[easybuild] running interproscan

[Christian Meesters]

Hi,

does anyone have experience running Interproscan using eb? Specifically, 
the easyconfig shows


# NOTE The data can be added manually afterwards with for example a 
symlink called *data*

# in %(installdir)s/
# But simpler to use the InterProScan_data-*.eb file. The regular 
InterProScan data package

# does not contain the lookup_service data way too large!

Is there an example? Does someone has a script to share? I did not find 
a command line flag to point this tool to an alternate location, is this 
really the case?


Any help is appreciated!

Cheers

Christian

Re: [easybuild] CCP4 and easybuild?

[Christian Meesters]

Hi,

I would be interested, too. Yet, if there is no working config 
miraculously hidden, perhaps we can sit (per video) on this together, 
Jürgen?


Cheers

Christian

On 8/23/22 13:42, juergen.hoffm...@univie.ac.at wrote:


Hello,

has anyone of you already installed ccp4 with easybuild and can give 
me the .eb file?
I found an old, very old version, but it seems that it has been 
discontinued.


Thank you,
Juergen



Juergen Hoffmann

University of Vienna

Department of Structural and Computational Biology

Campus-Vienna-Biocenter 5

1030 Wien

Austria

Tel.:    ++43 (1) 4277 DW 52213

Mobile: ++43 664 81 76 382

Fax:    ++43 (1) 4277 9522

Email: juergen.hoffm...@univie.ac.at 

[easybuild] installing pythonpackage fails

[Christian Meesters]

Dear List,

Any idea what might cause the install of a python package make fail with 
"Failed to copy file 
/easybuild/easyblocks/generic/pythonpackage.py to 
/tmp/eb-vmw07xz6/reprod_20201116214145_1540080/easyblocks/pythonpackage.py: 
[Errno 13] Permission denied"?


It gets funny when looking into the destination directory: the file 
already exists and has permissions '|-r--r--r--'. Hence, further 
attempts to install or copy '||pythonpackage.py' will fail.|


|We are running eb v4.3.1.|

|Any hint is appreciated!|

|Cheers|

|Christian|

Re: [easybuild] Autoconf run in ./src rather than .

[Christian Meesters]

Hi,

is there any update on this issue?

Cheers,

Christian


On 8/27/19 2:06 PM, Loris Bennett wrote:

Hi Åke,

Ah, thanks for the information.  The change must have happened
post 3.2.6, as I have a working easyconfig for that version.

I would in fact be happy to install an older version, but an apparently
bumpy transition from Sourceforge to Github seems to have broken all the
archived source 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 Bennett wrote:

Hi,

With EasyBuild 3.9.4 and the following easyconfig:

   name = 'MrBayes'
   version = '3.2.7'

   homepage = 'http://nbisweden.github.io'
   description = "MrBayes is a program for the Bayesian estimation of 
phylogeny."

   toolchain = {'name': 'foss', 'version': '2018b'}
   toolchainopts = {'usempi': True}

   source_urls = ['https://github.com/NBISweden/MrBayes/archive']
   sources = ['v%(version)s.tar.gz']

   dependencies = [
   ('beagle-lib', '3.0.2'),
   ('libreadline', '7.0'),
   ]

   builddependencies = [
   ('Autotools', '20180311'),
   ]

   moduleclass = 'bio'

I have the following error for a

   == 2019-08-27 13:12:36,748 run.py:173 DEBUG run_cmd: running cmd autoconf 
(in /trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/src)
   == 2019-08-27 13:12:36,748 run.py:192 INFO running cmd: autoconf
   == 2019-08-27 13:12:36,960 build_log.py:163 ERROR EasyBuild crashed with an
error (at
easybuild/software/EasyBuild/3.9.4/lib/python2.7/site-packages/vsc_base-2.8.4-py2.7.egg/vsc/utils/exceptions.py:124
in __init__): cmd "autoconf" exited with exit code 1 and output:
   autoconf: error: no input file

As the unpacked tarball has the structure

   /trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/
   ├── aclocal.m4
   ├── am-aux
   ├── am-macros
   ├── configure
   ├── configure.ac
   ├── COPYING
   ├── doc
   ├── examples
   ├── INSTALL
   ├── Makefile.am
   ├── Makefile.in
   ├── NEWS
   ├── README
   ├── src
   └── TODO

autoconf should be run in .../MrBayes-3.2.7, rather than
.../MrBayes-3.2.7/src

What am I doing wrong?

Cheers,

Loris

[easybuild] Rust applications and libraries in eb?

[Christian Meesters]

Hi,

The recent updates of easybuild brought forward the Rust compiler as a 
easyconfig. Is there anyone build modules for applications with it?


I would like to build a library and an application. For this: Would it 
be a good idea to have something similar to toolchain/compiler/pgi.py? 
Or is some more intricate approach involving a genuine toolchain better? 
Any ideas / remarks on this? Anyone already did some work, which did not 
find the way in the eb trunk?


Best regards,

Christian

Re: [easybuild] EB for make, make install but without configure?

[Christian Meesters]

my bad: LAST-914-intel-2017b.eb is what I meant - perils of copy & paste

sorry


On 5/15/19 4:25 PM, Christian Meesters wrote:

Hi,

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 provides a makefile with
an install step, but which does not have a configure file.

One the one hand, I could use 'ConfigureMake' and fake the configure
step somehow, but I'm not sure how to do this.  On the other hand, I
could use 'MakeCp' 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

Re: [easybuild] EB for make, make install but without configure?

[Christian Meesters]

Hi,

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 provides a makefile with
an install step, but which does not have a configure file.

One the one hand, I could use 'ConfigureMake' and fake the configure
step somehow, but I'm not sure how to do this.  On the other hand, I
could use 'MakeCp' 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

[easybuild] recent ipyrad

[Christian Meesters]

Hi,

This year has seen 2 updates of ipyrad 
(https://github.com/dereneaton/ipyrad/releases ). Does anyone have a 
working version of one of the current releases? With working I mean: one 
version, which works with the intended ip-cluster setup supporting MPI 
or a single-node version. If so any feedback would be appriciated, 
particularly:


 * a working easyconfig ;-)
 * hints on working software list (versions)
 * if tested: deviations on the docs for the submission script, if any
   - see https://ipyrad.readthedocs.io/HPC_script.html

Thanks a lot,

Best regards,

Christian Meesters

[easybuild] broken BLAST+ modules

[Christian Meesters]

Dear all,

Sites supporting life-science users might have realized, that modules 
installed with BLAST+* configfiles carry a glitch. I am writing in the 
event that you have not yet realized that:


The installed modules will provide perl scripts, e. g. update_blastdb.pl 
(which is a more frequently demanded script). These show the following 
interpreter directive: #!/usr/bin/perl . The issue at our side is, that 
our system Perl does not provide two of the libraries which are used by 
the script. Therefore, I changed the directive to #!/usr/bin/env perl 
and made a fitting Perl module a dependency.


Perhaps this is useful to someone.

I also wanted to raise some attention to the BLAST developers - to no 
avail, as there seemingly is no contact given (?).


The question for this community would be: Alter all BLAST+ easyconfigs 
accordingly? Or do you not face this issue, perhaps due to a different 
setup?


Best regards,

Christian

[easybuild] ipyrad 0.7.28

[Christian Meesters]

Dear All,

recently I tried installing ipyrad. The provided easyconfig is 
ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb. Installation with switching 
the toolchain to foss,2017a worked, when outcommenting the numba 
dependency (which is none, as ipyrad does not claim to have this 
dependency, if I am not mistaken).


However, the most recent version does not work: 0.7.28. The reason is, 
that the installation generates a 'binary' in /bin, hence 
'python -c "import ipyrad"', failes.


I tried tinkering around to no avail. Therefore: Does anyone have a 
working easyconfig, supporting a toolchain with MPI (which did not find 
its why into the canonical easyconfigs, yet)?


Any pointer will be highly appreciated.

Best regards,
Christian Meesters

Re: [easybuild] empty path overwritten and not restored

[Christian Meesters]

Dear Kenneth,


On 08/08/2017 09:15 PM, Kenneth Hoste wrote:

Dear Christian,

I would say this is a bug in the modules tool, not in EasyBuild 
itself, wouldn't you agree?
Indeed, I do. I was just hoping for a possible work around. (On the 
respective cluster modules is established for quite a while.) Yet, the 
move to Lmod is pending - as I have to admit.


Thank you,
Christian


All EasyBuild does is generate a module that includes "prepend-path 
MANPATH ".


If the modules tool does the prepend while not fully honoring the 
empty value in $MANPATH, there's little EasyBuild can do about this 
imho...


You may want to look into Lmod [1], a modern modules tool that does 
the right thing in this situation...



regards,

Kenneth

[1] https://www.tacc.utexas.edu/research-development/tacc-projects/lmod

On 08/08/2017 20:56, Christian Meesters wrote:

Dear all,

upon loading a module (C-Version), a preset variable (e.g. MANPATH) 
is prepended (depending on the module, of course). This overwrites 
the empty path, designated by a colon. E.g.:


$ echo $MANPATH
:/var/cfengine/share/man

$ man ls # works fine

$ module load tools/parallel/20170622
$ echo $MANPATH
/cluster/easybuild/software/tools/parallel/20170622/share/man:/var/cfengine/share/man 



$ man ls # does not work, because the empty path is missing

$ module purge

$ echo $MANPATH
/var/cfengine/share/man

$ man ls # still does not work, leading colon is missing

---

Now, my question is: Is there a way to ask Easybuild to set up module 
files, such that leading colons are preserved? If not, would that be 
worth a feature request?


Best regards,
Christian Meesters




--
Dr. Christian Meesters
Johannes Gutenberg-Universität Mainz
Zentrum für Datenverarbeitung
Anselm-Franz-von-Bentzelweg 12
55099 Mainz

tel. +49 (0)6131 39 26397

[easybuild] empty path overwritten and not restored

[Christian Meesters]

Dear all,

upon loading a module (C-Version), a preset variable (e.g. MANPATH) is 
prepended (depending on the module, of course). This overwrites the 
empty path, designated by a colon. E.g.:


$ echo $MANPATH
:/var/cfengine/share/man

$ man ls # works fine

$ module load tools/parallel/20170622
$ echo $MANPATH
/cluster/easybuild/software/tools/parallel/20170622/share/man:/var/cfengine/share/man

$ man ls # does not work, because the empty path is missing

$ module purge

$ echo $MANPATH
/var/cfengine/share/man

$ man ls # still does not work, leading colon is missing

---

Now, my question is: Is there a way to ask Easybuild to set up module 
files, such that leading colons are preserved? If not, would that be 
worth a feature request?


Best regards,
Christian Meesters