Hi Ole,
Ole Holm Nielsen writes:
> On 10/15/2018 01:54 PM, Loris Bennett wrote:
> ...
>> However, I found the following information regarding a newer version of
>> Lmod:
>>
>>https://lists.ugent.be/wws/arc/easybuild/2018-09/msg00030.html
>>
>> and
Dear Kenneth,
Kenneth Hoste writes:
> Dear Loris,
>
> On 12/10/2018 15:28, Loris Bennett wrote:
>> Hi,
>>
>> When tring to install via bootstrap_eb.py on CentOS 7 I get the
>> following error:
>>
>>[[INFO]] EasyBui
Hi,
When tring to install via bootstrap_eb.py on CentOS 7 I get the
following error:
[[INFO]] EasyBuild bootstrap script (version 20180925.01, MD5:
4e568883f293f94ade46a14d25cb6b94)
...
easybuild.tools.build_log.EasyBuildError: 'EasyBuild requires Lmod >= v6.6.3,
found v6.5.1'
The
n Tue, Oct 16, 2018 at 2:16 PM Loris Bennett
> wrote:
>
> Hi,
>
> I'm trying to install ORCA and have downloaded
>
> orca_4_0_1_2_linux_x86-64_openmpi202.tar.xz
>
> to my home directory. In this directory I run
>
> eb ORCA-4.0.1-OpenMPI-2.0.2.eb --robot --try-so
/tweaked_easyconfigs/o/ORCA/orca_4_0_1_2_linux_x86-64_openmpi202.tar.xz,
/tmp/eb-WkRm2h/tweaked_easyconfigs/ORCA/orca_4_0_1_2_linux_x86-64_openm
Where should I put the binary package or how should I tweak the
configuration, so that the package will be found?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT
ps://github.com/torch/ezinstall/issues/39#issuecomment-87905906
>
> Do you have that case where you are building on something which only has a
> single core?
>
> Alan
>
> On Fri, 9 Nov 2018 at 15:22, Loris Bennett wrote:
>
> Hi,
>
> I have just tried
>
'https://fossies.org/linux/misc/',
#'http://www.bzip.org/%(version)s/',
]
Why does it matter that the second URL is broken if the first is OK?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
rrectly:
buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"'
installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s"
Any idea what might be going wrong?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
htly pushed for time and probably have to recompile most
stuff anyway, I was wondering what is the most pragmatic way to
proceed.
Of the directories
apps/
build/
ebfiles_repo/
moduleData/
modules/
software/
sources/
could I just delete
build/
modules/
software/
?
Cheers,
could somehow be included by the current and all future
standard R easyconfigs?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
re1.eb ... softwareN.eb
> eb --job software1.eb ... softwareN.eb
> then EB will work out the dependencies for everything and parallelise the
> jobs where possible.
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
asybuild-life-sciences/blob/master/fh_easyconfigs/R-3.5.1-foss-2018b-fh1.eb
>
>
>
> John Dey
>
> On 1/18/19, 4:05 AM, "easybuild-requ...@lists.ugent.be on behalf of Loris
> Bennett" loris.benn...@fu-berlin.de> wrote:
>
> Hi,
>
> I'm instal
t;.
> https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/R-3.5.1-foss-2018b-fh1.eb
>
>
>
> John Dey
>
> On 1/18/19, 4:05 AM, "easybuild-requ...@lists.ugent.be on behalf of Loris
> Bennett" loris.benn...@fu-berlin.de> wrote:
>
&g
ven
> then you may still have a few corner cases that failand you will have to
> finish on the frontend.
>
> Alan
>
> On Fri, 18 Jan 2019 at 09:42, Loris Bennett
> wrote:
>
> Hi,
>
> As I need to build a lot of software in as short a time as possible I
> was c
Dear Kenneth,
Kenneth Hoste writes:
> Dear Loris,
>
> On 17/01/2019 11:07, Loris Bennett wrote:
>> Hi,
>>
>> I set up EasyBuild in my own home directory and managed to build a bunch
>> of software. I then copied the whole EasyBuild tree to a different
>>
overlooking the fact that either (a) there is some other problem
even if the modules don't overlap or (b) EasyBuild is even more
wonderful than I already think and can deal with this situation out of
the box?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email
ity/shared/easybuild/apps/lmod
and then linking
/etc/profile.d/z00_lmod.sh
to
/trinity/shared/easybuild/apps/lmod/init/profile
?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
Hi,
If the easyconfig for, say, Molden-5.8-foss-2018a.eb (Thanks, Kenneth!)
has been updated, my options seem to be
1. wait for the next EasyBuild update
2. run eb with --from-pr
Are there any other alternatives?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin
file into the o/ORCA/ subdirectory?
>
> What does "find /trinity/home/loris/shared/sources/o/ORCA -type f" print out?
>
>
> regards,
>
> Kenneth
>
> On 30/11/2018 13:26, Loris Bennett wrote:
>> Hi,
>>
>> I have
>>
>>export EASYBUI
Kenneth Hoste writes:
> On 04/12/2018 08:09, Loris Bennett wrote:
>> Dear Kenneth,
>>
>> I think the real problem is that the easyconfig is looking for
>>
>>orca_4_0_1_linux_x86-64_openmpi202.tar.xz
>>
>> whereas I have
>>
Kenneth Hoste writes:
> On 10/12/2018 07:39, Loris Bennett wrote:
>> Kenneth Hoste writes:
>>
>>> On 04/12/2018 08:09, Loris Bennett wrote:
>>>> Dear Kenneth,
>>>>
>>>> I think the real problem is that the easyconfig is looking
th (E) = /trinity/home/loris/shared/ebfiles_repo
robot-paths(D) =
/trinity/home/loris/shared/software/EasyBuild/3.7.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.7.1-py2.7.egg/easybuild/easyconfigs
sourcepath (E) = /trinity/home/loris/shared/sources
Cheers,
Loris
--
Dr. Loris Bennet
, say, rebuilding the modules?
2. Can a set of modules be defined which will be hidden by default?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
are you sure you want to hide the dependencies?
> I think it is useful for the users to know which deps are loaded, so
> they can avoid conflicts with other modules, even if it may look
> daunting to see 50+ modules loaded in some cases.
>
> Cheers,
> Sam
>
> On Fri, Nov 23, 201
ore this using "eb --ignore-checksums",
> but
> that's not recommended unless you're confident that you know what is causing
> the
> difference in checksum.
>
> On 19/11/2018 16:11, Loris Bennett wrote:
>>
>> Thanks, Alan. Next time I'll check the li
Kenneth Hoste writes:
> On 20/11/2018 07:43, Loris Bennett wrote:
>>
>> Yes, I can see that --ignore-checksums isn't ideal, particularly with
>> something like R with over 600 packages. It might be useful to be able
>> to configure how many failing checksums can be ig
':
['2ce542bcf841f722f34b936d44d859a53718a9de18ea24eb6ae843e042356795'],
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
he dependencies from being displayed if the installation of the
top-level packages has not been completed?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
Nov 2018 at 15:33, Loris Bennett
> wrote:
>
> Hi,
>
> The sha256 checksum for the R extension mgcv in R-3.5.1-foss-2018b.eb seems
> to
> be incorrect:
>
> == 2018-11-19 15:13:36,681 easyblock.py:517 INFO md5 checksum for
> /home/loris/
ache avail
>
> On Mon, 19 Nov 2018 at 15:47, Loris Bennett
> wrote:
>
> Hi,
>
> This maybe more of an Lmod problem. I have built two toolchains:
>
> [loris@admin ~]$ ll ~/shared/modules/toolchain/foss/
> total 0
> lrwxrwxrwx 1 loris loris 53 Nov 15 11:
the module files as
user 'build'. Is that correct?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
Åke Sandgren writes:
> It should work, I had no problems with it.
>
> But let's verify some things.
> Which version of EasyBuild are you using?
3.8.1
> On 4/1/19 4:31 PM, Loris Bennett wrote:
>> Hi,
>>
>> I have build QuantumESPRESSO using
>>
Hi,
I want to install a number of extra Perl packages. Is there an
equivalent of RPackage/PythonPackage for Perl? The easyblock PerlModule
seems to be aimed at installing a single module, rather than multiple
packages as extensions.
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie
ion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb
> .
>
>
> regards,
>
> Kenneth
>
> On 02/04/2019 15:47, Loris Bennett wrote:
>> Hi,
>>
>> I want to install a number of extra Perl packages. Is there an
>> equivalent of RPackage/PythonPackage for Perl? The
x-gnu
├── x86_64-unknown-linux-gnu_mpi
└── x86_64-unknown-linux-gnu_smp
What is the standard way of tweaking the PATH variable in such a case?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
Hi,
Ward Poelmans writes:
> Hi Loris,
>
> On 27/03/19 13:35, Loris Bennett wrote:
>
>>
>> However, the binaries are not directly under 'bin', but in the
>> subdirectories shown below:
>>
>> [build@admin bin]$ tree -L 1
>> .
>> ├── em64
e
mpiifort -mpi=sequential
Without the prebuildopts line, the package is built.
Does anyone know anything about the mixing of dynamic and static libs
in this case? Is it a real problem? If so, is there a more robust way
of dealing with it?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie
Hi Kenneth,
Kenneth Hoste writes:
> Dear Loris,
>
> On 02/04/2019 17:04, Loris Bennett wrote:
>> Dear Kenneth,
>>
>> OK, thanks for clarifying that point.
>>
>> One thing that surprised me in the context of trying to create a
>> extension-onl
est
I would assume this is just a dependency that I need to add to the list of
extensions, but when I mistakenly installed a whole Python along with
the extensions, I didn't see this error.
Is scipy.test part of some selftest within scipy, or is it something
EasyBuild is initiating?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
Hi Åke,
Thanks, that worked perfectly.
Cheers,
Loris
Åke Sandgren writes:
> See https://github.com/easybuilders/easybuild-easyconfigs/pull/7973 for
> a working PR for RDKit.
>
> On 4/1/19 3:05 PM, Loris Bennett wrote:
>> Hi,
>>
>> I am trying to write
with the HDF5 library being used.
Can anyone confirm that the Easyconfig is OK or should hdf5 be included
in the buildopts?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
ead_create'
collect2: error: ld returned 1 exit status
Any ideas?
Cheers,
Loris
PS: Is CMakePythonPackage the right easyblock? There don't seem to be
any easyconfigs which use it.
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
| |-- platform_common.zip
| `-- platform_glnxa64.zip
`-- R2018b_Update_2
|-- common
|-- glnxa64
|-- platform_common.zip
`-- platform_glnxa64.zip
How should the update be copied to the data extracted from the ISOs?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie
' in the easyconfig?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
/2018b as well
> (see https://github.com/easybuilders/easybuild-easyconfigs/pull/7759).
>
>
> regards,
>
> Kenneth
>
> On 27/02/2019 16:24, Loris Bennett wrote:
>> Hi,
>>
>> I am trying to build a tgz-file for MATLAB 2018b which EasyBuild can
>> digest.
. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
Computing
>
> Carl von Ossietzky University Oldenburg
> School of Mathematics and Natural Sciences
> 26111 Oldenburg, Germany
>
> Office: W03 1-139
> Phone: +49-441-798 3147
> E-Mail: stefan.har...@uni-oldenburg.de
> www: http://www.uni-oldenburg.de/fk5/wr
>
> -Ursp
cripts which
have been compiled with the MATLAB compiler
> We don't set any of them and things work perfectly as far as our users
> are concerned.
Do you use the MATLAB compiler?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
.
>
> What's your use-case?
>
> On 3/12/19 9:52 AM, Loris Bennett wrote:
>> Hi,
>>
>> I need to get $USER within an easyconfig. I found the documentation for
>> the Python module easybuild.tools.environment, but this doesn't seem to
>> be what I need.
>
implementation does not exist:
hooks/hpc_hooks.py
How should I be specifying the path?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
l requests and not so
much about maintaining local customisation.
Any thoughts?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
and complex, but it avoids having to
> create our own easyconfig for OpenMPI, IntelMPI, GROMACS at the moment.
>
> On 2/12/19 10:06 AM, Loris Bennett wrote:
>> Hi,
>>
>> I've just realised that I need to modify an easyconfig (I want to enable
>> the configuration for S
me think that there might be an
more suitable easyblock.
Any thoughts?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
is shown
has having been update dated 2017-07-17.
Any thoughts?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
or
> High Performance Research Computing
> TAMU Division of Research
> j-per...@tamu.eduhttp://hprc.tamu.edu
> HPRC Helpdesk: h...@hprc.tamu.edu
>
> On 4/12/19 2:59 AM, Loris Bennett wrote:
>> Hi,
>>
>> I'm trying to install
>>
>>NCL-6.5.0-intel-2
' and copy the files instead of letting 'make install'
be invoked, but then I would need to add the names of the scripts and
binaries to the EC explicitly.
What is the best approach?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
t;>
>> take and use an existing easyconfig? e.g. LASTZ-1.02.00-goolf-1.7.20.eb
>>
>> Best regards,
>>
>> Christian
>>
>> On 5/15/19 4:23 PM, Loris Bennett wrote:
>>> Hi,
>>>
>>> I have a program (http://last.cbrc.jp/) which prov
was a little
surprised not to find, say, version_revision as template.
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
Kenneth Hoste writes:
> On 17/05/2019 11:12, Loris Bennett wrote:
>> Hi,
>>
>> If I have a version
>>
>>1.2.3
>>
>> and for 'sources' need to convert this to
>>
>> v1r2.3
>>
>> is there a version template which wi
-DOPENBLASROOT=$EBROOTOPENBLAS"
> would be enough (seems like it just wants to know where it is).
>
> On Tue, 28 May 2019 at 10:29, Loris Bennett
> wrote:
>
> Hi,
>
> I'm writing an Easyconfig for OpenMolcas and am getting the error:
>
> -- Using OpenBLAS LAPACK+BLA
=ON -DOPENMP_ENABLE=ON -DLINALG=OpenBLAS"
sanity_check_paths = {
'files': [],
'dirs': [],
}
sanity_check_commands = []
modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
moduleclass = 'chem'
Cheers,
Loris
--
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ZEDAT, Freie Univ
i remember correctly, and that means MKL only.
>>
>> The OpenBLAS build does not generate an ilp64 version of the library at
>> the moment.
>>
>> On 5/31/19 10:38 AM, Loris Bennett wrote:
>>> Hi,
>>>
>>> I'm writing a easyconfig for OpenMolc
for the OpenBLAS module in
the foss-2018b toolchain, or is the error spurious?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
maybe you can
> improve upon it.
>
> Jack Perdue
> Lead Systems Administrator
> High Performance Research Computing
> TAMU Division of Research
> j-per...@tamu.eduhttp://hprc.tamu.edu
> HPRC Helpdesk: h...@hprc.tamu.edu
>
> On 6/6/19 9:20 AM, Loris Bennett wro
ng one of the above files. If "LAPACK"
provides a separate development package or SDK, be sure it has been
installed.
What am I doing wrong?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
* $CFGS1/c/CP2K/CP2K-5.1-intel-2018a.eb
* $CFGS1/c/CP2K/CP2K-6.1-foss-2019a.eb
* $CFGS1/c/CP2K/CP2K-6.1-intel-2018a.eb
Is there any particular reason why the buildopts don't just specify, say,
VERSION="sopt popt ssmp psmp"
?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie U
ted?
Note that I haven't had any problems reported to me which seem relevant
to this issue.
Note also that the commit referred to as being broken is nearly a year
old, so maybe the problem has been fixed in the meantime.
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin
Hi,
Ward Poelmans writes:
> Hi Loris,
>
> On 17/06/19 16:23, Loris Bennett wrote:
>>
>> Is there any particular reason why the buildopts don't just specify, say,
>>
>> VERSION="sopt popt ssmp psmp"
>>
>
> There is no speci
es such as C, C++, and Fortran."""
Isn't that a bit tendentious? It sounds like marketing blurb to me.
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
17/
Would it be possible to fix this?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
Hi Kenneth,
Kenneth Hoste writes:
> Hi Loris,
>
> On 09/05/2019 15:59, Loris Bennett wrote:
>> Hi,
>>
>> Having found the video, I was looking for the slide for Michael Bauers'
>> talk on "Containers in HPC with Singularity" from the 2nd EasyBuild Us
he refreshed
> R/3.5.1 PR.
>
> // Lars
>
> From: easybuild-requ...@lists.ugent.be on
> behalf of Loris Bennett
> Sent: Tuesday, May 14, 2019 16:58
> To: easybuild
> Subject: [easybuild] Installation of R/3.5.1-foss-2018b successful but
> incomplete
&
Loris Bennett writes:
> Dear Kenneth,
>
> Kenneth Hoste writes:
>
>> Dear Loris,
>>
>> On 30/04/2019 11:48, Loris Bennett wrote:
>>> Hi,
>>>
>>> I am trying t
.
There are only about 8 dependencies, so I can fix this by hand, but it
would be nice if I could rebuild the modules recursively.
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
Kenneth Hoste writes:
> On 15/05/2019 10:31, Loris Bennett wrote:
>> Hi Lars,
>>
>> Thanks for the info. I hadn't realised that the package list for a
>> specific version-toolchain combination could change.
>>
>> However, if I do '--force --skip' I get the
?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
therefore have to patch the install step into the
CMakeLists.txt file.
Or is there any alternative (besides getting the authors to fix their
program)?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
Hi,
I was looking at
https://github.com/easybuilders/easybuild-easyconfigs/pull/6917
and wondering what the current status is. Is there a
easyblock/easyconfig coming anytime soon? If not, I might have a look
at a Singularity-based solution.
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT
Dear Kenneth,
Kenneth Hoste writes:
> Dear Loris,
>
> On 30/04/2019 11:48, Loris Bennett wrote:
>> Hi,
>>
>> I am trying to write an easyconfig for RAxML-NG and have the following:
>>
>>
the following error: The following module(s) are
unknown: "CP2K/6.1-intel-2018a"
Aside from having a separate test system, what is the canonical way of
separating such speculative builds from the production setup?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universi
Loris Bennett writes:
> Hi,
> Ward Poelmans writes:
>
>> Hi Loris,
>>
>> On 17/06/19 16:23, Loris Bennett wrote:
>>>
>>> Is there any particular reason why the buildopts don't just specify, say,
>>>
>>> VERSION="sop
> toolchain = {'name': 'dummy', 'version': ''}
>
> See https://github.com/easybuilders/easybuild-framework/issues/2318
> and
> https://easybuild.readthedocs.io/en/latest/Concepts_and_Terminology.html?#dummy-toolchain
>
> Kind regards,
> Valentin
>
> On 2019-04-09 16
Loris Bennett writes:
> Hi,
>
> I want to write an easyconfig for SPM
>
> https://www.fil.ion.ucl.ac.uk/spm/software/spm12/
>
> which is a GPL toolbox for MATLAB. It comprises a bunch of MATLAB
> files, both in the top-level directory and in various subdir
',
('YAML', '1.29', {
'source_tmpl': 'YAML-%(version)s.tar.gz',
So is the YAML missing from the Perl 5.28.0 module or does BioPerl
depend on the wrong Perl module, or is something else going on?
Cheers,
Loris
--
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ZEDAT, Freie Universität Berlin
Dear Kenneth,
Kenneth Hoste writes:
> Dear Loris,
>
> On 21/08/2019 10:54, Loris Bennett wrote:
>> Hi,
>>
>> I'm trying to write an easyconfig for IOGA
>>
>>https://github.com/holmrenser/IOGA
>>
>> The setup script creates a python dicti
Hi Kenneth,
Kenneth Hoste writes:
> Hi Loris,
>
> On 16/08/2019 14:50, Loris Bennett wrote:
>> Hi,
>>
>> When I do
>>
>>$ module add BioPerl/1.7.2-foss-2018b-Perl-5.28.0
>>$ bp_genbank2gff3.pl -in test_in.gbff -out test_out.gff3
>>
>
ODO
autoconf should be run in .../MrBayes-3.2.7, rather than
.../MrBayes-3.2.7/src
What am I doing wrong?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
packages :-(
Cheers,
Loris
Åke Sandgren writes:
> You're not doing anything wrong, but since MrBayes changed layout
> between some 3.2 version and 3.2.7 the easyblock need to be updated.
>
> (Don't have time to look at this myself)
>
> On 8/27/19 1:23 PM, Loris Be
y also use -centos7.4-x86_64 as the version suffix, if you plan to
> submit this easyconfig upstream.
Added.
Cheers,
Loris
> Best regards, Mikael
>
> On Fri, Aug 9, 2019 at 2:55 PM Loris Bennett
> wrote:
>
> Hi Kenneth,
>
> Kenneth Hoste writes:
>
> &
y works. How should I create
the target directory (buildopts?) and how should I copy the files (I am
not really sure where the .so file should go relative to the .pm file)?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
> Cheers,
> Sam
>
> On Thu, Aug 29, 2019 at 4:10 PM Loris Bennett
> wrote:
>
> Dear Sam,
>
> Thanks for the suggestion, however I still don't get a 'lib' directory
> in the install dir. The log unfortunately doesn't give any indication
> that anything went wro
Loris Bennett writes:
> Hi,
>
> I'm looking at the following project:
>
> https://github.com/bcgsc/btl_bloomfilter
>
> which comprises a shared library and a corresponding Perl XS module.
>
> There is a Makefile, but it doesn't create the shared library or the
&
the Makefile should be
handling that?
Cheers,
Loris
Sam Moors writes:
> Dear Loris,
>
> Try this?
>
> files_to_copy = [(['swig/BloomFilter.pm', 'swig/BloomFilter.so'], 'lib')]
>
> Cheers,
> Sam
>
> On Thu, Aug 29, 2019 at 3:36 PM Loris Bennett
> wrote:
>
>
Footnotes:
[1] Would it make sense to consolidate the naming scheme, e.g. to replace
'postinstallcmds' with 'postinstall_cmd'?
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
> GPAW-19-8-1
> in the develop branch (or the merged pull request here:
> https://github.com/easybuilders/easybuild-easyconfigs/pull/8768/files )
>
> Best regards
>
> Jakob
>
>
>> On 26 Aug 2019, at 9:32, Loris Bennett wrote:
>>
>> Hi,
>>
>> If I ne
': ["IOGA.py", "IOGA_config.json" ],
'dirs': [''],
}
but the file IOGA_config.json isn't created and I can't see from the log
file why not.
Any ideas?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
ny
parameter names not conforming to the new convention could remain valid
but deprecated alternatives to new standardised names.
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
to deploy Singularity 3.3.0.
>
> Haven't cleaned it up enough for a PR, and there's new a new v3.4.0
> with support for encrypted containers that this EasyConfig should be
> adapted for, but I haven't had time to try it yet and see if any
> changes are needed.
>
> Kind regards,
> Va
on
> your site configuration/policies (e.g. dedicated software build user
> registered for restricted sudo commands, etc.).
>
> Kind regards,
> Valentin
>
> On 2019-09-12 13:16, Loris Bennett wrote:
>
> Hi Valentin,
>
> Thanks for the EasyConfig. I have modified it for
on
has appeared and have to disable the old version when I install a new
one. For the former I would just subscribe to the Singularity mailing
list. What would be the best approach for the latter? Would it be an
idea to have a constant, dummy version so that the existing version
would simply be repla
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