Mabon wrote, On 08/29/2012 10:08 AM:
> Looks like I forgot to reset that value. So making progress... I can install
> freebayes successfully (the front end timeout but it worked)
>
> However, samtools fails with the following message in web worker log:
>
> [localhost] local
You should be able to click on the link for the samtools dependency from the
"Installed tool shed repository" page for freebayes. Clicking the link will
allow you to browse the INSTALLATION.LOG on disk and see what caused the
error. Your environment is probably missing some component required
Looks like I forgot to reset that value. So making progress... I can
install freebayes successfully (the front end timeout but it worked)
However, samtools fails with the following message in web worker log:
[localhost] local: sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile
Warning: local() enco
Hi Philip,
What do you have for the following configuration setting in the [app:main]
section of your universe_wsgi.ini file? The config setting for
tool_dependency_dir should be a valid subdirectory that is writable by the user
that starts your Galaxy server.
# Location for installing tool d
I upgrade Galaxy to changeset 2531e085f262 and attempt to install freebayes
from the admin panel.
It installed the freebaye xml tool and appears in the tool panel but both
dependencies did not install (freebayes itself and samtools)
When I attempt to install either of them from the "Tool shed rep
Philip,
Is it possible for you to upgrade your Galaxy instance code base to at least
changeset 2531e085f262 (the human-readable changeset revision is 7503)? I'm
not sure what is causing the behavior in your environment, but I had to upgrade
the tool shed to this rev in order to deal with some
I already had that entry to the tool_data_table_conf.xml but still getting
the same error.
After some debugging and print statement, I found that it initially finds
the correct path to the 'sam_fa_indexes' when reading
tool_data_table_conf.xml in Galaxy installation directory but re-reads
another
Hi Phillip,
I'm not able to reproduce this behavior, so it's difficult to determine what
may be the cause. I have not seen others in the community encounter this
problem, but that may simply be due to the fact that no one is yet installing
the freebayes tool from the tool shed.
A possible wor
Any ideas anyone?
Philip Mabon
Senior Bioinformatician
National Microbiology Laboratory
Public Health Agency of Canada
On Tue, Aug 21, 2012 at 10:34 AM, Philip Mabon wrote:
> I just upgrade our galaxy to the latest release : 7487:be81990d148a and
> ran the migration tool script for freebayes.
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