Re: [easybuild] bcl2fastq2 easyblock help

I have written one also. bcl2fastq only seems to work with Boost 1.55. Please see: https://github.com/FredHutch/easybuild-life-sciences/ On Thu, Feb 16, 2017 at 4:39 PM, Robert Schmidt wrote: > I have an easyconfig here: > >

Re: [easybuild] Easyconfig extensions update tool

hought I'd mention the 'easy_update' > tool that John Dey has released, which will check through R, Perl and > Python easyconfigs and create new versions with updated extensions. > > > It's available at: > > > https://github.com/fizwit/easy_update.git > <https://github.com/fiz

[easybuild] scipy 1.18 fails sanity check

building Python-3.6.0 with scipy 0.18.1 easybuild Version 2.9.0 easyblocks 2.9.0 Ubuntu 14.04 LTS == FAILED: Installation ended unsuccessfully (build directory: /app/easybuild/build/Python/3.6.0/foss-2016b): build failed (first 300 chars): Sanity check failed: no file of

[easybuild] PythonModule

How do you add a Python module which is a wheel (whl) when building Python with easybuild? How can a Python wheel be installed as part of the exts_list ? This is a small section of my Python easyconfig file. use_pip = True exts_list = [ ... ('ont_albacore', '1.0.2', { 'source_tmpl':

Re: [easybuild] resume build R

/FredHutch/easybuild-life-sciences John Dey j...@fuzzdog.com On Tue, Nov 21, 2017 at 12:37 AM, Kenneth Hoste <kenneth.ho...@ugent.be> wrote: > Dear Yann, > > On 21/11/2017 09:34, Yann Sagon wrote: > > Hello, > > I'm trying to build R using R-3.3.1-foss-2016b.eb wit

[easybuild] Toolchains

to build packages and also for our computing environment.* *John Dey* *HPC Operations* SciComp Computing *O* *206.667.4308* *M* *360.649.2731* jf...@fredhutch.org Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N., Mail Stop J3-516 Seattle, WA 98109 *fredhutch.org* <h

[easybuild] R extensions failing sanity check

ciences/tree/master/fh_easyconfigs> /*R-3.5.1-foss-2016b-fh1.eb* John Dey j...@fuzzdog.com

[easybuild] sanity check for R

I have never seen a sanity check failure for R extensions until upgrading to EB 3.6.2. I now have 53 failures. How is EB testing sanity? Many of these packages output citation information, copyright notices, brief tutorials, etc... when loaded with library command. John Dey j...@fuzzdog.com

[easybuild] new release of easy_update

I have released a new version of easy_update. It is available https://github.com/FredHutch/easybuild-life-sciences/ John Dey j...@fuzzdog.com

Re: [easybuild] EasyBuild 3.5.3 PythonPackage IndexError: list index out of range

://github.com/FredHutch/easybuild-life-sciences John Dey j...@fuzzdog.com On Mon, Apr 16, 2018 at 11:26 AM, Dey, John F <jf...@fredhutch.org> wrote: > EasyBuild error. Package seems to build and test ok. Easybuild fails > during package install > > Easyconfig: https://github.com/F

Re: [easybuild] [ANN] 5th EasyBuild User Meeting: Wed-Fri 29-31 Jan 2020 in Barcelona

When is the tour of the Bacelona Super Computer? John Dey j...@fuzzdog.com On Mon, Jan 13, 2020 at 7:14 AM Kenneth Hoste wrote: > Dear EasyBuilders, > > The agenda for the 5th EasyBuild User Meeting is now almost complete, > see > > https://github.com/easybuilders/easybuild/

Re: [easybuild] BOINC, other distributed computing platforms for Coronavirus research?

our local cluster. https://bedford.io/blog/ <https://bedford.io/blog/> https://nextstrain.org/ncov <https://nextstrain.org/ncov> --  <> John Dey HPC Operations Scientific Computing O 206.667.4308 M 360.649.2731 E jf...@fredhutch.org <mailto:jf...@fredhutch.org>

Re: [easybuild] Build Biopython-1.75-foss-2019b-Python-2.7.16.eb failed

are you getting errors about poetry John Dey j...@fuzzdog.com > On Jul 1, 2020, at 8:27 AM, Yann Sagon wrote: > > Dear list, > > I'm trying to build Biopython-1.75-foss-2019b-Python-2.7.16.eb with > EeasyBuild 4.2.1 and it fails with a LOT of errors in the tests (

Re: [easybuild] Build failure with GCC 10.2.0: multiple definition of 'replica_index'

The default with GCC 10.2 is to compile with -fn-common which is causing many issues with packages. In every case, I have encountered the software should be patched. https://gcc.gnu.org/gcc-10/porting_to.html John Dey j...@fuzzdog.com On Mon, Feb 22, 2021 at 5:45 AM Loris Bennett wrote: >

Re: [easybuild] Convention for Recipe modifications

.github.io/easybuild-life-sciences/r/fhR-4.1.0-foss-2020b/ the scripts to create the site are in the "scripts" directory. John Dey j...@fuzzdog.com On Sat, Sep 18, 2021 at 5:51 PM Lev Lafayette wrote: > Hi Easybuilders, > > Where do you store your notes for modificati