IN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
>> PERL_MM_OPT=INSTALL_BASE=/root/perl5
>> XAUTHORITY=/tmp/.Xauthority.root
>> BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*`
>> }
>> _=/usr/bin/env
>> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@st
gerhard
*From:* Björn Grüning
*Sent:* 10 July 2018 08:49:04
*To:* Van Wageningen, GERHARD [gerha...@sun.ac.za];
galaxy-dev@lists.galaxyproject.org
*Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
environment
Which means
your input - must appreciated!
gerhard
From: Björn Grüning
Sent: 10 July 2018 08:49:04
To: Van Wageningen, GERHARD [gerha...@sun.ac.za];
galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Conda problems: Failed to activate conda environment
Which means
Wageningen, GERHARD [gerha...@sun.ac.za];
galaxy-dev@lists.galaxyproject.org
*Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
environment
Hi,
can you do:
. /home/.galaxy/tooldeps/_conda/bin/activate
'/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
And see if
problems: Failed to activate conda environment
Hi,
can you do:
. /home/.galaxy/tooldeps/_conda/bin/activate
'/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
And see if you can execute trim_galore from the commandline and get the
help?
Ciao,
Bjoern
Am 10.07.2018 um 08:34 schrie
ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
Björn Grüning ;
galaxy-dev@lists.galaxyproject.org
*From:* Björn Grüning
*Sent:* 05 July 2018 22:00:58
*To:* Van Wageningen, GERHARD [gerha...@sun.ac.za];
galaxy-dev@list
SAT2_ROOT_DIR
HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
export HISAT_ROOT_DIR
The conda environment with dependencies seems to be there:
/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
dencies/_conda/envs/*; do
> for link in conda activate deactivate; do
>\[ -h $env/bin/$link \] || ln -s "{{ galaxy_server_dir
> }}"/database/dependencies/_conda/bin/$link $env/bin/$link;
> done
> done
> ```
>
> Hope this helps.
&
helps.
Cheers,
Matthias
On 05.07.2018 18:00, galaxy-dev-requ...@lists.galaxyproject.org wrote:
Message: 1
Date: Thu, 5 Jul 2018 08:14:35 +0000
From: "Van Wageningen, GERHARD [gerha...@sun.ac.za]"
To:"galaxy-dev@lists.galaxyproject.org"
Subject: [galaxy-dev] C
8 08:14:35 +
> From: "Van Wageningen, GERHARD [gerha...@sun.ac.za]"
>
> To:"galaxy-dev@lists.galaxyproject.org"
>
> Subject: [galaxy-dev] Conda problems: Failed to activate conda
>environment
> Message-ID:
>
>
>
>
07.2018 18:00, galaxy-dev-requ...@lists.galaxyproject.org wrote:
Message: 1
Date: Thu, 5 Jul 2018 08:14:35 +
From: "Van Wageningen, GERHARD [gerha...@sun.ac.za]"
To:"galaxy-dev@lists.galaxyproject.org"
Subject: [galaxy-dev] Conda problems: Failed to activate conda
Hi Gerhard,
it seems your tool is picking up the old tool_dependency version and not
the conda version of python.
Have a look at
https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample
to configure the order of dependency resolution in Galaxy.
Cheers,
B
Hi All
I have recently started learning the Galaxy setup starting with an upgrade.
Made some headway but I was wondering if someone could comment on a problem
that has emerged.
The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair
PBS scheduler with drmaa setup (working)
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