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galaxybot
@galaxybot
[clements] Hi All, just a reminder that * talk abstracts for GCCBOSC are due this Friday.* https://galaxyproject.org/galaxy-updates/2018-03/#abstract-submission-registration-and-housing-are-open
[mrscribe] Title: March 2018 Galaxy News (at galaxyproject.org)
[clements] And, we'll be announcing conference-subsidized childcare later this week. So, don't let that hold you back.
Martin Cech
@martenson
@jmchilton I will kill it for now
Nicola Soranzo
@nsoranzo
Is there any good reason to show composite datatypes in the Type dropdown of the upload window when the Regular tab is selected?
Martin Cech
@martenson
probably not
Nicola Soranzo
@nsoranzo
@emily9542 I'd suggest to the tool authors to use Conda for tool dependencies instead of ToolShed packages
Micropathology
@Micropathology
Is there anything indicative of all newly installed tools giving command not found errors?
selten
@selten
Apart from running the tool that would fail?
or the i button showing 'command not found'?
Micropathology
@Micropathology
Sorry that read wrong. I meant is there an obvious problem which would cause all newly installed tools to produce this error?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
Something wrong with your conda installation ? Anything in the logs ?
Micropathology
@Micropathology
I checked the galaxy logs and its saying that python and conda need to be updated. I'm not sure why this is suddenly the case. The only thing I have done recently to the cluster is to resize the partition.
Martin Page
@doomedramen
Hey all, got a bug question for you, I know you love them
Ghost
@ghost~5772e7e2c2f0db084a206e1b
shoot
Martin Page
@doomedramen
Adding datasets to galaxy ("from path"), when selecting "Link files instead of copying" I had assumed it would make a symbolic link...
Ghost
@ghost~5772e7e2c2f0db084a206e1b
@Micropathology what exactly are the logs saying ?
Martin Page
@doomedramen
turns out this is not the case
Ghost
@ghost~5772e7e2c2f0db084a206e1b
it should be, unless you also checked line ending conversion
Martin Page
@doomedramen
I dont see an option for that here
Micropathology
@Micropathology

galaxy.tools.deps.conda_util DEBUG 2018-03-15 07:58:26,700 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel r --channel bioconda --channel iuc --name __unicycler@0.4.4 unicycler=0.4.4
Fetching package metadata: ......
Error: No packages found in current linux-64 channels matching: python 2.7*

You can search for this package on anaconda.org with

anaconda search -t conda python 2.7*

You may need to install the anaconda-client command line client with

conda install anaconda-client
Martin Page
@doomedramen
"Preserve directory structure AND Link files instead of copying"
Micropathology
@Micropathology
this what happened when i tried to run unicyler
Ghost
@ghost~5772e7e2c2f0db084a206e1b
and that was working fine previously ?
@wookoouk what galaxy version is that ?
Micropathology
@Micropathology
no there are a number of tools that I installed recently that have this error, but tools installed in the past work
Ghost
@ghost~5772e7e2c2f0db084a206e1b
right, so unicycler is python3 only, but also your channel order is not correct
Martin Page
@doomedramen
@mvdbeek 15.10
Ghost
@ghost~5772e7e2c2f0db084a206e1b
hmm, i've been using the link form filesystem option with recent galaxy versions and that worked fine
but 15.10 is pretty old
it's possible this was fixed in the meantime
@Micropathology I'd suggest updating conda and galaxy to the latest versions respectively. Now unicycler is a bad example because it is python3 only
Micropathology
@Micropathology
is it possible that conda broke somehow and cannot install too dependencies? what is channel order?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
yes, conda is being actively developed, and the channel order changes
every now and then. we account for this in galaxy, but we don't automatically upgrade installed conda versions
Micropathology
@Micropathology
so periodically I have to update conda? will this sort out the channel order?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
no, that is a galaxy setting
and yes, often new packages can't be installed with old conda versions
The channel order is configured with https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L228
galaxybot
@galaxybot
[mrscribe] Title: galaxy/galaxy.yml.sample at dev · galaxyproject/galaxy · GitHub (at github.com)
Ghost
@ghost~5772e7e2c2f0db084a206e1b
at the time of a galaxy release we ship the current default order, but this can change as I mentioned
now old galaxy versions don't entirely respect the configured channel order, that's why I'd advise to also upgrade galaxy
which would come with the correct default channel order
Micropathology
@Micropathology
I'm using 17.09
Ghost
@ghost~5772e7e2c2f0db084a206e1b
right, and the default channel order changed after the 17.09 release
and the bug fix to respect the specified channel order was also applied after the 17.09 release
it should be as simple as git pull if you're on the 17.09 branch
Micropathology
@Micropathology
right ok I think I'm understanding now. I need to keep galaxy upto date or I'm going to get tool install problems.
Ghost
@ghost~5772e7e2c2f0db084a206e1b
now for the case of unicycler you can probably install it with /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channels defaults --name __unicycler@0.4.4 unicycler=0.4.4 python=3
note that i've change the channel order and added python=3