Dear list,

found a solution (aka dirty hack), if anybody is interested:

The problem is that our cluster uses environment modules (http://modules.sourceforge.net/) to provide software (basically by setting and unsetting PATHs...). Because python needs bz2 support for galaxy I needed to load bzip2 as module since the dynamic library was not available otherwise. This module also provides a bunzip2 binary which led to a clash when the LD_LIBRARY_PATH was unset during conda installation (the module's bunzip2 still wanted to have the dynamic library and the systems bunzip2 was later in the PATH).

Solution:

I created a copy of the module which appends the needed paths to the various environment variables (instead of prepending). Then the systems bunzip2 used and the shared object is still available.

Cheers, Matthias

On 19.04.2017 18:15, Marius van den Beek wrote:

That's a little weird, I don't think relying on the system's LD_LIBRARY_PATH is good practice. Maybe you could try what was suggested in the last answer here: https://serverfault.com/questions/372987/centos-usr-local-lib-system-wide-ld....

On 19 April 2017 at 17:57, Matthias Bernt <m.bernt@ufz.de mailto:m.bernt@ufz.de> wrote:

Dear list,

Just found out that conda is not installing on our CentOS6.8
installation (might be related to earlier messages).

The problem is that the shell script installing conda unsets the
LD_LIBRARY_PATH which makes tar dysfunctional (tar is called by the
installer).

The command line that is executed during galaxy's installation is

wget -q --recursive -O '/tmp/conda_install7tWo7r.sh'
'https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh
<https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh>'
&& bash '/tmp/conda_install7tWo7r.sh' -b -p
'/gpfs1/data/galaxy_server/galaxy-dev/_conda' &&
/gpfs1/data/galaxy_server/galaxy-dev/_conda/bin/conda install -y -q
conda=4.2.13

Removing the unset LD_LIBRARY_PATH line (and fiddling around with
some file size checks) is (seemingly) successful.

There is an open issue on the conda github:
https://github.com/conda/conda/issues/3632
<https://github.com/conda/conda/issues/3632>

Any suggestions? The line removal procedure seems to be quite
complicated in an automated ansible installation which I try to achieve.

Cheers,
Matthias

--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>,
m.bernt@ufz.de <mailto:m.bernt@ufz.de>, www.ufz.de <http://www.ufz.de>

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
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Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
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