[easybuild] bcl2fastq2 easyblock help

[Siddiqui, Shahzeb]

Hello,

I need to install bcl2fastq2 for a user and I was wondering if someone can help 
me get this working in EasyBuild. It uses a configure make to install the 
package, with a slight variation. The configure script is placed in inside  a 
"src" directory and it doesn't build in current directory but it can be 
bypassed with -force-builddir.

I have been able to install it with a custom easyblock, but I think the command 
"bcl2fastq" is not configured properly. I am not an expert on this tool so I 
have no way of testing it.

Please see: https://github.com/hpcugent/easybuild-easyblocks/issues/1110

Thanks

Shahzeb Siddiqui
HPC Linux Engineer
B2220-447.2
Groton, CT

Re: [easybuild] Playlist from 2nd EasyBuild User Meeting

[Vanzo, Davide]

Alan,
thank you from this side of the pond!

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu

On Feb 16 2017, at 4:46 am, Alan O'Cais  wrote:
Dear all,

I finished editing the videos from the 2nd User Meeting. You can find the full 
playlist at
https://www.youtube.com/playlist?list=PLVA9BuLC1j-yfxp2w-wraAGDCmhjb3o5Y

Enjoy!

Alan

--
Dr. Alan O'Cais
E-CAM Software Manager
Juelich Supercomputing Centre
Forschungszentrum Juelich GmbH
52425 Juelich, Germany

Phone: +49 2461 61 5213
Fax: +49 2461 61 6656
E-mail: a.oc...@fz-juelich.de
WWW:http://www.fz-juelich.de/ias/jsc/EN




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

Re: [easybuild] Issue with Matlab 2016b sources

[Jure Pečar]

On Thu, 16 Feb 2017 14:23:36 +0100
Kenneth Hoste  wrote:

> I would assume that the contents of both ISOs can simply be combined 
> into a single .tar.gz?
> 
> Long-term, we should look into support for unpacking .iso files 
> directly, but since this only pops up for MATLAB (afaik), this hasn't 
> received much attention.

Ansys has similar issue. Last time I did it, there were 4 dvd isos already that 
needed to be bundled into one tarball.


-- 

  Jurij Pečar
  HPC Engineer, IT Operations, IT Services
  EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
  Room 13-401

Re: [easybuild] Issue with Matlab 2016b sources

[Kenneth Hoste]

On 15/02/2017 21:13, Vanzo, Davide wrote:

Hello,
I have a question about the Matlab source files. In the 
Matlab easyconfig files the sources are expected to be in tar.gz 
format. However I have always received the installer in as an 
iso image. Until version 2016a it wasn't that big of a deal since i 
have generated the tar.gz by mounting the iso and creating the 
archive. With 2016b the installer is split into two iso disks.
So do you know if there is a way to get the tar.gz instead of the iso? 
If not, how would you suggest to tackle the issue?


I would assume that the contents of both ISOs can simply be combined 
into a single .tar.gz?


Long-term, we should look into support for unpacking .iso files 
directly, but since this only pops up for MATLAB (afaik), this hasn't 
received much attention.


Some work was done in refactoring the unpack support, but it never got 
finished, cfr. https://github.com/hpcugent/easybuild-framework/pull/864



regards,

Kenneth


--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu

[easybuild] Playlist from 2nd EasyBuild User Meeting

[Alan O'Cais]

Dear all,

I finished editing the videos from the 2nd User Meeting. You can find the full 
playlist at
https://www.youtube.com/playlist?list=PLVA9BuLC1j-yfxp2w-wraAGDCmhjb3o5Y

Enjoy!

Alan

--
Dr. Alan O'Cais
E-CAM Software Manager
Juelich Supercomputing Centre
Forschungszentrum Juelich GmbH
52425 Juelich, Germany

Phone: +49 2461 61 5213
Fax: +49 2461 61 6656
E-mail: a.oc...@fz-juelich.de
WWW:http://www.fz-juelich.de/ias/jsc/EN




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

Re: [easybuild] Stream for EasyBuild User Meeting

[Alan O'Cais]

Hi Maxime,

All your dreams have come true, I edited out the call drops in Barts
presentation. You can find the final result here (once youtube has finished
digesting it):
https://www.youtube.com/watch?v=ldsXmIuowtc

I'm making a playlist of the entire meeting now.

Alan

On 10 February 2017 at 17:43, Maxime Boissonneault <
maxime.boissonnea...@calculquebec.ca> wrote:

> Thanks.
> Are you planning to do some video edition (of Bart's presentation in
> particular) ?
>
> Maxime
>
>
> On 17-02-10 11:35, Kenneth Hoste wrote:
>
>
>
> On 10/02/2017 16:40, Maxime Boissonneault wrote:
>
> Hi Alan and Kenneth,
> Are the streams from yesterday available ?
>
>
> Wednesday:
>
> opening+Singularity+EasyBuild update: https://www.youtube.com/watch?
> v=Pjv2UppJANo
> Rob's + Damian's talk: https://www.youtube.com/watch?v=Pjv2UppJANo
> Lmod + XALT update: https://www.youtube.com/watch?v=r4gH7cPt-UI
>
> Thursday:
>
> easyblocks tutorial: https://www.youtube.com/watch?v=iDXsYP2PVJs
> site presentations: https://www.youtube.com/watch?v=6ve8U4ph5eM
> Bart's presentation (incl. the chipmunk mode):
> https://www.youtube.com/watch?v=5VcWnVbJIR0
>
> See also http://hpcugent.github.io/easybuild/files/EUM17/ for links to
> the slides (I'll still need to get my hands on Bart's slides...)
>
> We hope to clean up the recordings a bit sometime soon, i.e. trimming
> start/end, split up into individual talks.
>
>
> K.
>
>
> Maxime
>
> On 17-02-08 03:58, Alan O'Cais wrote:
>
> Dear all,
>
> For those who couldn't make it, the stream for the EasyBuild User Meeting
> is available at
> https://youtu.be/Pjv2UppJANo
>
> We will try hard to keep to the schedule
> .
>
> Alan
>
> --
> Dr. Alan O'Cais
> E-CAM Software Manager
> Juelich Supercomputing Centre
> Forschungszentrum Juelich GmbH
> 52425 Juelich, Germany
>
> Phone: +49 2461 61 5213 <02461%20615213>
> Fax: +49 2461 61 6656 <02461%20616656>
> E-mail: a.oc...@fz-juelich.de
> WWW:http://www.fz-juelich.de/ias/jsc/EN
>
>
> 
> 
> 
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> 
> 
> 
> 
>
>
>
> --
> -
> Maxime Boissonneault
> Analyste de calcul - Calcul Québec, Université Laval
> Président - Comité de coordination du soutien à la recherche de Calcul Québec
> Team lead - Research Support National Team, Compute Canada
> Instructeur Software Carpentry
> Ph. D. en physique
>
>
>
>


-- 
Dr. Alan O'Cais
E-CAM Software Manager
Juelich Supercomputing Centre
Forschungszentrum Juelich GmbH
52425 Juelich, Germany

Phone: +49 2461 61 5213
Fax: +49 2461 61 6656
E-mail: a.oc...@fz-juelich.de
WWW:http://www.fz-juelich.de/ias/jsc/EN