conda installation fails

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conda installation fails

Matthias Bernt
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' 
&& 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

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,
[hidden email], 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:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------


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Re: conda installation fails

Marius van den Beek
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-library-path.

On 19 April 2017 at 17:57, Matthias Bernt <[hidden email]> 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' && 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

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 <a href="tel:%2B49%20341%20235%20482296" value="+49341235482296" target="_blank">+49 341 235 482296,
[hidden email], 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: MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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  http://galaxyproject.org/search/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: conda installation fails

Björn Grüning-3
In reply to this post by Matthias Bernt
Hi,

I second Marius here, I would not try to fix the miniconda installation,
but rather fix the `tar` installation. This is not the original COS6.8
behaviour right?

Ciao,
Bjoern

Am 19.04.2017 um 17:57 schrieb Matthias Bernt:

> 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'
> && 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
>
> Any suggestions? The line removal procedure seems to be quite
> complicated in an automated ansible installation which I try to achieve.
>
> Cheers,
> Matthias
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: conda installation fails

Matthias Bernt
In reply to this post by Marius van den Beek
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-library-path.
>
> On 19 April 2017 at 17:57, Matthias Bernt <[hidden email]
> <mailto:[hidden email]>> 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>,
>     [hidden email] <mailto:[hidden email]>, 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:
>     MinDirig Wilfried Kraus
>     Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
>     Prof. Dr. Dr. h.c. Georg Teutsch
>     Administrative Geschäftsführerin/ Administrative Managing Director:
>     Prof. Dr. Heike Graßmann
>     -------------------------------------------
>
>
>     ___________________________________________________________
>     Please keep all replies on the list by using "reply all"
>     in your mail client.  To manage your subscriptions to this
>     and other Galaxy lists, please use the interface at:
>       https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>
>
>     To search Galaxy mailing lists use the unified search at:
>       http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
>
>
--

-------------------------------------------
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,
[hidden email], 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:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

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